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Li YQ, Ma H, Wang QY, Liu DS, Wang W, Li SX, Zuo RX, Shen T, Zhu BS, Sa YL. Low frequency of SLC26A4 c.919-2A > G variant among patients with nonsyndromic hearing loss in Yunnan of Southwest China. BMC Med Genomics 2024; 17:55. [PMID: 38378613 PMCID: PMC10877886 DOI: 10.1186/s12920-024-01829-3] [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: 02/10/2023] [Accepted: 02/09/2024] [Indexed: 02/22/2024] Open
Abstract
BACKGROUND Gene variants are responsible for more than half of hearing loss, particularly in nonsyndromic hearing loss (NSHL). The most common pathogenic variant in SLC26A4 gene found in East Asian populations is c.919-2A > G followed by c.2168A > G (p.H723R). This study was to evaluate their variant frequencies in patients with NSHL from special education schools in nine different areas of Southwest China's Yunnan. METHODS We performed molecular characterization by PCR-products directly Sanger sequencing of the SLC26A4 c.919-2AG and c.2168 A > G variants in 1167 patients with NSHL including 533 Han Chinese and 634 ethnic minorities. RESULTS The SLC26A4 c.919-2A > G variant was discovered in 8 patients with a homozygous state (0.69%) and twenty-five heterozygous (2.14%) in 1167 patients with NSHL. The total carrier rate of the c.919-2A > G variant was found in Han Chinese patients with 4.50% and ethnic minority patients with 1.42%. A significant difference existed between the two groups (P < 0.05). The c.919-2A > G allele variant frequency was ranged from 3.93% in Kunming to zero in Lincang and Nvjiang areas of Yunnan. We further detected the SLC26A4 c.2168 A > G variant in this cohort with one homozygotes (0.09%) and seven heterozygotes (0.60%), which was detected in Baoshan, Honghe, Licang and Pu`er areas. Between Han Chinese group (0.94%) and ethnic minority group (0.47%), there was no statistical significance (P > 0.05). Three Han Chinese patients (0.26%) carried compound heterozygosity for c.919-2A > G and c.2168 A > G. CONCLUSION These data suggest that the variants in both SLC26A4 c.919-2A > G and c.2168 A > G were relatively less frequencies in this cohort compared to the average levels in most regions of China, as well as significantly lower than that in Han-Chinese patients. These results broadened Chinese population genetic information resources and provided more detailed information for regional genetic counselling for Yunnan.
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Affiliation(s)
- Yan-Qiong Li
- Center for Clinical Medicine Research (Yunnan Provincial Key Laboratory of Clinical Virology, 202205AG070053, L-2019003), The First People's Hospital of Yunnan Province (The Affiliated Hospital of Kunming University of Science and Technology/School of Medicine), Kunming, 650032, Yunnan, China
- Central Sterile Supply Department, The First People's Hospital of Yunnan Province, (The Affiliated Hospital of Kunming University of Science and Technology/School of Medicine), Kunming, 650032, Yunnan, China
| | - Heng Ma
- The Outpatient Department of Yanan Hospital Affiliated to Kunming Medical University, Kunming, 650051, Yunnan, China
| | - Qin-Yao Wang
- Center for Clinical Medicine Research (Yunnan Provincial Key Laboratory of Clinical Virology, 202205AG070053, L-2019003), The First People's Hospital of Yunnan Province (The Affiliated Hospital of Kunming University of Science and Technology/School of Medicine), Kunming, 650032, Yunnan, China
| | - De-Sheng Liu
- Center for Clinical Medicine Research (Yunnan Provincial Key Laboratory of Clinical Virology, 202205AG070053, L-2019003), The First People's Hospital of Yunnan Province (The Affiliated Hospital of Kunming University of Science and Technology/School of Medicine), Kunming, 650032, Yunnan, China
- The Emergency Department of Traditional Chinese Medicine Hospital of Sichuan Province, (The Affiliated Hospital of Chengdu University of Traditional Chinese Medicine), Chengdu, 610075, Sichuan, China
| | - Wei Wang
- Center for Clinical Medicine Research (Yunnan Provincial Key Laboratory of Clinical Virology, 202205AG070053, L-2019003), The First People's Hospital of Yunnan Province (The Affiliated Hospital of Kunming University of Science and Technology/School of Medicine), Kunming, 650032, Yunnan, China
| | - Shi-Xin Li
- Center for Clinical Medicine Research (Yunnan Provincial Key Laboratory of Clinical Virology, 202205AG070053, L-2019003), The First People's Hospital of Yunnan Province (The Affiliated Hospital of Kunming University of Science and Technology/School of Medicine), Kunming, 650032, Yunnan, China
| | - Rong-Xia Zuo
- Center for Clinical Medicine Research (Yunnan Provincial Key Laboratory of Clinical Virology, 202205AG070053, L-2019003), The First People's Hospital of Yunnan Province (The Affiliated Hospital of Kunming University of Science and Technology/School of Medicine), Kunming, 650032, Yunnan, China
| | - Tao Shen
- Center for Clinical Medicine Research (Yunnan Provincial Key Laboratory of Clinical Virology, 202205AG070053, L-2019003), The First People's Hospital of Yunnan Province (The Affiliated Hospital of Kunming University of Science and Technology/School of Medicine), Kunming, 650032, Yunnan, China
| | - Bao-Sheng Zhu
- Center of Genetic Diagnosis (Yunnan Provincial Key Laboratory for Birth Defects and Genetic Diseases), The First People's Hospital of Yunnan Province (The Affiliated Hospital of Kunming University of Science and Technology/School of Medicine), Kunming, 650032, Yunnan, China
| | - Ya-Lian Sa
- Center for Clinical Medicine Research (Yunnan Provincial Key Laboratory of Clinical Virology, 202205AG070053, L-2019003), The First People's Hospital of Yunnan Province (The Affiliated Hospital of Kunming University of Science and Technology/School of Medicine), Kunming, 650032, Yunnan, China.
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Feng J, Zeng Z, Luo S, Liu X, Luo Q, Yang K, Zhang G, Liu J. Carrier frequencies, trends, and geographical distribution of hearing loss variants in China: The pooled analysis of 2,161,984 newborns. Heliyon 2024; 10:e24850. [PMID: 38322914 PMCID: PMC10845244 DOI: 10.1016/j.heliyon.2024.e24850] [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: 08/08/2023] [Revised: 12/07/2023] [Accepted: 01/16/2024] [Indexed: 02/08/2024] Open
Abstract
The aim of this study is to comprehensively investigate the prevalence and distribution patterns of three common genetic variants associated with hearing loss (HL) in Chinese neonatal population. Methods: Prior to June 30, 2023, an extensive search and screening process was conducted across multiple literature databases. R software was utilized for conducting meta-analyses, cartography, and correlation analyses. Results: Firstly, our study identified a total of 99 studies meeting the inclusion criteria. Notably, provinces such as Qinghai, Tibet, Jilin, and Heilongjiang lack large-scale genetic screening data for neonatal deafness. Secondly, in Chinese newborns, the carrier frequencies of GJB2 variants (c.235delC, c.299_300delAT) were 1.63 % (95 %CI 1.52 %-1.76 %) and 0.33 % (95 %CI 0.30 %-0.37 %); While SLC26A4 variants (c.919-2A > G, c.2168A > G) exhibited carrier rates of 0.95 % (95 %CI 0.86 %-1.04 %) and 0.17 % (95 %CI 0.15 %-0.19 %); Additionally, Mt 12S rRNA m.1555 A > G variant was found at a rate of 0.24 % (95 % CI 0.22 %-0.26 %). Thirdly, the mutation rate of GJB2 c.235delC was higher in the east of the Heihe-Tengchong line, whereas the mutation rate of Mt 12S rRNA m.1555 A > G variant exhibited the opposite pattern. Forthly, no significant correlation exhibited the opposite pattern of GJB2 variants, but there was a notable correlation among SLC26A4 variants. Lastly, strong regional distribution correlations were evident between mutation sites from different genes, particularly between SLC26A4 (c.919-2A > G and c.2168A > G) and GJB c.299_300delAT. Conclusions: The most prevalent deafness genes among Chinese neonates were GJB2 c.235delC variant, followed by SLC26A4 c.919-2A > G variant. These gene mutation rates exhibit significant regional distribution characteristics. Consequently, it is imperative to enhance genetic screening efforts to reduce the incidence of deafness in high-risk areas.
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Affiliation(s)
- Jia Feng
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Sichuan Province Engineering Technology Research Center of Molecular Diagnosis of Clinical Diseases, Molecular Diagnosis of Clinical Diseases Key Laboratory of Luzhou, Sichuan, China
| | - Zhangrui Zeng
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Sichuan Province Engineering Technology Research Center of Molecular Diagnosis of Clinical Diseases, Molecular Diagnosis of Clinical Diseases Key Laboratory of Luzhou, Sichuan, China
| | - Sijian Luo
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Sichuan Province Engineering Technology Research Center of Molecular Diagnosis of Clinical Diseases, Molecular Diagnosis of Clinical Diseases Key Laboratory of Luzhou, Sichuan, China
| | - Xuexue Liu
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Sichuan Province Engineering Technology Research Center of Molecular Diagnosis of Clinical Diseases, Molecular Diagnosis of Clinical Diseases Key Laboratory of Luzhou, Sichuan, China
| | - Qing Luo
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Sichuan Province Engineering Technology Research Center of Molecular Diagnosis of Clinical Diseases, Molecular Diagnosis of Clinical Diseases Key Laboratory of Luzhou, Sichuan, China
| | - Kui Yang
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Sichuan Province Engineering Technology Research Center of Molecular Diagnosis of Clinical Diseases, Molecular Diagnosis of Clinical Diseases Key Laboratory of Luzhou, Sichuan, China
| | - Guanbin Zhang
- Department of Laboratory Medicine, Fujian Medical University, Fuzhou 350122, China
- National Engineering Research Center for Beijing Biochip Technology, Beijing, 102206 ,China
| | - Jinbo Liu
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Sichuan Province Engineering Technology Research Center of Molecular Diagnosis of Clinical Diseases, Molecular Diagnosis of Clinical Diseases Key Laboratory of Luzhou, Sichuan, China
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Yu K, Liu X, Yang B. The correlation between deafness progression and SLC26A4 mutations in enlarged vestibular aqueduct patients. Eur Arch Otorhinolaryngol 2024; 281:649-654. [PMID: 37477685 DOI: 10.1007/s00405-023-08123-5] [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: 05/02/2023] [Accepted: 07/04/2023] [Indexed: 07/22/2023]
Abstract
BACKGROUND The relationship between the hearing phenotype and the SLC26A4 mutation in enlarged vestibular aqueduct cases has not been fully elucidated. OBJECTIVES To detect SLC26A4 mutation in a group of cases with enlarged vestibular aqueduct who received cochlear implantation and to analyze the correlation between the SLC26A4 genotype and the progression of deafness. MATERIALS AND METHODS Twenty-nine enlarged vestibular aqueduct patients were selected. Using the Sanger sequence to analyze SLC26A4 gene mutations. The 29 cases were divided into group A (carrying the c.919-2A > G mutation) and group B (not carrying the c.919-2A > G mutation). The difference in the duration of deafness was analyzed between the two groups. RESULTS The detection rate of the c.1174A > T mutation in the postlingual deafness group was 37.5%, higher than that in the prelingual deafness group (0%). The difference in the duration of deafness between groups A and B was not statistically significant by the Mann-Whitney U test (p > 0.05). CONCLUSIONS The correlation between the SLC26A4 genotype and the duration of deafness in cases with enlarged vestibular aqueduct is not yet clear. However, the c.1174A > T mutation may be linked to delayed hearing loss and the progression of deafness may be relatively slow in some cases of c.919-2A > G mutation.
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Affiliation(s)
- Kejia Yu
- The Fourth Affiliated Hospital, International Institutes of Medicine, Zhejiang University School of Medicine, Yiwu, China
| | - Xiao Liu
- Department of Otorhinolaryngology, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Beibei Yang
- Department of Otorhinolaryngology, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
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Yu Y, Zhang J, Zhan Y, Luo G. A novel method for detecting nine hotspot mutations of deafness genes in one tube. Sci Rep 2024; 14:454. [PMID: 38172427 PMCID: PMC10764868 DOI: 10.1038/s41598-023-50928-1] [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: 07/06/2023] [Accepted: 12/28/2023] [Indexed: 01/05/2024] Open
Abstract
Deafness is a common sensory disorder. In China, approximately 70% of hereditary deafness originates from four common deafness-causing genes: GJB2, SLC26A4, GJB3, and MT-RNR1. A single-tube rapid detection method based on 2D-PCR technology was established for nine mutation sites in the aforementioned genes, and Sanger sequencing was used to verify its reliability and accuracy. The frequency of hotspot mutations in deafness genes was analysed in 116 deaf students. 2D-PCR identified 27 genotypes of nine loci according to the melting curve of the FAM, HEX, and Alexa568 fluorescence channels. Of the 116 deaf patients, 12.9% (15/116) carried SLC26A4 mutations, including c.919-2A > G and c.2168A > G (allele frequencies, 7.3% and 2.2%, respectively). The positivity rate (29.3%; 34/116) was highest for GJB2 (allele frequency, 15.9% for c.235delC, 6.0% for c.299_300delAT, and 2.6% for c.176-191del16). Sanger sequencing confirmed the consistency of results between the detection methods based on 2D-PCR and DNA sequencing. Common pathogenic mutations in patients with non-syndromic deafness in Changzhou were concentrated in GJB2 (c.235delC, c.299_300delAT, and c.176-191del16) and SLC26A4 (c.919-2A > G and c.2168 A > G). 2D-PCR is an effective method for accurately and rapidly identifying deafness-related genotypes using a single-tube reaction, and is superior to DNA sequencing, which has a high cost and long cycle.
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Affiliation(s)
- Yang Yu
- Comprehensive Laboratory, The Third Affiliated Hospital of Soochow University, Changzhou, 213003, People's Republic of China
| | - Jun Zhang
- Comprehensive Laboratory, The Third Affiliated Hospital of Soochow University, Changzhou, 213003, People's Republic of China
| | - Yuxia Zhan
- Comprehensive Laboratory, The Third Affiliated Hospital of Soochow University, Changzhou, 213003, People's Republic of China
| | - Guanghua Luo
- Comprehensive Laboratory, The Third Affiliated Hospital of Soochow University, Changzhou, 213003, People's Republic of China.
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Xiong Y, Chen M, Wang H, Chen L, Huang H, Xu L. Mutation analysis of GJB2, SLC26A4, GJB3 and mtDNA12SrRNA genes in 251 non-syndromic hearing loss patients in Fujian, China. Int J Pediatr Otorhinolaryngol 2024; 176:111777. [PMID: 38029595 DOI: 10.1016/j.ijporl.2023.111777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 10/23/2023] [Accepted: 11/03/2023] [Indexed: 12/01/2023]
Abstract
OBJECTIVES The molecular etiology of non-syndromic hearing loss (NSHL) in Southeastern China (Fujian) has not been precisely identified. our study selected patients with NSHL and analyzed their causative genes, which helped to improve the accuracy of the diagnosis of hereditary hearing loss (HHL) and its treatment. METHODS 251 unrelated patients who attended the otolaryngology clinic of Fujian Maternal and Child Health Hospital with hearing loss were enrolled to our study. All patients had genetic tests and listening tests, of which 251 were diagnosed with NSHL. In addition, we used whole-exome sequencing (WES) in a patient who has a significant family history of HHL but negative for gene chip testing, as well as in his family members. RESULT Among of 251 patients, Nucleotide changes were found in 63 cases (25.09%), including 34 located in GJB2(13.5%, including 235delC and 299_300delAT), 13 located in SLC26A4(5.18%, including c.919-2G > A and 2168 A > G), 1 located in GJB3(0.4%,538C > T) and 16 located in mtDNA12SrRNA (6.37%,1555 A > G). In addition, we discuss the process of identifying novel PLS1 mutations from 251 patients. CONCLUSION Our results demonstrate the conventional deafness gene mutation in 251 NSHL patients in Fujian, China. Compared with the other area of China, we have a lower detection rate, but GJB2 235delC remains the most common mutation in Fujian. In addition, we discuss the process of discovering novel mutation locus for deafness, which provides an understanding for deafness diagnosis and genetic testing.
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Affiliation(s)
- Yikang Xiong
- The Frist Department of Clinical Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, 350122, Fujian Province, China
| | - Meihuan Chen
- Medical Genetic Diagnosis and Therapy Center of Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Provincial Key Laboratory of Prenatal Diagnosis and Birth Defect, Fuzhou, 350001, Fujian Province, China
| | - Haiwei Wang
- Medical Genetic Diagnosis and Therapy Center of Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Provincial Key Laboratory of Prenatal Diagnosis and Birth Defect, Fuzhou, 350001, Fujian Province, China
| | - Lingji Chen
- Medical Genetic Diagnosis and Therapy Center of Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Provincial Key Laboratory of Prenatal Diagnosis and Birth Defect, Fuzhou, 350001, Fujian Province, China
| | - Hailong Huang
- Medical Genetic Diagnosis and Therapy Center of Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Provincial Key Laboratory of Prenatal Diagnosis and Birth Defect, Fuzhou, 350001, Fujian Province, China.
| | - Liangpu Xu
- The Frist Department of Clinical Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, 350122, Fujian Province, China; Medical Genetic Diagnosis and Therapy Center of Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Provincial Key Laboratory of Prenatal Diagnosis and Birth Defect, Fuzhou, 350001, Fujian Province, China.
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Takahashi S, Homma K. The molecular principles underlying diverse functions of the SLC26 family of proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.10.570988. [PMID: 38106153 PMCID: PMC10723444 DOI: 10.1101/2023.12.10.570988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Mammalian SLC26 proteins are membrane-based anion transporters that belong to the large SLC26/SulP family, and many of their variants are associated with hereditary diseases. Recent structural studies revealed a strikingly similar homodimeric molecular architecture for several SLC26 members, implying a shared molecular principle. Now a new question emerges as to how these structurally similar proteins execute diverse physiological functions. In this study we sought to identify the common vs. distinct molecular mechanism among the SLC26 proteins using both naturally occurring and artificial missense changes introduced to SLC26A4, SLC26A5, and SLC26A9. We found: (i) the basic residue at the anion binding site is essential for both anion antiport of SLC26A4 and motor functions of SLC26A5, and its conversion to a nonpolar residue is crucial but not sufficient for the fast uncoupled anion transport in SLC26A9; (ii) the conserved polar residues in the N- and C-terminal cytosolic domains are likely involved in dynamic hydrogen-bonding networks and are essential for anion antiport of SLC26A4 but not for motor (SLC26A5) and uncoupled anion transport (SLC26A9) functions; (iii) the hydrophobic interaction between each protomer's last transmembrane helices, TM14, is not of functional significance in SLC26A9 but crucial for the functions of SLC26A4 and SLC26A5, likely contributing to optimally orient the axis of the relative movements of the core domain with respect to the gate domains within the cell membrane. These findings advance our understanding of the molecular mechanisms underlying the diverse physiological roles of the SLC26 family of proteins.
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苏 栋, 娄 凡, 黄 锐, 李 霞, 林 垦, 李 果, 马 静. [Analysis of 59 cases of large vestibular aqueduct syndrome SLC26A4gene mutation frequency and new mutation sites]. LIN CHUANG ER BI YAN HOU TOU JING WAI KE ZA ZHI = JOURNAL OF CLINICAL OTORHINOLARYNGOLOGY, HEAD, AND NECK SURGERY 2023; 37:909-915. [PMID: 37905486 PMCID: PMC10985661 DOI: 10.13201/j.issn.2096-7993.2023.11.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 09/13/2023] [Indexed: 11/02/2023]
Abstract
Objective:To study the frequency of SLC26A4 gene mutation sites in children with enlarged vestibular aqueduct deafness in Yunnan, report the new mutation sites of SLC26A4 gene, further clarify the mutation spectrum of SLC26A4gene, and explore the association between biallelic and monoallelic mutations of SLC26A4 gene and CT phenotype of inner ear, so as to provide basis for clinical and genetic diagnosis of deafness. Methods:Review the results of temporal bone CT examination of 390 children after cochlear implantation in the Department of Otolaryngology, Kunming Children's Hospital from August 2016 to September 2021. Sanger sequencing of SLC26A4 gene was performed in 59 children with enlarged vestibular aqueduct. According to the genetic test results, the children who underwent temporal bone CT examination were divided into two groups: SLC26A4 biallelic mutation group(homozygous mutation and compound heterozygous mutation), monoallelic mutation group, and the association with inner ear CT phenotype was analyzed, and the new sites were summarized and analyzed. Results:The c.919-2a>g mutation was the most common mutation in children with enlarged vestibular aqueduct with SLC26A4 gene mutation. Three new variants of SLC26A4 gene were found; CT examination combined with genetic testing found that a part of children with enlarged vestibular aqueduct was associated with SLC26A4 monoallelic mutation or no SLC26A4 gene mutation was detected. Further research is needed to investigate the involvement of other pathogenic factors in the pathogenesis of EVA.
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Affiliation(s)
- 栋 苏
- 昆明市儿童医院耳鼻咽喉头颈外科 昆明市儿童先天出生缺陷防控研究重点实验室 云南省儿童重大疾病研究重点实验室(昆明,650228)Department of Otorhinolaryngology Head and Neck Surgery, Kunming Children's Hospital, Kunming Key Laboratory for Prevention and Control of Congenital Birth Defects of Children, Yunnan Key Laboratory of Children's Major Disease Research, Kunming, 650228, China
| | - 凡 娄
- 昆明市儿童医院耳鼻咽喉头颈外科 昆明市儿童先天出生缺陷防控研究重点实验室 云南省儿童重大疾病研究重点实验室(昆明,650228)Department of Otorhinolaryngology Head and Neck Surgery, Kunming Children's Hospital, Kunming Key Laboratory for Prevention and Control of Congenital Birth Defects of Children, Yunnan Key Laboratory of Children's Major Disease Research, Kunming, 650228, China
| | - 锐 黄
- 昆明市儿童医院耳鼻咽喉头颈外科 昆明市儿童先天出生缺陷防控研究重点实验室 云南省儿童重大疾病研究重点实验室(昆明,650228)Department of Otorhinolaryngology Head and Neck Surgery, Kunming Children's Hospital, Kunming Key Laboratory for Prevention and Control of Congenital Birth Defects of Children, Yunnan Key Laboratory of Children's Major Disease Research, Kunming, 650228, China
| | - 霞 李
- 昆明市儿童医院耳鼻咽喉头颈外科 昆明市儿童先天出生缺陷防控研究重点实验室 云南省儿童重大疾病研究重点实验室(昆明,650228)Department of Otorhinolaryngology Head and Neck Surgery, Kunming Children's Hospital, Kunming Key Laboratory for Prevention and Control of Congenital Birth Defects of Children, Yunnan Key Laboratory of Children's Major Disease Research, Kunming, 650228, China
| | - 垦 林
- 昆明市儿童医院耳鼻咽喉头颈外科 昆明市儿童先天出生缺陷防控研究重点实验室 云南省儿童重大疾病研究重点实验室(昆明,650228)Department of Otorhinolaryngology Head and Neck Surgery, Kunming Children's Hospital, Kunming Key Laboratory for Prevention and Control of Congenital Birth Defects of Children, Yunnan Key Laboratory of Children's Major Disease Research, Kunming, 650228, China
| | - 果 李
- 昆明市儿童医院耳鼻咽喉头颈外科 昆明市儿童先天出生缺陷防控研究重点实验室 云南省儿童重大疾病研究重点实验室(昆明,650228)Department of Otorhinolaryngology Head and Neck Surgery, Kunming Children's Hospital, Kunming Key Laboratory for Prevention and Control of Congenital Birth Defects of Children, Yunnan Key Laboratory of Children's Major Disease Research, Kunming, 650228, China
| | - 静 马
- 昆明市儿童医院耳鼻咽喉头颈外科 昆明市儿童先天出生缺陷防控研究重点实验室 云南省儿童重大疾病研究重点实验室(昆明,650228)Department of Otorhinolaryngology Head and Neck Surgery, Kunming Children's Hospital, Kunming Key Laboratory for Prevention and Control of Congenital Birth Defects of Children, Yunnan Key Laboratory of Children's Major Disease Research, Kunming, 650228, China
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Huang Y, Li L, Pan L, Ling X, Wang C, Huang C, Huang Y. Non-syndromic enlarged vestibular aqueduct caused by novel compound mutations of the SLC26A4 gene: a case report and literature review. Front Genet 2023; 14:1240701. [PMID: 37745850 PMCID: PMC10512862 DOI: 10.3389/fgene.2023.1240701] [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: 06/15/2023] [Accepted: 08/18/2023] [Indexed: 09/26/2023] Open
Abstract
Enlarged vestibular aqueduct is an autosomal genetic disease mainly caused by mutations in the SLC26A4 gene and includes non-syndromic and syndromic types. This study aimed to identify genetic defects in a Chinese patient with non-syndromic enlarged vestibular aqueduct (NSEVA) and to investigate the impact of variants on the severity of non-syndromic enlarged vestibular aqueduct. A male patient with NSEVA, aged approximately 6 years, was recruited for this study. The clinical characteristics and results of auxiliary examinations, including laboratory and imaging examinations, were collected, and 127 common hereditary deafness genes were detected by chip capture high-throughput sequencing. Protein structure predictions, the potential impact of mutations, and multiple sequence alignments were analyzed in silico. Compound heterozygote mutations c.1523_1528delinsAC (p.Thr508Asnfs*3) and c.422T>C (p.Phe141Ser) in the SLC26A4 gene were identified. The novel frameshift mutation c.1523_1528delinsAC produces a severely truncated pendrin protein, and c.422T>C has been suggested to be a disease-causing mutation. Therefore, this study demonstrates that the novel mutation c.1523_1528delinsAC in compound heterozygosity with c.422T>C in the SLC26A4 gene is likely to be the cause of NSEVA. Cochlear implants are the preferred treatment modality for patients with NSEVA and severe-to-profound sensorineural hearing loss Genetic counseling and prenatal diagnosis are essential for early diagnosis. These findings expand the mutational spectrum of SLC26A4 and improve our understanding of the molecular mechanisms underlying NSEVA.
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Affiliation(s)
- Yunhua Huang
- Department of Clinical Laboratory, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
- Key Laboratory of Clinical Laboratory Medicine of Guangxi Department of Education, Guangxi Medical University, Nanning, Guangxi, China
| | - Linlin Li
- Department of Clinical Laboratory, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
- Key Laboratory of Clinical Laboratory Medicine of Guangxi Department of Education, Guangxi Medical University, Nanning, Guangxi, China
| | - Liqiu Pan
- Department of Clinical Laboratory, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
- Key Laboratory of Clinical Laboratory Medicine of Guangxi Department of Education, Guangxi Medical University, Nanning, Guangxi, China
| | - Xiaoting Ling
- Department of Clinical Laboratory, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
- Key Laboratory of Clinical Laboratory Medicine of Guangxi Department of Education, Guangxi Medical University, Nanning, Guangxi, China
| | - Chenghan Wang
- Department of Clinical Laboratory, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
- Key Laboratory of Clinical Laboratory Medicine of Guangxi Department of Education, Guangxi Medical University, Nanning, Guangxi, China
| | - Chaoyu Huang
- Department of Clinical Laboratory, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
- Key Laboratory of Clinical Laboratory Medicine of Guangxi Department of Education, Guangxi Medical University, Nanning, Guangxi, China
| | - Yifang Huang
- Department of Clinical Laboratory, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
- Key Laboratory of Clinical Laboratory Medicine of Guangxi Department of Education, Guangxi Medical University, Nanning, Guangxi, China
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9
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Danilchenko VY, Zytsar MV, Maslova EA, Orishchenko KE, Posukh OL. Insight into the Natural History of Pathogenic Variant c.919-2A>G in the SLC26A4 Gene Involved in Hearing Loss: The Evidence for Its Common Origin in Southern Siberia (Russia). Genes (Basel) 2023; 14:genes14040928. [PMID: 37107686 PMCID: PMC10137394 DOI: 10.3390/genes14040928] [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: 03/19/2023] [Revised: 04/10/2023] [Accepted: 04/12/2023] [Indexed: 04/29/2023] Open
Abstract
Pathogenic variants in the SLC26A4 gene leading to nonsyndromic recessive deafness (DFNB4), or Pendred syndrome, are some of the most common causes of hearing loss worldwide. Earlier, we found a high proportion of SLC26A4-related hearing loss with prevailing pathogenic variant c.919-2A>G (69.3% among all mutated SLC26A4 alleles that have been identified) in Tuvinian patients belonging to the indigenous Turkic-speaking Siberian people living in the Tyva Republic (Southern Siberia, Russia), which implies a founder effect in the accumulation of c.919-2A>G in Tuvinians. To evaluate a possible common origin of c.919-2A>G, we genotyped polymorphic STR and SNP markers, intragenic and flanking SLC26A4, in patients homozygous for c.919-2A>G and in healthy controls. The common STR and SNP haplotypes carrying c.919-2A>G were revealed, which convincingly indicates the origin of c.919-2A>G from a single ancestor, supporting a crucial role of the founder effect in the c.919-2A>G prevalence in Tuvinians. Comparison analysis with previously published data revealed the identity of the small SNP haplotype (~4.5 kb) in Tuvinian and Han Chinese carriers of c.919-2A>G, which suggests their common origin from founder chromosomes. We assume that c.919-2A>G could have originated in the geographically close territories of China or Tuva and subsequently spread to other regions of Asia. In addition, the time intervals of the c.919-2A>G occurrence in Tuvinians were roughly estimated.
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Affiliation(s)
- Valeriia Yu Danilchenko
- Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Marina V Zytsar
- Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Ekaterina A Maslova
- Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Konstantin E Orishchenko
- Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Olga L Posukh
- Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Novosibirsk State University, 630090 Novosibirsk, Russia
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10
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Fang Y, Li J, Zhang M, Cheng Y, Wang C, Zhu J. Clinical application value of expanded carrier screening in the population of childbearing age. Eur J Med Res 2023; 28:151. [PMID: 37031186 PMCID: PMC10082524 DOI: 10.1186/s40001-023-01112-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 03/30/2023] [Indexed: 04/10/2023] Open
Abstract
OBJECTIVE The objective of this study was to explore the clinical utility of the implementation of expanded carrier screening (ECS) in Chinese population of childbearing age. MATERIALS AND METHODS Based on capillary electrophoresis, a first-generation sequencing technology, a prospective screening study of carriers of 15 single-gene diseases was carried out in 327 subjects in Anhui Province, including 84 couples and 159 women of childbearing age, the disease carrier rate, types of screened pathogenic genes, and incidence of both partners carrying the same pathogenic genes were summarized and analyzed. RESULTS In 320 people with normal phenotypes who underwent ECS for 15 genetic diseases and 7 spouses who underwent targeted gene sequencing, 65 carriers of at least one disease were detected, with a total carrier rate of 20.31% (65/320). Among the 65 carriers, 81.54% (53/65) carried one genetic variant, 16.92% (11/65) carried two genetic variants, and 1.54% (1/65) carried three genetic variants. In this study, the three diseases with the highest carrier rates were hereditary deafness (8.13%, 26/320), Wilson's disease (4.06%, 13/320), and phenylketonuria (3.13%, 10/320). One high-risk couple (1.19%, 1/84) was detected. CONCLUSIONS It has certain clinical application value to implement ECS in the population of childbearing age in China.
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Affiliation(s)
- Yuqin Fang
- Affiliated Maternity and Child Health Hospital of Anhui Medical University, Hefei, China
- Maternity and Child Health Hospital of Anhui Province, Hefei, China
| | - Jingran Li
- Maternity and Child Health Hospital of Anhui Province, Hefei, China
| | - Miaomiao Zhang
- Maternity and Child Health Hospital of Anhui Province, Hefei, China
| | - Yuan Cheng
- Maternity and Child Health Hospital of Anhui Province, Hefei, China
| | - Chaohong Wang
- Maternity and Child Health Hospital of Anhui Province, Hefei, China
| | - Jiansheng Zhu
- Affiliated Maternity and Child Health Hospital of Anhui Medical University, Hefei, China.
- Maternity and Child Health Hospital of Anhui Province, Hefei, China.
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11
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Wang Q, Hu J, Bian P, Chen C, Wang Y, Cheng S, Guo Y, Xu B. The effect of SLC26A4 gene mutations on long-term rehabilitative outcomes in cochlear implant patients. Acta Otolaryngol 2023; 143:156-162. [PMID: 36780306 DOI: 10.1080/00016489.2023.2174592] [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: 02/14/2023]
Abstract
BACKGROUND SLC26A4 gene mutations related to hearing loss patients can obtain good hearing and speech rehabilitation effects after cochlear implantation (CI). OBJECTIVE To explore the long-term rehabilitative outcomes of CI in patients with different SLC26A4 mutation groups. MATERIAL AND METHODS Clinical data of 71 patients with SLC26A4 gene mutations who received CI in the Second Hospital of Lanzhou University from 2012 to 2015 were retrospectively reviewed. According to the genetic test results, use One-way ANOVA analysis to compare the differences in auditory results, categories of auditory performance (CAP) and speech intelligibility rating (SIR) index questionnaire scores and speech recognition rates among different groups in 4-5 years after CI. RESULT Compared with other genotypes of SLC26A4, the patients with homozygous mutation of c.919-2A > G in SLC26A4 had better hearing aid threshold at 500 Hz and better recognition rates of Yangyang words than other monoallelic mutation groups after CI (p < .05). CONCLUSIONS AND SIGNIFICANCE The most common hot spot mutation of SLC26A4 gene is c.919-2A > G. The patients with homozygous mutation of c.919-2A > G in SLC26A4 gene had partly better hearing and speech rehabilitation than other monoallelic mutation groups after CI.
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Affiliation(s)
- Qin Wang
- Department of Otolaryngology-Head & Neck Surgery, Lanzhou University Second Hospital, Lanzhou, China
| | - Jian Hu
- Department of Otorhinolaryngology Head and Neck Surgery, Xijing Hospital, Airforce Military Medical University, Xi'an, Shaanxi Province, China
| | - Panpan Bian
- Department of Otolaryngology-Head & Neck Surgery, Lanzhou University Second Hospital, Lanzhou, China
| | - Chi Chen
- Department of Otolaryngology-Head & Neck Surgery, Lanzhou University Second Hospital, Lanzhou, China
| | - Yanli Wang
- Department of Otolaryngology-Head & Neck Surgery, Lanzhou University Second Hospital, Lanzhou, China
| | - Shihong Cheng
- Department of Otolaryngology-Head & Neck Surgery, Lanzhou University Second Hospital, Lanzhou, China
| | - Yufen Guo
- Department of Otolaryngology-Head & Neck Surgery, Lanzhou University Second Hospital, Lanzhou, China
| | - Baicheng Xu
- Department of Otolaryngology-Head & Neck Surgery, Lanzhou University Second Hospital, Lanzhou, China
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12
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Tan Y, Jian H, Zhang R, Wang J, Zhou C, Xiao Y, Liang W, Wang L. Applying amplification refractory mutation system technique to detecting cell-free fetal DNA for single-gene disorders purpose. Front Genet 2023; 14:1071406. [PMID: 37113995 PMCID: PMC10128035 DOI: 10.3389/fgene.2023.1071406] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Accepted: 03/15/2023] [Indexed: 04/29/2023] Open
Abstract
Non-invasive prenatal diagnosis for single-gene disorders (NIPD) is still in development and deserves further study. The advent of next-generation sequencing technology significantly improved the detection of multiple mutations for non-invasive prenatal diagnosis for single-gene disorder purposes. However, bespoke amplicon-based NGS assays are costly. In this study, we developed a new strategy for non-invasive prenatal screening for single-gene disorders based on a capillary electrophoresis (CE) platform using an amplification refractory mutation system (ARMS)-PCR technique. Allele-specific primers for several disease-correlated mutations were designed, and subsequently, sensitivity and specificity assays were conducted. Assays on simulated two-person DNA mixtures showed that three primers targeting the mutant allele could detect minor DNA components in 1:500 mixtures. All primers showed positive results at 0.01 ng of the template DNA. Cell-free fetal DNA was extracted from a pregnant woman's peripheral blood for the detection of paternally inherited mutations. Our results showed that one primer successfully amplified the mutant allele of fetal DNA in maternal plasma, which was confirmed by genotyping the genomic DNA extracted from amniotic fluid. This study suggested that the ARMS-PCR technique, a fast and cost-effective method, might be a promising method used to target de novo or paternally inherited pathogenic mutations in maternal plasma.
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Affiliation(s)
- Yu Tan
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan, China
| | - Hui Jian
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan, China
- Department of Laboratory Medicine, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Ranran Zhang
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, China
| | - Jing Wang
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan, China
| | - Cong Zhou
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan, China
| | - Yuanyuan Xiao
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan, China
| | - Weibo Liang
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, China
- *Correspondence: Weibo Liang, ; Li Wang,
| | - Li Wang
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan, China
- *Correspondence: Weibo Liang, ; Li Wang,
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Danilchenko VY, Zytsar MV, Maslova EA, Posukh OL. Selection of Diagnostically Significant Regions of the SLC26A4 Gene Involved in Hearing Loss. Int J Mol Sci 2022; 23:ijms232113453. [PMID: 36362242 PMCID: PMC9655724 DOI: 10.3390/ijms232113453] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 10/23/2022] [Accepted: 11/01/2022] [Indexed: 11/06/2022] Open
Abstract
Screening pathogenic variants in the SLC26A4 gene is an important part of molecular genetic testing for hearing loss (HL) since they are one of the common causes of hereditary HL in many populations. However, a large size of the SLC26A4 gene (20 coding exons) predetermines the difficulties of its complete mutational analysis, especially in large samples of patients. In addition, the regional or ethno-specific prevalence of SLC26A4 pathogenic variants has not yet been fully elucidated, except variants c.919-2A>G and c.2168A>G (p.His723Arg), which have been proven to be most common in Asian populations. We explored the distribution of currently known pathogenic and likely pathogenic (PLP) variants across the SLC26A4 gene sequence presented in the Deafness Variation Database for the selection of potential diagnostically important parts of this gene. As a result of this bioinformatic analysis, we found that molecular testing ten SLC26A4 exons (4, 6, 10, 11, 13−17 and 19) with flanking intronic regions can provide a diagnostic rate of 61.9% for all PLP variants in the SLC26A4 gene. The primary sequencing of these SLC26A4 regions may be applied as an initial effective diagnostic testing in samples of patients of unknown ethnicity or as a subsequent step after the targeted testing of already-known ethno- or region-specific pathogenic SLC26A4 variants.
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Affiliation(s)
- Valeriia Yu. Danilchenko
- Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Marina V. Zytsar
- Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Ekaterina A. Maslova
- Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Olga L. Posukh
- Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Novosibirsk State University, 630090 Novosibirsk, Russia
- Correspondence:
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14
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徐 小, 龚嘎 蓝, 蔡 舜, 巴 罗, 郑 宏, 余 力, 索朗 卓. [Summary of experience in cochlear implantation surgery in Tibet and analysis of postoperative rehabilitation effect]. LIN CHUANG ER BI YAN HOU TOU JING WAI KE ZA ZHI = JOURNAL OF CLINICAL OTORHINOLARYNGOLOGY, HEAD, AND NECK SURGERY 2022; 36:793-797. [PMID: 36217661 PMCID: PMC10128555 DOI: 10.13201/j.issn.2096-7993.2022.10.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Indexed: 06/16/2023]
Abstract
Cochlear implant surgery is now recognized as the most effective intervention for patients with severe and profound sensorineural hearing loss. Due to various factors such as high altitude, low oxygen content, and ethnic differences in Tibet, the early hearing screening found that the incidence of neonatal hearing loss was significantly higher than in the mainland. With the great assistance of the China Disabled Persons' Federation, the first cochlear implant surgery was carried out in Tibet in 2011, and a total of 116 cases have been completed. This article aims to summarize the clinical experience of cochlear implant surgery in Tibet for ten years and retrospectively analyze the postoperative rehabilitation effect, so as to improve the understanding of cochlear implant surgery in plateau areas.
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Affiliation(s)
- 小东 徐
- 西藏大学医学院(拉萨,850000)School of Medicine, Tibet University, Lhasa, Tibet, 850000, China
| | - 蓝孜 龚嘎
- 西藏大学医学院(拉萨,850000)School of Medicine, Tibet University, Lhasa, Tibet, 850000, China
| | - 舜玉 蔡
- 西藏自治区人民医院耳鼻喉科Department of Otolaryngology, People's Hospital of Tibet Autonomous Region
| | - 罗 巴
- 西藏自治区人民医院耳鼻喉科Department of Otolaryngology, People's Hospital of Tibet Autonomous Region
| | - 宏伟 郑
- 北京大学人民医院耳鼻咽喉头颈外科Peking University People's Hospital
| | - 力生 余
- 北京大学人民医院耳鼻咽喉头颈外科Peking University People's Hospital
| | - 卓嘎 索朗
- 西藏自治区残疾人联合会听力康复中心Hearing Rehabilitation Center, Tibet Autonomous Region Disabled Persons' Federation
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15
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He X, Zhao S, Shi L, Lu Y, Yang Y, Zhang X. Compound heterozygous variants of the SLC26A4 gene in a Chinese family with enlarged vestibular aqueducts. BMC Med Genomics 2022; 15:152. [PMID: 35804348 PMCID: PMC9270741 DOI: 10.1186/s12920-022-01271-3] [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: 01/17/2022] [Accepted: 05/10/2022] [Indexed: 11/21/2022] Open
Abstract
Background To investigate the genetic causes of hearing loss in patients with enlarged vestibular aqueduct (EVA), the SLC26A4-related genotypes and phenotypes were analyzed. SLC26A4 gene is closely associated with EVA and its homozygous mutations or compound heterozygous mutations may cause deafness and strongly affect quality of life. Methods The patients who came to our hospital for hearing test and accompanied by bilateral hearing abnormalities were collected for fifteen deafness-related gene mutations detection. Those who are positive will be verified by Sanger sequencing, combined with family history, hearing test, and computerized tomography (CT) of the temporal bone, aiming to diagnose the enlarged vestibular aqueducts. Whole-exome sequencing were performed when necessary. Results Our patient failed hearing screening on both sides twice, and EVA (> 1.5 mm) was diagnosed by CT. This study has identified a novel missense mutation in the SLC26A4 gene, c.2069T>A, which in compound heterozygosity with c.1174A>T is likely to be the cause of hearing loss. The novel heterozygous c.2069T>A mutation of SLC26A4 gene has been submitted to Clinvar with Variation ID 1,048,780. Conclusion Our findings expand the gene mutation spectrum of SLC26A4 and provide additional knowledge for diagnosis and genetic counseling associated with EVA-induced hearing loss. Supplementary Information The online version contains supplementary material available at 10.1186/s12920-022-01271-3.
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Affiliation(s)
- Xiaohui He
- Xi'an People's Hospital (Xi'an Fourth Hospital), Xi'an, China
| | - Shaozhi Zhao
- Xi'an People's Hospital (Xi'an Fourth Hospital), Xi'an, China
| | - Lin Shi
- Xi'an People's Hospital (Xi'an Fourth Hospital), Xi'an, China
| | - Yitong Lu
- Xi'an People's Hospital (Xi'an Fourth Hospital), Xi'an, China
| | - Yintong Yang
- Xi'an People's Hospital (Xi'an Fourth Hospital), Xi'an, China
| | - Xinwen Zhang
- Xi'an People's Hospital (Xi'an Fourth Hospital), Xi'an, China.
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16
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Li MM, Tayoun AA, DiStefano M, Pandya A, Rehm HL, Robin NH, Schaefer AM, Yoshinaga-Itano C. Clinical evaluation and etiologic diagnosis of hearing loss: A clinical practice resource of the American College of Medical Genetics and Genomics (ACMG). Genet Med 2022; 24:1392-1406. [PMID: 35802133 DOI: 10.1016/j.gim.2022.03.018] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 03/28/2022] [Indexed: 11/26/2022] Open
Abstract
Hearing loss is a common and complex condition that can occur at any age, can be inherited or acquired, and is associated with a remarkably wide array of etiologies. The diverse causes of hearing loss, combined with the highly variable and often overlapping presentations of different forms of hearing loss, challenge the ability of traditional clinical evaluations to arrive at an etiologic diagnosis for many deaf and hard-of-hearing individuals. However, identifying the etiology of hearing loss may affect clinical management, improve prognostic accuracy, and refine genetic counseling and assessment of the likelihood of recurrence for relatives of deaf and hard-of-hearing individuals. Linguistic and cultural identities associated with being deaf or hard-of-hearing can complicate access to and the effectiveness of clinical care. These concerns can be minimized when genetic and other health care services are provided in a linguistically and culturally sensitive manner. This clinical practice resource offers information about the frequency, causes, and presentations of hearing loss and suggests approaches to the clinical and genetic evaluation of deaf and hard-of-hearing individuals aimed at identifying an etiologic diagnosis and providing informative and effective patient education and genetic counseling.
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Affiliation(s)
- Marilyn M Li
- Department of Pathology and Laboratory Medicine, Department of Pediatrics, Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Ahmad Abou Tayoun
- Al Jalila Genomics Center, Al Jalila Children's Specialty Hospital, Mohammed Bin Rashid University, Dubai, United Arab Emirates
| | | | - Arti Pandya
- Department of Pediatrics, University of North Carolina School of Medicine, Chapel Hill, NC
| | - Heidi L Rehm
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Nathaniel H Robin
- Departments of Genetics and Pediatrics, University of Alabama at Birmingham, Birmingham, AL
| | - Amanda M Schaefer
- Department of Otolaryngology-Head & Neck Surgery, Molecular Otolaryngology and Renal Research Laboratories, University of Iowa, Iowa City, IA
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17
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A capillary electrophoresis-based multiplex PCR assay for expanded carrier screening in the eastern Han Chinese population. NPJ Genom Med 2022; 7:6. [PMID: 35079019 PMCID: PMC8789796 DOI: 10.1038/s41525-021-00280-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 12/20/2021] [Indexed: 12/05/2022] Open
Abstract
Expanded carrier screening, a type of reproductive genetic testing for couples, has gained tremendous popularity for assessing the risk of passing on certain genetic conditions to offspring. Here, a carrier screening assay for 448 pathogenic variants was developed using capillary electrophoresis-based multiplex PCR technology. The capillary electrophoresis-based multiplex PCR assay achieved a sensitivity, specificity, and accuracy of 97.4%, 100%, and 99.6%, respectively, in detecting the specific variants. Among the 1915 couples (3830 individuals), 708 individuals (18.5%) were identified as carriers for at least one condition. Of the 708 carriers, 633 (89.4%) were heterozygous for one condition, 71 (10.0%) for two disorders, 3 (0.4%) for three disorders, and 1 (0.1%) for four disorders. Meanwhile, 30 (1.57%) couples were identified as at‐risk couples. This study describes an inexpensive and effective method for expanded carrier screening. The simplicity and accuracy of this approach will facilitate the clinical implementation of expanded carrier screening.
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18
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Jin X, Huang S, An L, Zhang C, Dai P, Gao H, Ma X. Variant analysis of 92 Chinese Han families with hearing loss. BMC Med Genomics 2022; 15:12. [PMID: 35062939 PMCID: PMC8781451 DOI: 10.1186/s12920-022-01158-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 01/07/2022] [Indexed: 01/31/2024] Open
Abstract
Abstract
Background
Hearing loss (HL) is the most frequent sensory deficit in humans, HL has strong genetic heterogeneity. The genetic diagnosis of HL is very important to aid treatment decisions and to provide prognostic information and genetic counseling for the patient’s family.
Methods
We undertook pedigree analysis in 92 Chinese non-syndromic HL patients by targeted next-generation sequencing and Sanger sequencing.
Results
Among the 92 HL patients, 18 were assigned a molecular diagnosis with 33 different variants in 14 deafness genes. Eighteen of the variants in 12 deafness genes were novel. Variants in TMC1, CDH23, LOXHD1 and USH2A were each detected in two probands, and variants in POU3F4, OTOA, GPR98, GJB6, TRIOBP, SLC26A4, MYO15A, TNC, STRC and TMPRSS3 were each detected in one proband.
Conclusion
Our findings expand the spectrum of deafness gene variation, which will inform genetic diagnosis of deafness and add to the theoretical basis for the prevention of deafness.
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Hu CJ, Lu YC, Tsai CY, Chan YH, Lin PH, Lee YS, Yu IS, Lin SW, Liu TC, Hsu CJ, Yang TH, Cheng YF, Wu CC. Insights into phenotypic differences between humans and mice with p.T721M and other C-terminal variants of the SLC26A4 gene. Sci Rep 2021; 11:20983. [PMID: 34697379 PMCID: PMC8545921 DOI: 10.1038/s41598-021-00448-7] [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: 06/01/2021] [Accepted: 09/22/2021] [Indexed: 11/17/2022] Open
Abstract
Recessive variants of the SLC26A4 gene are an important cause of hereditary hearing impairment. Several transgenic mice with different Slc26a4 variants have been generated. However, none have recapitulated the auditory phenotypes in humans. Of the SLC26A4 variants identified thus far, the p.T721M variant is of interest, as it appears to confer a more severe pathogenicity than most of the other missense variants, but milder pathogenicity than non-sense and frameshift variants. Using a genotype-driven approach, we established a knock-in mouse model homozygous for p.T721M. To verify the pathogenicity of p.T721M, we generated mice with compound heterozygous variants by intercrossing Slc26a4+/T721M mice with Slc26a4919-2A>G/919-2A>G mice, which segregated the c.919-2A > G variant with abolished Slc26a4 function. We then performed serial audiological assessments, vestibular evaluations, and inner ear morphological studies. Surprisingly, both Slc26a4T721M/T721M and Slc26a4919-2A>G/T721M showed normal audiovestibular functions and inner ear morphology, indicating that p.T721M is non-pathogenic in mice and a single p.T721M allele is sufficient to maintain normal inner ear physiology. The evidence together with previous reports on mouse models with Slc26a4 p.C565Y and p.H723R variants, support our speculation that the absence of audiovestibular phenotypes in these mouse models could be attributed to different protein structures at the C-terminus of human and mouse pendrin.
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Affiliation(s)
- Chin-Ju Hu
- Department of Otolaryngology, National Taiwan University Hospital, 7 Chung-Shan S. Rd., Taipei, 100, Taiwan.,Program in Speech and Hearing Bioscience and Technology, Harvard Medical School, Boston, MA, 02115, USA
| | - Ying-Chang Lu
- Department of Otolaryngology, National Taiwan University Hospital, 7 Chung-Shan S. Rd., Taipei, 100, Taiwan
| | - Cheng-Yu Tsai
- Department of Otolaryngology, National Taiwan University Hospital, 7 Chung-Shan S. Rd., Taipei, 100, Taiwan
| | - Yen-Hui Chan
- Department of Otolaryngology, National Taiwan University Hospital, 7 Chung-Shan S. Rd., Taipei, 100, Taiwan.,Department of Otolaryngology, Taichung Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Taichung, 427, Taiwan
| | - Pei-Hsuan Lin
- Department of Otolaryngology, National Taiwan University Hospital, 7 Chung-Shan S. Rd., Taipei, 100, Taiwan
| | - Yi-Shan Lee
- Department of Otolaryngology, National Taiwan University Hospital, 7 Chung-Shan S. Rd., Taipei, 100, Taiwan
| | - I-Shing Yu
- Transgenic Mouse Models Core (TMMC), Division of Genomic Medicine, Research Center for Medical Excellence, National Taiwan University, Taipei, 100, Taiwan
| | - Shu-Wha Lin
- Transgenic Mouse Models Core (TMMC), Division of Genomic Medicine, Research Center for Medical Excellence, National Taiwan University, Taipei, 100, Taiwan
| | - Tien-Chen Liu
- Department of Otolaryngology, National Taiwan University Hospital, 7 Chung-Shan S. Rd., Taipei, 100, Taiwan.,Department of Otolaryngology, College of Medicine, National Taiwan University, Taipei, 100, Taiwan
| | - Chuan-Jen Hsu
- Department of Otolaryngology, National Taiwan University Hospital, 7 Chung-Shan S. Rd., Taipei, 100, Taiwan.,Department of Otolaryngology, Taichung Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Taichung, 427, Taiwan
| | - Ting-Hua Yang
- Department of Otolaryngology, National Taiwan University Hospital, 7 Chung-Shan S. Rd., Taipei, 100, Taiwan.
| | - Yen-Fu Cheng
- Department of Medical Research, Taipei Veteran General Hospital, 201, Sec.2, Shi-Pai Rd, Taipei, 112, Taiwan. .,Department of Otolaryngology-Head and Neck Surgery, Taipei Veteran General Hospital, Taipei, 112, Taiwan. .,School of Medicine, National Yang Ming Chiao Tung University, Taipei, 112, Taiwan.
| | - Chen-Chi Wu
- Department of Otolaryngology, National Taiwan University Hospital, 7 Chung-Shan S. Rd., Taipei, 100, Taiwan. .,Department of Otolaryngology, College of Medicine, National Taiwan University, Taipei, 100, Taiwan. .,Department of Medical Research, National Taiwan University Hospital Hsin-Chu Branch, Hsinchu, 302, Taiwan.
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Liang P, Chen F, Wang S, Li Q, Li W, Wang J, Chen J, Zha D. Whole exome sequencing of six Chinese families with hereditary non-syndromic hearing loss. Int J Pediatr Otorhinolaryngol 2021; 148:110817. [PMID: 34265623 DOI: 10.1016/j.ijporl.2021.110817] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 06/03/2021] [Accepted: 06/24/2021] [Indexed: 11/29/2022]
Abstract
OBJECTIVES Hereditary non-syndromic hearing loss (NSHL) has a high genetic heterogeneity with about 152 genes identified as associated molecular causes. The present study aimed to detect the possible damaging variants of the deaf probands from six unrelated Chinese families. METHODS After excluding the pathogenic/likely pathogenic variants in the most common genes, GJB2 and SLC26A4, 12 probands with prelingual deafness and autosomal recessive inheritance were evaluated by whole-exome sequencing (WES). All the candidate variants were verified by Sanger sequencing in all patients and their parents. RESULTS Biallelic variants were identified in all deaf patients. Among these six families, 10 potentially causative variants, including 3 reported and 7 novel variants, in 3 different deafness-associated autosomal recessive (DFNB) genes (MYO15A, COL11A2, and CDH23) were identified. These novel variants are thought to be pathogenic or likely pathogenic for theirs predicted damage function upon the protein as while as cosegregated with the deafness phenotype. The variants in MYO15A were frequent with 7/10 candidate ones. CONCLUSION Next-generation sequencing (NGS) approach becomes more cost-effective and efficient when analyzing large-scale genes compared to the conventional polymerase chain reaction-based Sanger sequencing, which is often used to screen common deafness-related genes. The current findings further extend the pathogenic/likely pathogenic variants spectrum of hearing loss in the Chinese population, which has a positive significance for genetic counseling.
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Affiliation(s)
- Pengfei Liang
- Department of Otolaryngology-Head and Neck Surgery, Xijing Hospital, Air Force Medical University, Xi'an, China
| | - Fengping Chen
- Department of Otolaryngology-Head and Neck Surgery, Xijing Hospital, Air Force Medical University, Xi'an, China
| | - Shujuan Wang
- Department of Otolaryngology-Head and Neck Surgery, Xijing Hospital, Air Force Medical University, Xi'an, China
| | - Qiong Li
- Department of Otolaryngology-Head and Neck Surgery, Xijing Hospital, Air Force Medical University, Xi'an, China
| | - Wei Li
- Department of Otolaryngology-Head and Neck Surgery, Xijing Hospital, Air Force Medical University, Xi'an, China
| | - Jian Wang
- Department of Otolaryngology-Head and Neck Surgery, Xijing Hospital, Air Force Medical University, Xi'an, China
| | - Jun Chen
- Department of Otolaryngology-Head and Neck Surgery, Xijing Hospital, Air Force Medical University, Xi'an, China
| | - Dingjun Zha
- Department of Otolaryngology-Head and Neck Surgery, Xijing Hospital, Air Force Medical University, Xi'an, China.
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21
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Tian Y, Xu H, Liu D, Zhang J, Yang Z, Zhang S, Liu H, Li R, Tian Y, Zeng B, Li T, Lin Q, Wang H, Li X, Lu W, Shi Y, Zhang Y, Zhang H, Jiang C, Xu Y, Chen B, Liu J, Tang W. Increased diagnosis of enlarged vestibular aqueduct by multiplex PCR enrichment and next-generation sequencing of the SLC26A4 gene. Mol Genet Genomic Med 2021; 9:e1734. [PMID: 34170635 PMCID: PMC8404235 DOI: 10.1002/mgg3.1734] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 04/30/2021] [Accepted: 05/24/2021] [Indexed: 12/11/2022] Open
Abstract
Background The enlarged vestibular aqueduct (EVA) is the commonest malformation of inner ear accompanied by sensorineural hearing loss in children. Three genes SLC26A4, FOXI1, and KCNJ10 have been associated with EVA, among them SLC26A4 being the most common. Yet, hotspot mutation screening can only diagnose a small number of patients. Methods Thus, in this study, we designed a new molecular diagnosis panel for EVA based on multiplex PCR enrichment and next‐generation sequencing of the exon and flanking regions of SLC26A4. A total of 112 hearing loss families with EVA were enrolled and the pathogenicity of the rare variants detected was interpreted according to the American College of Medical Genetics and Genomics (ACMG) guidelines. Results Our results showed that 107/112 (95.54%) families carried SLC26A4 biallelic mutations, 4/112 (3.57%) carried monoallelic variants, and 1/112 (0.89%) had none variant, resulting in a diagnostic rate of 95.54%. A total of 49 different variants were detected in those patients and we classified 30 rare variants as pathogenic/likely pathogenic, of which 13 were not included in the Clinvar database. Conclusion Our diagnostic panel has an increased diagnostic yield with less cost, and the curated list of pathogenic variants in the SLC26A4 gene can be directly used to aid the genetic counseling to patients.
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Affiliation(s)
- Yongan Tian
- BGI College, Zhengzhou University, Zhengzhou, China.,Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China.,Precision Medicine Center, Academy of Medical Science, Zhengzhou University, Zhengzhou, China
| | - Hongen Xu
- The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Danhua Liu
- The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Juanli Zhang
- Henan Province Medical Instrument Testing Institute, Zhengzhou, China
| | | | - Sen Zhang
- School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Huanfei Liu
- Precision Medicine Center, Academy of Medical Science, Zhengzhou University, Zhengzhou, China
| | - Ruijun Li
- Precision Medicine Center, Academy of Medical Science, Zhengzhou University, Zhengzhou, China
| | | | - Beiping Zeng
- BGI College, Zhengzhou University, Zhengzhou, China.,Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Tong Li
- BGI College, Zhengzhou University, Zhengzhou, China.,Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Qianyu Lin
- School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Haili Wang
- National Health Commission Key Laboratory of Birth Defects Prevention, Henan Key Laboratory of Population Defects Prevention, Zhengzhou, China
| | - Xiaohua Li
- Department of Otology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Wei Lu
- Department of Otology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Ying Shi
- The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yan Zhang
- The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Hui Zhang
- The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Chang Jiang
- Department of Otology, Henan Provincial People's Hospital, Zhengzhou, China
| | - Ying Xu
- Zhengzhou Children's Hospital, Zhengzhou, China
| | - Bei Chen
- Department of Otology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jun Liu
- Department of Otology, Henan Provincial People's Hospital, Zhengzhou, China
| | - Wenxue Tang
- The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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22
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Duan S, Guo Y, Chen X, Li Y. Genetic mutations in patients with nonsyndromic hearing impairment of minority and Han Chinese ethnicities in Qinghai, China. J Int Med Res 2021; 49:3000605211000892. [PMID: 33827324 PMCID: PMC8040579 DOI: 10.1177/03000605211000892] [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] [Indexed: 11/17/2022] Open
Abstract
Objective Mutations in GJB2, SLC26A4, and mitochondrial (mt)DNA 12S rRNA genes are the main cause of nonsyndromic hearing impairment. The present study analyzed these mutations in ethnic minority and Han Chinese patients with nonsyndromic hearing impairment from Qinghai, China. Methods The SNPscan assay was used to analyze mutation spectra and frequencies in the two patient groups. Results GJB2 mutations were detected in 9.5% (20/210) of minority patients and 20.88% (48/230) of Han Chinese patients. The most common Han Chinese GJB2 variants were c.235delC and c.299_300delAT, whereas c.235delC and c.109G > A were the most prevalent in minority patients. SLC26A4 mutations were detected in 5.71% (12/210) of minority patients and 14.35% (33/230) of Han Chinese patients, and mtDNA 12S rRNA mutations were detected in 4.28% (9/210) of minority patients and 9.13% (21/230) of Han Chinese patients. Conclusions These data indicate that the mutation frequencies of three deafness-associated genes were significantly higher in Han Chinese patients than in minority patients. Moreover, the GJB2 mutation spectrum was shown to differ between these two patient groups.
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Affiliation(s)
- Shihong Duan
- Department of Otolaryngology-Head and Neck Surgery, Second Hospital of Lanzhou University, Lanzhou, China
| | - Yufen Guo
- Department of Otolaryngology-Head and Neck Surgery, Second Hospital of Lanzhou University, Lanzhou, China
| | - Xingjian Chen
- Department of Otolaryngology-Head and Neck Surgery, Second Hospital of Lanzhou University, Lanzhou, China
| | - Yong Li
- Department of Otolaryngology-Head and Neck Surgery, Second Hospital of Lanzhou University, Lanzhou, China
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23
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Koohiyan M, Hashemzadeh-Chaleshtori M, Tabatabaiefar MA. Molecular diagnosis of SLC26A4-related hereditary hearing loss in a group of patients from two provinces of Iran. Intractable Rare Dis Res 2021; 10:23-30. [PMID: 33614372 PMCID: PMC7882080 DOI: 10.5582/irdr.2020.03090] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
The SLC26A4 gene has been described as the second gene involved in most cases of autosomal recessive non-syndromic hearing loss (ARNSHL), after GJB2. Over 500 different SLC26A4 mutations have been reported, with each ethnic population having its own distinctive mutations. Here, we aimed to determine the frequency and mutation profile of the SLC26A4 gene from two different provinces (center and west) of Iran. This study included 50 nuclear families with two or more siblings segregating presumed ARNSHL. All affected tested negative for mutations in GJB2 at the DFNB1 locus and were therefore screened for autozygosity by descent using short tandem repeat polymorphisms (STRPs) of DFNB4. Sanger sequencing was performed to screen the 20 exons of the SLC26A4 gene for the families linked to this locus. In silico analyses were also performed using available software tools. Four out of 25 (16%) and 3 of 25 (12%) studied families of Isfahan and Hamedan provinces, respectively. were linked to DFNB4. Sanger sequencing led to the identification of six different mutations, one of which (c.919-2A>G) was recurrent and accounted for 31% of all mutant alleles. One out of 7 (14.3%) families with mutations were confirmed to be Pendred syndrome (PS). The SLC26A4 mutations have a high carrying rate in ARNSHL Iranian patients. The identification of a disease causing mutation can be used to establish a genotypic diagnosis and provide important information to the patients and their families.
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Affiliation(s)
- Mahbobeh Koohiyan
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
- Cancer Research Center, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Morteza Hashemzadeh-Chaleshtori
- Cellular and Molecular Research Center, Basic Health Research Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Mohammad Amin Tabatabaiefar
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
- Pediatric Inherited Diseases Research Center, Research Institute for Primordial Prevention of Noncommunicable Disease, Isfahan University of Medical Sciences, Isfahan, Iran
- Address correspondence to:Mohammad Amin Tabatabaiefar, Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Hezarjarib St., Isfahan 81746-7346, Iran. E-mail:
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24
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Kınoğlu K, Orhan KS, Kara H, Öztürk O, Polat B, Aydoğan H, Çelik M, Ceviz AB, Güldiken Y. Investigation of DFNB4 SLC26A4 mutation in patients with enlarged vestibular aquaduct. Int J Pediatr Otorhinolaryngol 2020; 138:110379. [PMID: 33152970 DOI: 10.1016/j.ijporl.2020.110379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 08/02/2020] [Accepted: 09/09/2020] [Indexed: 11/30/2022]
Abstract
OBJECTIVES Mutations of the SLC26A4 gene causing enlarged vestibular aqueduct (EVA) syndrome have not yet been fully elucidated. The study aimed to investigate SLC26A4 mutations in patients with EVA syndrome in the Turkish population. Identifying these mutations may play an essential role in determining the prognosis, follow-up, and management options of these patients. METHODS Whole exome sequencing and/or Sanger sequencing of SLC26A4 in 22 patients with sensorineural hearing loss associated with isolated EVA without inner ear anomalies, and 22 controls were performed. RESULTS Twenty-two patients and 22 control subjects were included in the study. The onset of hearing loss was pre-lingual in 15 patients, and post-lingual in 7. The mean (standard deviation) vestibular aqueduct width of the patients was 3.23 mm (1.28). Twenty SLC26A4 variants, 15 of them unique, were identified in 22 patients. Among them, seven variants were heterozygous, and 13 were homozygous. The variants p.E37X (c.109G > T), p.Y27H (c.79T > C), p.C706Y (c.2117G > A) have not been previously reported. CONCLUSION The detection of rare and previously unreported mutations in our study showed that studies with a larger number of patients with EVA might reveal more role of the SLC26A4 gene. Besides, to understand the etiopathogenesis of the disease, other related genes also should be investigated.
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Affiliation(s)
- Kubilay Kınoğlu
- Istanbul University, Aziz Sancar Institute of Experimental Medicine, Turkey
| | - Kadir Serkan Orhan
- Istanbul University, Istanbul Faculty of Medicine, Department of Otorhinolaryngology
| | - Hakan Kara
- Istanbul University, Istanbul Faculty of Medicine, Department of Otorhinolaryngology.
| | - Oğuz Öztürk
- Istanbul University, Aziz Sancar Institute of Experimental Medicine, Turkey
| | - Beldan Polat
- Istanbul University, Istanbul Faculty of Medicine, Department of Otorhinolaryngology
| | - Hülya Aydoğan
- Istanbul University, Aziz Sancar Institute of Experimental Medicine, Turkey
| | - Mehmet Çelik
- Istanbul University, Istanbul Faculty of Medicine, Department of Otorhinolaryngology
| | - Ayşe Begüm Ceviz
- Istanbul University, Aziz Sancar Institute of Experimental Medicine, Turkey
| | - Yahya Güldiken
- Istanbul University, Istanbul Faculty of Medicine, Department of Otorhinolaryngology
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25
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Zhou K, Huang L, Feng M, Li X, Zhao Y, Liu F, Wei J, Qin D, Lu Q, Shi M, Qu S, Tang F. A novel SLC26A4 splicing mutation identified in two deaf Chinese twin sisters with enlarged vestibular aqueducts. Mol Genet Genomic Med 2020; 8:e1447. [PMID: 32770655 PMCID: PMC7549568 DOI: 10.1002/mgg3.1447] [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: 05/21/2020] [Revised: 07/15/2020] [Accepted: 07/16/2020] [Indexed: 12/13/2022] Open
Abstract
Background Variants in the SLC26A4 gene are correlated with nonsyndromic hearing loss with an enlarged vestibular aqueduct (EVA). This study aimed to identify the genetic causes in a Chinese family with EVA, and the pathogenicity of the detected variants. Methods We collected blood samples and clinical data from a pair of deaf twin sisters with EVA and their family members. As controls, a group of 500 normal‐hearing people were enrolled in our study. Twenty‐one exons and flanking splice sites of the SLC26A4 gene were screened for pathogenic mutations by polymerase chain reaction and bidirectional Sanger sequencing. Minigene assays were used to verify whether the novel SLC26A4 intronic mutation influenced the normal splicing of mRNA. Results Hearing loss in the twins with EVA was diagnosed using auditory tests and imaging examinations. Two pathogenic mutations, c.919‐2A>G and c.1614+5G>A were detected in SLC26A4, the latter of which has not been reported in the literature. The minigene expression in vitro confirmed that c.1614+5G>A could cause aberrant splicing, resulting in skipping over exon 14. Conclusions On the SLC26A4 gene, c.1614+5G>A is a pathogenic mutation. This finding enriches the mutational spectrum of the SLC26A4 gene and provides a basis for the genetic diagnosis of EVA.
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Affiliation(s)
- Kai Zhou
- Department of Otolaryngology & Head and Neck, The People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, China.,Guangxi Medical University, Nanning, Guangxi, China
| | - Lancheng Huang
- Department of Otolaryngology & Head and Neck, The People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, China.,Guangxi Medical University, Nanning, Guangxi, China
| | - Menglong Feng
- Department of Otolaryngology & Head and Neck, The People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, China.,Guangxi University of Chinese Medicine, Nanning, Guangxi, China
| | - Xinlei Li
- Medical Genetics Center, Southwest Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Yi Zhao
- Medical Genetics Center, Southwest Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Fei Liu
- Research Center of Medical Sciences, The People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Jiazhang Wei
- Department of Otolaryngology & Head and Neck, The People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Danxue Qin
- Department of Otolaryngology & Head and Neck, The People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Qiutian Lu
- Department of Otolaryngology & Head and Neck, The People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Min Shi
- Department of Otolaryngology & Head and Neck, The People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Shenhong Qu
- Department of Otolaryngology & Head and Neck, The People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Fengzhu Tang
- Department of Otolaryngology & Head and Neck, The People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
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Kanavy DM, McNulty SM, Jairath MK, Brnich SE, Bizon C, Powell BC, Berg JS. Comparative analysis of functional assay evidence use by ClinGen Variant Curation Expert Panels. Genome Med 2019; 11:77. [PMID: 31783775 PMCID: PMC6884856 DOI: 10.1186/s13073-019-0683-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 11/05/2019] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The 2015 American College of Medical Genetics and Genomics (ACMG) and the Association for Molecular Pathology (AMP) guidelines for clinical sequence variant interpretation state that "well-established" functional studies can be used as evidence in variant classification. These guidelines articulated key attributes of functional data, including that assays should reflect the biological environment and be analytically sound; however, details of how to evaluate these attributes were left to expert judgment. The Clinical Genome Resource (ClinGen) designates Variant Curation Expert Panels (VCEPs) in specific disease areas to make gene-centric specifications to the ACMG/AMP guidelines, including more specific definitions of appropriate functional assays. We set out to evaluate the existing VCEP guidelines for functional assays. METHODS We evaluated the functional criteria (PS3/BS3) of six VCEPs (CDH1, Hearing Loss, Inherited Cardiomyopathy-MYH7, PAH, PTEN, RASopathy). We then established criteria for evaluating functional studies based on disease mechanism, general class of assay, and the characteristics of specific assay instances described in the primary literature. Using these criteria, we extensively curated assay instances cited by each VCEP in their pilot variant classification to analyze VCEP recommendations and their use in the interpretation of functional studies. RESULTS Unsurprisingly, our analysis highlighted the breadth of VCEP-approved assays, reflecting the diversity of disease mechanisms among VCEPs. We also noted substantial variability between VCEPs in the method used to select these assays and in the approach used to specify strength modifications, as well as differences in suggested validation parameters. Importantly, we observed discrepancies between the parameters VCEPs specified as required for approved assay instances and the fulfillment of these requirements in the individual assays cited in pilot variant interpretation. CONCLUSIONS Interpretation of the intricacies of functional assays often requires expert-level knowledge of the gene and disease, and current VCEP recommendations for functional assay evidence are a useful tool to improve the accessibility of functional data by providing a starting point for curators to identify approved functional assays and key metrics. However, our analysis suggests that further guidance is needed to standardize this process and ensure consistency in the application of functional evidence.
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Affiliation(s)
- Dona M Kanavy
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Shannon M McNulty
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Meera K Jairath
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Sarah E Brnich
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Chris Bizon
- Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Bradford C Powell
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jonathan S Berg
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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27
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Koohiyan M. A systematic review of SLC26A4 mutations causing hearing loss in the Iranian population. Int J Pediatr Otorhinolaryngol 2019; 125:1-5. [PMID: 31228605 DOI: 10.1016/j.ijporl.2019.06.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 05/19/2019] [Accepted: 06/12/2019] [Indexed: 11/16/2022]
Abstract
OBJECTIVES The genetics of sensorineural hearing loss is characterized by a high degree of heterogeneity. In spite of this, mutations in the SLC26A4 gene, have been reported to be the second most common contributor after those of GJB2 in many populations. However, different results have been reported for the frequency of SLC26A4 mutations in Iran, which varies between 0 and 12.3%. Here, we have taken together and reviewed the spectrum and frequency of the reported SLC26A4 mutations to provide a comprehensive collection of data for SLC26A4 mutations and HL in the Iranian population and considered founder mutations. METHODS A systematic literature review of the PubMed, Google Scholar, Web of Science, and Science Direct databases was conducted for articles published before March 2019. The primary data of these studies including the number of samples, mutation frequency and so on were extracted. RESULTS Nine studies involved 827 unrelated families were included and analyzed for the type and prevalence of the SLC26A4 gene mutations. Altogether 39 different genetic mutations were detected. SLC26A4 mutations were found to be 6.39% in the population studied which is significantly lower than that identified in the east Asia. However, c.1334T > G was the most common mutation accounting for 10% of the populations studied. CONCLUSIONS This data gives an overview of the SLC26A4 mutations in Iran, which could be used for screening, diagnostic programs of live births and genetic counseling.
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Affiliation(s)
- Mahbobeh Koohiyan
- Cancer Research Center, Shahrekord University of Medical Sciences, Rahmatieh, Shahrekord, 8813833435, Iran.
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Oza AM, DiStefano MT, Hemphill SE, Cushman BJ, Grant AR, Siegert RK, Shen J, Chapin A, Boczek NJ, Schimmenti LA, Murry JB, Hasadsri L, Nara K, Kenna M, Booth KT, Azaiez H, Griffith A, Avraham KB, Kremer H, Rehm HL, Amr SS, Abou Tayoun AN. Expert specification of the ACMG/AMP variant interpretation guidelines for genetic hearing loss. Hum Mutat 2019; 39:1593-1613. [PMID: 30311386 DOI: 10.1002/humu.23630] [Citation(s) in RCA: 285] [Impact Index Per Article: 57.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 07/23/2018] [Accepted: 08/25/2018] [Indexed: 12/23/2022]
Abstract
Due to the high genetic heterogeneity of hearing loss (HL), current clinical testing includes sequencing large numbers of genes, which often yields a significant number of novel variants. Therefore, the standardization of variant interpretation is crucial to provide consistent and accurate diagnoses. The Hearing Loss Variant Curation Expert Panel was created within the Clinical Genome Resource to provide expert guidance for standardized genomic interpretation in the context of HL. As one of its major tasks, our Expert Panel has adapted the American College of Medical Genetics and Genomics/Association for Molecular Pathology (ACMG/AMP) guidelines for the interpretation of sequence variants in HL genes. Here, we provide a comprehensive illustration of the newly specified ACMG/AMP HL rules. Three rules remained unchanged, four rules were removed, and the remaining 21 rules were specified. These rules were further validated and refined using a pilot set of 51 variants assessed by curators and disease experts. Of the 51 variants evaluated in the pilot, 37% (19/51) changed category based upon application of the expert panel specified rules and/or aggregation of evidence across laboratories. These HL-specific ACMG/AMP rules will help standardize variant interpretation, ultimately leading to better care for individuals with HL.
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Affiliation(s)
- Andrea M Oza
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts.,Department of Otolaryngology and Communication Enhancement, Boston Children's Hospital, Boston, Massachusetts
| | - Marina T DiStefano
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts.,Harvard Medical School, Boston, Massachusetts
| | - Sarah E Hemphill
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts
| | - Brandon J Cushman
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts
| | - Andrew R Grant
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts
| | - Rebecca K Siegert
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts
| | - Jun Shen
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts.,Harvard Medical School, Boston, Massachusetts.,Department of Pathology, Brigham & Women's Hospital, Boston, Massachusetts
| | | | - Nicole J Boczek
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Lisa A Schimmenti
- Department of Otorhinolaryngology, Clinical Genomics and Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota
| | - Jaclyn B Murry
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts
| | - Linda Hasadsri
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Kiyomitsu Nara
- Division of Hearing and Balance Research, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, Tokyo, Japan
| | - Margaret Kenna
- Department of Otolaryngology and Communication Enhancement, Boston Children's Hospital, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts
| | - Kevin T Booth
- Molecular Otolaryngology and Renal Research Laboratories, Department of Otolaryngology, University of Iowa Hospital and Clinics, Iowa City, Iowa.,The Interdisciplinary Graduate Program in Molecular Medicine, Carver College of Medicine, University of Iowa, Iowa City, Iowa
| | - Hela Azaiez
- Molecular Otolaryngology and Renal Research Laboratories, Department of Otolaryngology, University of Iowa Hospital and Clinics, Iowa City, Iowa
| | - Andrew Griffith
- Audiology Unit, National Institute on Deafness and Other Communication Disorders (NIDCD), NIH, Bethesda, Maryland
| | - Karen B Avraham
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Hannie Kremer
- Department of Otorhinolaryngology and Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Heidi L Rehm
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts.,Harvard Medical School, Boston, Massachusetts.,Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts.,The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Sami S Amr
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts.,Harvard Medical School, Boston, Massachusetts.,Department of Pathology, Brigham & Women's Hospital, Boston, Massachusetts
| | - Ahmad N Abou Tayoun
- The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,The University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
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Xiang YB, Tang SH, Li HZ, Xu CY, Chen C, Xu YZ, Ding LR, Xu XQ. Mutation analysis of common deafness-causing genes among 506 patients with nonsyndromic hearing loss from Wenzhou city, China. Int J Pediatr Otorhinolaryngol 2019; 122:185-190. [PMID: 31035178 DOI: 10.1016/j.ijporl.2019.04.024] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 04/16/2019] [Accepted: 04/16/2019] [Indexed: 12/17/2022]
Abstract
OBJECTIVES The frequency and spectrum of mutations in deafness-causing genes differs significantly according to the ethnic population and region under investigation. The molecular etiology of nonsyndromic hearing loss (NSHL) in Wenzhou, China, has not yet been systematically elucidated. To provide accurate genetic testing and counseling in this area, we investigated the molecular etiology of NSHL in a deaf population from Wenzhou. METHODS A total 506 unrelated patients with NSHL were enrolled in this study. Nine hotspot mutations in four major deafness genes were investigated by sequencing (Group I: 187 patients enrolled between 2011 and 2015) or allele-specific PCR-based universal array (Group II: 319 patients enrolled between 2016 and 2017). The investigated genes included GJB2 (c.35delG, c.176_191del16, c.235delC, c.299-300delAT), SLC26A4 (c.2168A > G, c.919-2A > G), mtDNA 12SrRNA (m.1555A > G, m.1494C > T), and GJB3 (c.538C > T). Furthermore, whole coding region sequencing or improved multiplex ligation detection reaction (IMLDR) were performed for patients who carried mono-allelic variants of GJB2 and SLC26A4, in order to detect other mutations among these patients. RESULTS GJB2 mutations were detected in 22.92% (116/506) of the entire cohort and SLC26A4 mutations were found in 6.52% (33/506) of the cohort. GJB3 mutations were detected in 0.79% (4/506) of the cohort. The mutation rate of mitochondrial DNA 12SrRNA in our patients was 17.40% (88/506), including 17.00% (86/506) with the m.1555A > G mutation and 0.40% (2/506) with the m.1494C > T mutation. The allelic frequency of the c.235delC mutation was 14.62% (148/1012), which is significantly higher than that of c.109G > A (33/1012, 3.26%), c.299_300delAT (13/1012, 1.28%), and c.176_191del16 (6/1012, 0.59%). The most common pathogenic mutation of SLC26A4 was the c.919-2A > G mutation (37/1012, 3.66%), followed by c.2168A > G (6/1012, 0.59%), and c.1229C > T (4/1012, 0.40%). Moreover, five rare pathogenic variants of GJB2 and eight rare pathogenic variants of SLC26A4 were identified. CONCLUSION GJB2 is the primary deafness-causing gene in deaf patients from Wenzhou, China; this is consistent with what is observed in most Chinese populations. However, the surprisingly high rate of the m.1555A > G mutation (17.00%) in patients from Wenzhou was significantly higher than in other populations in China. These findings highlight the specificity of the common deafness-causing gene mutation spectrum in the Wenzhou area. This information may be of benefit for genetic counseling and risk assessment for deaf patients from this area.
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Affiliation(s)
- Yan-Bao Xiang
- Key Laboratory of Birth Defects, Department of Genetics, Wenzhou Central Hospital, 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.
| | - Huan-Zheng Li
- 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.
| | - Chong Chen
- 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.
| | - Li-Rong Ding
- 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.
| | - Xue-Qin Xu
- Key Laboratory of Birth Defects, Department of Genetics, Wenzhou Central Hospital, Wenzhou, China.
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Wen Z, Zhu H, Li Z, Zhang S, Zhang A, Zhang T, Fu X, Sun D, Zhang J, Gao J. A knock-in mouse model of Pendred syndrome with Slc26a4 L236P mutation. Biochem Biophys Res Commun 2019; 515:359-365. [PMID: 31155292 DOI: 10.1016/j.bbrc.2019.05.157] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 05/25/2019] [Indexed: 11/25/2022]
Abstract
SLC26A4 gene mutations lead to Pendred syndrome and non-syndromic hearing loss (DFNB4). The mouse model is well used to study the pathology of Pendred syndrome, however, mice with different Slc26a4 mutations exhibit different phenotypes, and these mice have severe deafness and inner ear malformations that are not imitated less severely Human phenotype. In this study, we generated a knock-in mouse model of Pendred syndrome with Slc26a4 L236P mutation to mimic the most common mutation found in human. Some L236P mice were observed to have significant vestibular dysfunction including torticollis and circling, the giant otoconia and destruction of the otoconial membrane was observed in L236P mice. Unlike other profoundly deafness in Slc26a4 mouse model, L236P mice present mild to profound hearing loss, consistent with the hearing threshold, inner ear hair cells also lost from slight to significant. Together, these data demonstrate that the L236P mouse phenotype is more similar to the human phenotype and should be used as a tool for further research into the human Pendred syndrome.
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Affiliation(s)
- Zongzhuang Wen
- Institute of Developmental Biology, School of Life Science, Shandong University, Jinan, Shandong, China
| | - Haixia Zhu
- State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, College of Pharmacy, Harbin Medical University, Harbin, Heilongjiang, China
| | - Zhenzu Li
- Department of Bioengineering, Shandong Polytechnic, Jinan, Shandong, China
| | - Sen Zhang
- Institute of Developmental Biology, School of Life Science, Shandong University, Jinan, Shandong, China
| | - Aizhen Zhang
- Institute of Developmental Biology, School of Life Science, Shandong University, Jinan, Shandong, China
| | - Tingting Zhang
- Institute of Developmental Biology, School of Life Science, Shandong University, Jinan, Shandong, China
| | - Xiaolong Fu
- Institute of Developmental Biology, School of Life Science, Shandong University, Jinan, Shandong, China
| | - Daqing Sun
- Department of Paediatric Surgery, Tianjin Medical University General Hospital, Tianjin, China.
| | - Jian Zhang
- Institute of Developmental Biology, School of Life Science, Shandong University, Jinan, Shandong, China.
| | - Jiangang Gao
- Institute of Developmental Biology, School of Life Science, Shandong University, Jinan, Shandong, China.
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A rapid improved multiplex ligation detection reaction method for the identification of gene mutations in hereditary hearing loss. PLoS One 2019; 14:e0215212. [PMID: 30973918 PMCID: PMC6459514 DOI: 10.1371/journal.pone.0215212] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 03/28/2019] [Indexed: 12/27/2022] Open
Abstract
Hearing loss (HL) is a common sensory disorder. More than half of HL cases can be attributed to genetic causes. There is no effective therapy for genetic HL at present, early diagnosis to reduce the incidence of genetic HL is important for clinical intervention in genetic HL. Previous studies have identified 111 nonsyndromic hearing loss genes. The most frequently mutated genes identified in NSHL patients in China include GJB2, SLC26A4, and the mitochondrial gene MT-RNR1. It is important to develop HL gene panels in Chinese population, which allow for etiologic diagnosis of both SHL and NSHL. In this study, a total of 220 unrelated Han Chinese patients with bilateral progressive SNHL and 50 unrelated healthy controls were performed Single nucleotide polymorphism (SNP) genotyping using an improved multiplex ligation detection reaction (iMLDR) technique, is to simultaneously detect a total of 32 mutations in ten HL genes, covering all currently characterized mutations involved in the etiology of nonsyndromic or syndromic hearing loss in the Chinese population. The 49 positive samples with known mutations were successfully detected using the iMLDR Technique. For 171 SNHL patients, gene variants were found in 57 cases (33.33%), among which, 30 patients carried mutations in GJB2, 14 patients carried mutations in SLC26A4, seven patients carried mutations in GJB3, and six patients carried mutations in MT-RNR1. The molecular etiology of deafness was confirmed in 12.9% (22/171) of patients carried homozygous variants. These results were verified by Sanger sequencing, indicating that the sensitivity and specificity of the iMLDR technique was 100%. We believe that the implementation of this population-specific technology at an efficient clinical level would have great value in HL diagnosis and treatment.
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Zhao X, Huang L, Wang X, Wang X, Zhao L, Cheng X, Ruan Y. Genotyping and audiological characteristics of infants with a single-allele SLC26A4 mutation. Int J Pediatr Otorhinolaryngol 2019; 116:153-158. [PMID: 30554688 DOI: 10.1016/j.ijporl.2018.10.046] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 10/26/2018] [Accepted: 10/28/2018] [Indexed: 11/16/2022]
Abstract
OBJECTIVES To identify second-allele variant in infants with a known single-allele mutation of the SLC26A4 gene and to determine the frequency of their occurrence; and to investigate the clinical audiological characteristics of infants with bi-allelic mutations in SLC26A4. METHODS The study subjects were 371 patients with a single-allele SLC26A4 mutation detected by neonatal deafness gene screening (4 genes and 9 pathogenic variants) who were treated at the otology outpatient department of Beijing Tongren Hospital. The exonic and flanking splice site regions of the SLC26A4 gene were sequenced for all patients. All patients with bi-allelic SLC26A4 mutations underwent audiological evaluation, and some also underwent temporal bone computed tomography and/or inner ear magnetic resonance imaging. RESULTS Of the 371 patients, 314 (84.64%) had an c.919-2A > G heterozygous mutation and 57 (15.36%) had a c.2168A > G (p.H723R) heterozygous mutation. 13 patients (3.50%) had a second-allele variant, including 11 (2.96%) with pathogenic mutations and 1 (0.27%) with a likely benign variant. Of the 13 patients with bi-allelic mutations, 11 had hearing loss and 2 had normal hearing, the latter of whom had c.919-2A > G/c.1766A > G and c.919-2A > G/c.757A > G compound heterozygous mutations, respectively. Four of the 13 patients with bi-allelic mutations had passed the universal newborn hearing screening, including 2 cases (15.38%) with hearing loss. The most prevalent degree of hearing loss was profound (40.91%), followed by severe (36.36%). The most prevalent audiometric configuration was sloping hearing loss (50.00%), followed by flat-type hearing loss (40.91%). CONCLUSIONS This is the first report in China of the frequency of occurrence of second-allele variant in infants with a known single-allele mutation of the SLC26A4 gene; the frequency was 3.50% for any type of variant and 2.96% for pathogenic mutations. A novel variant, c.1766A > G (p.Q589R), which is likely benign, was identified. The pathogenicity of c.757A > G (p.I253V) mutation deserves more in-depth research. For infants with bi-allelic SLC26A4 mutations, the degree of hearing loss was mainly severe-to-profound and the audiometric configuration was mainly sloping.
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Affiliation(s)
- Xuelei Zhao
- Beijing Tongren Hospital, Capital Medical University, Beijing, China; Beijing Institute of Otolaryngology, Beijing, China; Key Laboratory of Otolaryngology, Head and Neck Surgery, Ministry of Education, Beijing, China
| | - Lihui Huang
- Beijing Tongren Hospital, Capital Medical University, Beijing, China; Beijing Institute of Otolaryngology, Beijing, China; Key Laboratory of Otolaryngology, Head and Neck Surgery, Ministry of Education, Beijing, China.
| | - Xueyao Wang
- Beijing Tongren Hospital, Capital Medical University, Beijing, China; Beijing Institute of Otolaryngology, Beijing, China; Key Laboratory of Otolaryngology, Head and Neck Surgery, Ministry of Education, Beijing, China
| | - Xianlei Wang
- Beijing Tongren Hospital, Capital Medical University, Beijing, China; Beijing Institute of Otolaryngology, Beijing, China; Key Laboratory of Otolaryngology, Head and Neck Surgery, Ministry of Education, Beijing, China
| | - Liping Zhao
- Beijing Tongren Hospital, Capital Medical University, Beijing, China; Beijing Institute of Otolaryngology, Beijing, China; Key Laboratory of Otolaryngology, Head and Neck Surgery, Ministry of Education, Beijing, China
| | - Xiaohua Cheng
- Beijing Tongren Hospital, Capital Medical University, Beijing, China; Beijing Institute of Otolaryngology, Beijing, China; Key Laboratory of Otolaryngology, Head and Neck Surgery, Ministry of Education, Beijing, China
| | - Yu Ruan
- Beijing Tongren Hospital, Capital Medical University, Beijing, China; Beijing Institute of Otolaryngology, Beijing, China; Key Laboratory of Otolaryngology, Head and Neck Surgery, Ministry of Education, Beijing, China
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Ming L, Wang Y, Lu W, Sun T. A Mutational Analysis of GJB2, SLC26A4, MT-RNA1, and GJB3 in Children with Nonsyndromic Hearing Loss in the Henan Province of China. Genet Test Mol Biomarkers 2018; 23:51-56. [PMID: 30589569 DOI: 10.1089/gtmb.2018.0146] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Hearing impairment is one of the most common neurosensory disorders afflicting humans. Approximately half of all cases have a genetic etiology. The distribution and frequency of genetic mutations that cause deafness differ significantly by ethnic group and geographic region. METHODS 130 sporadic nonsyndromic hearing loss (NSHL) children from the Henan province were subjected to microarray-based mutation detection. Nine pathogenic mutations were detected in four of the most common deafness-related genes (GJB2, GJB3, SLC26A4, and MT-RNA1). RESULTS Fifty percent of the analyzed patients (65/130) were shown to have genetic defects known to be related to deafness. Slightly >30% (41/130) had biallelic pathogenic mutations. One patient had pathogenic mutations in their mitochondrial genes (MT-RNA1); no mutations were detected in the GJB3 gene. Twenty-three (17.69%) patients were carriers of a single mutation in a recessive gene; these findings alone, however, cannot be interpreted as a cause of hearing loss. Utilizing this molecular strategy, we were able to arrive at a conclusive diagnosis for 42 of the NSHL children. CONCLUSION Genetic factors play a major role in sporadic NSHL patients from the Henan province, but it is clear that our screen needs to be expanded to include additional genes and alleles. Screening of potential pathogenic genes is important for patient risk assessment.
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Affiliation(s)
- Liang Ming
- 1 Key Clinical Laboratory of Henan Province, Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University , Zhengzhou, China
| | - Yangxia Wang
- 1 Key Clinical Laboratory of Henan Province, Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University , Zhengzhou, China
| | - Wei Lu
- 2 Department of Otology, The First Affiliated Hospital of Zhengzhou University , Zhengzhou, China
| | - Ting Sun
- 1 Key Clinical Laboratory of Henan Province, Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University , Zhengzhou, China
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Li H, Qiu J, Zhu J, Huang Y. Gene mutation analysis and genetic counseling for patients with non-syndromic hearing loss in Linyi region. Exp Ther Med 2018; 17:413-417. [PMID: 30651814 PMCID: PMC6307381 DOI: 10.3892/etm.2018.6927] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 10/25/2018] [Indexed: 11/06/2022] Open
Abstract
Through gene mutation analysis of patients with non-syndromic hearing loss (NSHL) correct genetic counseling for patients with NSHL and their family members were provided. A total of 116 patients suffering from NSHL were selected, and Sanger sequencing was applied to analyze 31 mutation sites in four deafness genes [gap junction β-2 (GJB2), solute carrier family 26, member 4 (SLC26A4), GJB3 and mitochondria 12S ribosomal ribonucleic acid (12SrRNA)]. Based on detection results, for the families with reproductive needs, amniotic fluid was extracted from pregnant women during proper gestational weeks to identify fetal genotypes and predict hearing state. Among 116 patients with NSHL, 51 patients carrying definite pathogenic mutation were found, including 35 patients with GJB2 mutations, 14 patients with SLC26A4 gene mutations and 2 patients with mitochondrial deoxyribonucleic acid 12SrRNA (mtDNA 12SrRNA) mutations. No GJB3 gene mutation site was detected. In addition, prenatal diagnosis to 17 pregnant women who had given birth to babies with deafness was performed, and results suggested that genotypes of 6 fetuses were consistent with those of probands, genotypes of 8 fetuses were consistent with those of their parents, and no mutation was found in the other 3 fetuses. Gene mutation analysis of patients with NSHL can identify the etiology and provide appropriate genetic counseling and birth guiding for patients with NSHL and their family members. In addition, prenatal diagnosis to the families who plan to give birth again can avoid the natality of fetuses with hearing loss.
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Affiliation(s)
- Huafeng Li
- Genetics Laboratory, Women and Children's Health Care Hospital of Linyi, Linyi, Shandong 276014, P.R. China
| | - Jigang Qiu
- Genetics Laboratory, Women and Children's Health Care Hospital of Linyi, Linyi, Shandong 276014, P.R. China
| | - Jinping Zhu
- Genetics Laboratory, Women and Children's Health Care Hospital of Linyi, Linyi, Shandong 276014, P.R. China
| | - Yuqiang Huang
- Genetics Laboratory, Women and Children's Health Care Hospital of Linyi, Linyi, Shandong 276014, P.R. China
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Targeted Next-Generation Sequencing Facilitates Genetic Diagnosis and Provides Novel Pathogenetic Insights into Deafness with Enlarged Vestibular Aqueduct. J Mol Diagn 2018; 21:138-148. [PMID: 30268946 DOI: 10.1016/j.jmoldx.2018.08.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 08/13/2018] [Accepted: 08/30/2018] [Indexed: 12/24/2022] Open
Abstract
Enlarged vestibular aqueduct (EVA) is an inner-ear malformation associated with sensorineural hearing impairment. Most EVAs are associated with Pendred syndrome and nonsyndromic autosomal recessive deafness-4 (DFNB4), two autosomal-recessive disorders caused by mutations in SLC26A4. However, many EVA patients cannot have a confirmed diagnosis by screening common SLC26A4 mutations, constituting an enigma in genetic diagnosis. To enable comprehensive genetic examination and explore the etiologies of EVA, we designed a next-generation sequencing panel targeting the entire length of 3 Pendred syndrome/DFNB4 genes (SLC26A4, FOXI1, and KCNJ10) and exons of 10 other genes related to EVA and performed genetic testing in 50 EVA families without confirmative results on screening for SLC26A4 hotspots (c.919-2A>G and p.H723R). Bi-allelic SLC26A4 mutations were identified in 34 families and EYA1 mutations in two families, yielding a diagnostic rate of 72% (36 of 50). In addition, two variants were identified in KCNJ10 and FOXI1, but findings did not support the previous hypothesis that mutations in these two genes are probable contributors to EVA through recessive inheritance or digenic inheritance with SLC26A4. Of note, a large SLC26A4 deletion was confirmed in one step using our panel. These results show the utility of a next-generation sequencing-based panel to address EVA families by identifying various types of gene mutations with satisfactory diagnostic yields and provide novel insights into the pathogenesis of EVA.
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Zhao P, Lin L, Lan L. Analysis of mutation spectrum of common deafness-causing genes in Hakka newborns in southern China by semiconductor sequencing. Medicine (Baltimore) 2018; 97:e12285. [PMID: 30235673 PMCID: PMC6160144 DOI: 10.1097/md.0000000000012285] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 08/15/2018] [Indexed: 11/27/2022] Open
Abstract
Hearing loss is a common neurosensory disorder, approximately half of the cases are caused by genetic factors, and approximately 70% of hereditary hearing impairments are nonsyndromic hearing loss (NSHL). The mutations of GJB2 (gap junction beta-2 protein), GJB3 (gap junction beta-3 protein), SLC26A4 (solute carrier family 26 member 4), and MT-RNR1 (mitochondrially encoded 12S RNA) are the most common inherited causes of NSHL. Because of different genetic backgrounds, the mutation spectrum of these common deafness-causing genes varies among different regions in China. Because no data are known on these mutations among the Hakka population of Southern China, we aim to investigate the mutation spectrum to add these to neonatal screening and genetic counseling. A total of 1252 blood samples from newborns have been detected by semiconductor sequencing for 100 mutations loci of 18 deafness-causing genes. Of the participants, 95 subjects carried deafness-causing genes mutations with the carrier rate of 7.59%. The mutation frequencies of GJB2, SLC26A4, GJB3, and mitochondrial genes were 3.04%, 3.51%, 0.16%, and 0.88%, respectively. We followed up subjects with single-gene homozygous or compound heterozygous mutations. Our study firstly analyzed deafness-causing genes mutation spectrum in Hakka population, providing evidence for future neonatal screening and genetic counseling in this area.
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Affiliation(s)
- Pingsen Zhao
- Clinical Core Laboratory
- Center for Precision Medicine, Meizhou People's Hospital (Huangtang Hospital), Meizhou Hospital Affiliated to Sun Yat-sen University
- Guangdong Provincial Engineering and Technology Research Center for Molecular Diagnostics of Cardiovascular Diseases
- Meizhou Municipal Engineering and Technology Research Center for Molecular Diagnostics of Cardiovascular Diseases
- Meizhou Municipal Engineering and Technology Research Center for Molecular Diagnostics of Major Genetic Disorders
- Prenatal Diagnosis Center, Meizhou People's Hospital (Huangtang Hospital), Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, P. R. China
| | - Lifang Lin
- Clinical Core Laboratory
- Center for Precision Medicine, Meizhou People's Hospital (Huangtang Hospital), Meizhou Hospital Affiliated to Sun Yat-sen University
- Guangdong Provincial Engineering and Technology Research Center for Molecular Diagnostics of Cardiovascular Diseases
- Meizhou Municipal Engineering and Technology Research Center for Molecular Diagnostics of Cardiovascular Diseases
- Meizhou Municipal Engineering and Technology Research Center for Molecular Diagnostics of Major Genetic Disorders
- Prenatal Diagnosis Center, Meizhou People's Hospital (Huangtang Hospital), Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, P. R. China
| | - Liubing Lan
- Prenatal Diagnosis Center, Meizhou People's Hospital (Huangtang Hospital), Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, P. R. China
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Kuwabara MF, Wasano K, Takahashi S, Bodner J, Komori T, Uemura S, Zheng J, Shima T, Homma K. The extracellular loop of pendrin and prestin modulates their voltage-sensing property. J Biol Chem 2018; 293:9970-9980. [PMID: 29777056 DOI: 10.1074/jbc.ra118.001831] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 04/24/2018] [Indexed: 12/21/2022] Open
Abstract
Pendrin and prestin belong to the solute carrier 26 (SLC26) family of anion transporters. Prestin is unique among the SLC26 family members in that it displays voltage-driven motor activity (electromotility) and concurrent gating currents that manifest as nonlinear cell membrane electrical capacitance (nonlinear capacitance (NLC)). Although the anion transport mechanism of the SLC26 proteins has begun to be elucidated, the molecular mechanism of electromotility, which is thought to have evolved from an ancestral ion transport mechanism, still remains largely elusive. Here, we demonstrate that pendrin also exhibits large NLC and that charged residues present in one of the extracellular loops of pendrin and prestin play significant roles in setting the voltage-operating points of NLC. Our results suggest that the molecular mechanism responsible for sensing voltage is not unique to prestin among the members of the SLC26 family and that this voltage-sensing mechanism works independently of the anion transport mechanism.
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Affiliation(s)
- Makoto F Kuwabara
- From the Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Koichiro Wasano
- the Department of Otolaryngology-Head and Neck Surgery, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611
| | - Satoe Takahashi
- the Department of Otolaryngology-Head and Neck Surgery, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611
| | | | - Tomotaka Komori
- From the Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Sotaro Uemura
- From the Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Jing Zheng
- the Department of Otolaryngology-Head and Neck Surgery, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611.,The Hugh Knowles Center for Clinical and Basic Science in Hearing and Its Disorders, Northwestern University, Evanston, Illinois 60608
| | - Tomohiro Shima
- From the Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan,
| | - Kazuaki Homma
- the Department of Otolaryngology-Head and Neck Surgery, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, .,The Hugh Knowles Center for Clinical and Basic Science in Hearing and Its Disorders, Northwestern University, Evanston, Illinois 60608
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38
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Large scale newborn deafness genetic screening of 142,417 neonates in Wuhan, China. PLoS One 2018; 13:e0195740. [PMID: 29634755 PMCID: PMC5892933 DOI: 10.1371/journal.pone.0195740] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 03/28/2018] [Indexed: 11/19/2022] Open
Abstract
Almost one third of the three million people in China suffering severe deafness are children, and 50% of these cases are believed to have genetic components to their etiology. Newborn hearing genetic screening can complement Universal Neonatal Hearing Screening for the diagnosis of congenital hearing loss as well as identifying children at risk for late-onset and progressive hearing impairment. The aim of this joint academic and Ministry of Health project was to prototype a cost effective newborn genetic screen in a community health setting on a city-wide level, and to ascertain the prevalence of variation at loci that have been associated with non-syndromic hearing loss. With the participation of 143 local hospitals in the city of Wuhan, China we screened 142,417 neonates born between May 2014 and Dec. 2015. The variants GJB2 c.235delC, SLC26A4 c.919-2A>G, and mitochondrial variants m.1555A>G and m.1494C>T were assayed using real time PCR. Newborns found to carry a variant were re-assayed by sequencing in duplicate. Within a subset of 707 newborns we assayed using real-time PCR and ARMS-PCR to compare cost, sensitivity and operating procedure. The most frequent hearing loss associated allele detected in this population was the 235delC variant in GJB2 gene. In total, 4289 (3.01%) newborns were found to carry at least one allele of either GJB2 c.235delC, SLC26A4 c.919-2A>G or two assayed MT-RNR1 variants. There was complete accordance between the real-time PCR and the ARMS PCR, though the real-time PCR had a much lower failure rate. Real-time PCR had a lower cost and operating time than ARMS PCR. Ongoing collaboration with the participating hospitals will determine the specificity and sensitivity of the association of the variants with hearing loss at birth and arising in early childhood, allowing an estimation of the benefits of newborn hearing genetic screening in a large-scale community setting.
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Duan SH, Ma JL, Yang XL, Guo YF. Simultaneous multi‑gene mutation screening using SNPscan in patients from ethnic minorities with nonsyndromic hearing‑impairment in Northwest China. Mol Med Rep 2017; 16:6722-6728. [PMID: 28901477 PMCID: PMC5865789 DOI: 10.3892/mmr.2017.7431] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 05/11/2017] [Indexed: 12/31/2022] Open
Abstract
The present study aimed to investigate the molecular etiology of nonsyndromic hearing impairment (HI) in hearing impaired populations of Hui, Tibetan, and Tu ethnicities in northwest China. A total of 283 unrelated subjects with HI who attended special education schools in northwest China were enrolled in the present study. Single-nucleotide polymorphisms (SNPs) in three common deafness-related genes, gap junction protein β2 (GJB2), solute carrier family 26 member 4 (SLC26A4) and mitochondrially encoded 12S RNA (mtDNA12SrRNA), were detected using a SNPscan technique. GJB2 mutations were detected in 14.89% of Hui patients, 9.37% of Tibetan patients and 11.83% of Tu patients. The most prevalent GJB2 mutation in the Hui and Tu patients was c.235delC. In the Tibetan patients, the c.109G>A SNP exhibited the highest allele frequency. SLC26A4 mutations were detected in 10.64% of Hui patients, 6.25% of Tibetan patients, and 8.6% of Tu patients. The most common SLC26A4 mutation was c.919-2A>Gin the Hui, Tibetan, and Tu patients, and the second most common SLC26A4 mutations in these patients were c.1517T>G, c.1226G>A andc.2168A>G, respectively. The mutation rates ofmtDNA12SrRNA in the Hui, Tibetan, and Tu patients were 1.06, 5.21, and 5.38%, respectively. These findings demonstrate that the mutation spectra of these deafness-related genes are unique amongst these three ethnic groups. This information will be helpful in designing a protocol for genetic testing for deafness and for achieving accurate molecular diagnoses in northwest China.
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Affiliation(s)
- Shi-Hong Duan
- Department of Otolaryngology‑Head and Neck Surgery, Second Hospital of Lanzhou University, Lanzhou, Gansu 730030, P.R. China
| | - Jian-Li Ma
- Department of Otolaryngology‑Head and Neck Surgery, Second Hospital of Lanzhou University, Lanzhou, Gansu 730030, P.R. China
| | - Xiao-Long Yang
- Department of Otolaryngology‑Head and Neck Surgery, Second Hospital of Lanzhou University, Lanzhou, Gansu 730030, P.R. China
| | - Yu-Fen Guo
- Department of Otolaryngology‑Head and Neck Surgery, Second Hospital of Lanzhou University, Lanzhou, Gansu 730030, P.R. China
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40
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Luo J, Bai X, Zhang F, Xiao Y, Gu L, Han Y, Fan Z, Li J, Xu L, Wang H. Prevalence of Mutations in Deafness-Causing Genes in Cochlear Implanted Patients with Profound Nonsyndromic Sensorineural Hearing Loss in Shandong Province, China. Ann Hum Genet 2017; 81:258-266. [PMID: 28786104 DOI: 10.1111/ahg.12207] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Revised: 06/29/2017] [Accepted: 06/30/2017] [Indexed: 11/27/2022]
Abstract
The mutations of GJB2, SLC26A4, and mtDNA12SrRNA are the most common inherited causes of nonsyndromic sensorineural hearing loss (NSHL) in China, yet previous genetic screenings were mainly carried on patients with moderate-to-profound impairment. We aimed to detect the mutation frequencies in NSHL population within a more specified range of severity. Patients with profound NSHL who had undergone cochlear implantation in the Shandong Provincial Hospital (Shandong, China) were recruited. The majority (n = 472) were between 0.7 and 6 years old, and the remaining (n = 63) were between 6 and 70 years old. In total, 115 mutation alleles of the three genes were screened with SNP scan assay. Of the patients, 19.44% (104/535) were found to have GJB2 mutations, and the most common allele was c.235delC, followed by c.299_300delAT and c.109G>A. SLC26A4 mutations were detected in 13.46% patients (72/535), and the most common allele was c.919-2A>G (IVS7-2A>G), followed by c.1174A>T and c.2168A>G. Seven patients (1.31%) carried mutations in mtDNA12SrRNA, with the alleles of m.1555A>G and m.1494C>T. We found the allele frequency of c.109G>A (GJB2) was relatively lower in the profound NSHL population in comparison to the moderate-to-profound ones, and the c.1174A>T (SLC26A4) relatively higher. It suggests those mutations may be connected with the degree of deafness, which needs more observations and analyses to support.
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Affiliation(s)
- Jianfen Luo
- Department of Otorhinolaryngology Head and Neck Surgery, Shandong Provincial Hospital Affiliated to Shandong University, Shandong, China.,Shandong Provincial Key Laboratory of Otology, Shandong, China
| | - Xiaohui Bai
- Department of Otorhinolaryngology Head and Neck Surgery, Shandong Provincial Hospital Affiliated to Shandong University, Shandong, China.,Shandong Provincial Key Laboratory of Otology, Shandong, China
| | - Fengguo Zhang
- Department of Otorhinolaryngology Head and Neck Surgery, Shandong Provincial Hospital Affiliated to Shandong University, Shandong, China.,Shandong Provincial Key Laboratory of Otology, Shandong, China
| | - Yun Xiao
- Department of Otorhinolaryngology Head and Neck Surgery, Shandong Provincial Hospital Affiliated to Shandong University, Shandong, China.,Shandong Provincial Key Laboratory of Otology, Shandong, China
| | - Lintao Gu
- Department of Otorhinolaryngology Head and Neck Surgery, Shandong Provincial Hospital Affiliated to Shandong University, Shandong, China
| | - Yuechen Han
- Department of Otorhinolaryngology Head and Neck Surgery, Shandong Provincial Hospital Affiliated to Shandong University, Shandong, China.,Shandong Provincial Key Laboratory of Otology, Shandong, China
| | - Zhaomin Fan
- Department of Otorhinolaryngology Head and Neck Surgery, Shandong Provincial Hospital Affiliated to Shandong University, Shandong, China.,Shandong Provincial Key Laboratory of Otology, Shandong, China
| | - Jianfeng Li
- Department of Otorhinolaryngology Head and Neck Surgery, Shandong Provincial Hospital Affiliated to Shandong University, Shandong, China.,Shandong Provincial Key Laboratory of Otology, Shandong, China
| | - Lei Xu
- Department of Otorhinolaryngology Head and Neck Surgery, Shandong Provincial Hospital Affiliated to Shandong University, Shandong, China.,Shandong Provincial Key Laboratory of Otology, Shandong, China
| | - Haibo Wang
- Department of Otorhinolaryngology Head and Neck Surgery, Shandong Provincial Hospital Affiliated to Shandong University, Shandong, China.,Shandong Provincial Key Laboratory of Otology, Shandong, China
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41
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Abstract
Mutations in gap junction proteins encoding beta connexions are believed to be a major cause for congenital hearing loss. The purpose of this study was to do comparative analyses of frequencies of most prominent mutations responsible for congenital deafness. Using fluorescence PCR method, the entire coding region of GJB2 gene, GJB3 gene, and SLC26A4 was analyzed. Direct DNA sequencing was used to analyze mutations in these genes among unrelated 2,674 cases of newborns. Also, 12S rRNA mutation was also studied in these cases. In 2,674 cases of newborns from June 2013 to June 2014, found deafness mutation in 137 cases (5.12 % of carrier rate), carrying GJB2 mutations in 68 cases (2.54 % of carry rate), GJB3 mutations in 10 cases (0.37 % of carry rate), SLC26A4 mutations in 54 cases (2.02 % of carry rate), and mitochondrial 12S rRNA mutations in five cases (0.19 % of carry rate). The study concludes that GJB2 gene mutation is the most common and mitochondrial 12S rRNA mutations are the least common mutation for congenital hearing loss in Chinese newborns.
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42
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Lebeko K, Manyisa N, Chimusa ER, Mulder N, Dandara C, Wonkam A. A Genomic and Protein-Protein Interaction Analyses of Nonsyndromic Hearing Impairment in Cameroon Using Targeted Genomic Enrichment and Massively Parallel Sequencing. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2017; 21:90-99. [PMID: 28075205 DOI: 10.1089/omi.2016.0171] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Hearing impairment (HI) is one of the leading causes of disability in the world, impacting the social, economic, and psychological well-being of the affected individual. This is particularly true in sub-Saharan Africa, which carries one of the highest burdens of this condition. Despite this, there are limited data on the most prevalent genes or mutations that cause HI among sub-Saharan Africans. Next-generation technologies, such as targeted genomic enrichment and massively parallel sequencing, offer new promise in this context. This study reports, for the first time to the best of our knowledge, on the prevalence of novel mutations identified through a platform of 116 HI genes (OtoSCOPE®), among 82 African probands with HI. Only variants OTOF NM_194248.2:c.766-2A>G and MYO7A NM_000260.3:c.1996C>T, p.Arg666Stop were found in 3 (3.7%) and 5 (6.1%) patients, respectively. In addition and uniquely, the analysis of protein-protein interactions (PPI), through interrogation of gene subnetworks, using a custom script and two databases (Enrichr and PANTHER), and an algorithm in the igraph package of R, identified the enrichment of sensory perception and mechanical stimulus biological processes, and the most significant molecular functions of these variants pertained to binding or structural activity. Furthermore, 10 genes (MYO7A, MYO6, KCTD3, NUMA1, MYH9, KCNQ1, UBC, DIAPH1, PSMC2, and RDX) were identified as significant hubs within the subnetworks. Results reveal that the novel variants identified among familial cases of HI in Cameroon are not common, and PPI analysis has highlighted the role of 10 genes, potentially important in understanding HI genomics among Africans.
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Affiliation(s)
- Kamogelo Lebeko
- 1 Division of Human Genetics, Department of Pathology, Faculty of Health Sciences - University of Cape Town , Cap Town, South Africa
| | - Noluthando Manyisa
- 1 Division of Human Genetics, Department of Pathology, Faculty of Health Sciences - University of Cape Town , Cap Town, South Africa
| | - Emile R Chimusa
- 1 Division of Human Genetics, Department of Pathology, Faculty of Health Sciences - University of Cape Town , Cap Town, South Africa
| | - Nicola Mulder
- 2 Division of Computational Biology, Faculty of Health Sciences - University of Cape Town , Cap Town, South Africa
| | - Collet Dandara
- 1 Division of Human Genetics, Department of Pathology, Faculty of Health Sciences - University of Cape Town , Cap Town, South Africa
| | - Ambroise Wonkam
- 1 Division of Human Genetics, Department of Pathology, Faculty of Health Sciences - University of Cape Town , Cap Town, South Africa .,3 Department of Medicine, Faculty of Health Sciences - University of Cape Town , Cap Town, South Africa
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43
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Mapping pathogenic mutations suggests an innovative structural model for the pendrin (SLC26A4) transmembrane domain. Biochimie 2016; 132:109-120. [PMID: 27771369 DOI: 10.1016/j.biochi.2016.10.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 10/03/2016] [Indexed: 12/16/2022]
Abstract
Human pendrin (SLC26A4) is an anion transporter mostly expressed in the inner ear, thyroid and kidney. SLC26A4 gene mutations are associated with a broad phenotypic spectrum, including Pendred Syndrome and non-syndromic hearing loss with enlarged vestibular aqueduct (ns-EVA). No experimental structure of pendrin is currently available, making phenotype-genotype correlations difficult as predictions of transmembrane (TM) segments vary in number. Here, we propose a novel three-dimensional (3D) pendrin transmembrane domain model based on the SLC26Dg transporter. The resulting 14 TM topology was found to include two non-canonical transmembrane segments crucial for pendrin activity. Mutation mapping of 147 clinically validated pathological mutations shows that most affect two previously undescribed TM regions.
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44
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Franzè A, Esposito G, Di Domenico C, Iossa S, Sauchelli G, Fioretti T, Cavaliere M, Auletta G, Corvino V, Laria C, Malesci R, Marciano E, Salvatore F. SLC26A4 genotypes associated with enlarged vestibular aqueduct malformation in south Italian children with sensorineural hearing loss. Clin Chem Lab Med 2016; 54:e259-63. [PMID: 26894580 DOI: 10.1515/cclm-2015-1216] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 01/08/2016] [Indexed: 01/26/2023]
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45
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Lebeko K, Sloan-Heggen CM, Noubiap JJN, Dandara C, Kolbe DL, Ephraim SS, Booth KT, Azaiez H, Santos-Cortez RLP, Leal SM, Smith RJH, Wonkam A. Targeted genomic enrichment and massively parallel sequencing identifies novel nonsyndromic hearing impairment pathogenic variants in Cameroonian families. Clin Genet 2016; 90:288-90. [PMID: 27246798 DOI: 10.1111/cge.12799] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 04/19/2016] [Accepted: 05/01/2016] [Indexed: 01/22/2023]
Abstract
In sub-Saharan Africa GJB2-related nonsyndromic hearing impairment (NSHI) is rare. Ten Cameroonian families was studied using a platform (OtoSCOPE®) with 116 genes. In seven of 10 families (70%), 12 pathogenic variants were identified in six genes. Five of the 12 (41.6%) variants are novel. These results confirm the efficiency of comprehensive genetic testing in defining the causes of NSHI in sub-Saharan Africa.
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Affiliation(s)
- K Lebeko
- Division of Human Genetics, Department of Pathology, Faculty of Health Sciences University of Cape Town, Cape Town, South Africa
| | - C M Sloan-Heggen
- Department of Otolaryngology, Molecular Otolaryngology and Renal Research Laboratories, The University of Iowa, Iowa City, IA, USA
| | - J J N Noubiap
- Department of Medicine, Faculty of Health Sciences University of Cape Town, Cape Town, South Africa
| | - C Dandara
- Division of Human Genetics, Department of Pathology, Faculty of Health Sciences University of Cape Town, Cape Town, South Africa
| | - D L Kolbe
- Department of Otolaryngology, Molecular Otolaryngology and Renal Research Laboratories, The University of Iowa, Iowa City, IA, USA
| | - S S Ephraim
- Department of Otolaryngology, Molecular Otolaryngology and Renal Research Laboratories, The University of Iowa, Iowa City, IA, USA
| | - K T Booth
- Department of Otolaryngology, Molecular Otolaryngology and Renal Research Laboratories, The University of Iowa, Iowa City, IA, USA
| | - H Azaiez
- Department of Otolaryngology, Molecular Otolaryngology and Renal Research Laboratories, The University of Iowa, Iowa City, IA, USA
| | - R L P Santos-Cortez
- Center for Statistical Genetics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - S M Leal
- Center for Statistical Genetics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - R J H Smith
- Department of Otolaryngology, Molecular Otolaryngology and Renal Research Laboratories, The University of Iowa, Iowa City, IA, USA
| | - A Wonkam
- Division of Human Genetics, Department of Pathology, Faculty of Health Sciences University of Cape Town, Cape Town, South Africa.,Department of Medicine, Faculty of Health Sciences University of Cape Town, Cape Town, South Africa
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46
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Ma D, Zhang J, Luo C, Lin Y, Ji X, Hu P, Xu Z. Genetic counseling for patients with nonsyndromic hearing impairment directed by gene analysis. Mol Med Rep 2016; 13:1967-74. [PMID: 26783197 PMCID: PMC4769003 DOI: 10.3892/mmr.2016.4769] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2015] [Accepted: 11/10/2015] [Indexed: 11/06/2022] Open
Abstract
The aim of the present study was to investigate the genetic etiology of patients with nonsyndromic hearing impairment through gene analysis, and provide accurate genetic counseling and prenatal diagnosis for deaf patients and families with deaf children. Previous molecular etiological studies have demonstrated that the most common molecular changes in Chinese patients with nonsyndromic hearing loss (NSHL) involved gap junction protein β 2, solute carrier family 26, member 4 (SLC26A4), and mitochondrial DNA 12S rRNA. A total of 117 unrelated NSHL patients were included. Mutation screening was performed by Sanger sequencing in GJB2, 12S rRNA, and the hot‑spot regions of SLC26A4. In addition, patients with a single mutation of SLC26A4 in the hot‑spot regions underwent complete exon sequencing to identify a mutation in the other allele. A total of 36 of the 117 deaf patients were confirmed to have two pathogenic mutations, which included 4 deaf couples, husband or wife in 11 deaf couples and 17 deaf individuals. In addition, prenatal diagnoses was performed in 7 pregnant women at 18‑21 weeks gestation who had previously given birth to a deaf child, and the results showed that two fetal genotypes were the same as the proband's genotypes, four fetuses carried one pathogenic gene from their parents, and one fetus was identified to have no mutations. Taken together, the genetic testing of deaf patients can provide reasonable guidance to deaf patients and families with deaf children.
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Affiliation(s)
- Dingyuan Ma
- Department of Prenatal Diagnosis, State Key Laboratory of Reproductive Medicine, Nanjing Maternity and Child Health Care Hospital Affiliated to Nanjing Medical University, Nanjing, Jiangsu 210029, P.R. China
| | - Jingjing Zhang
- Department of Prenatal Diagnosis, State Key Laboratory of Reproductive Medicine, Nanjing Maternity and Child Health Care Hospital Affiliated to Nanjing Medical University, Nanjing, Jiangsu 210029, P.R. China
| | - Chunyu Luo
- Department of Prenatal Diagnosis, State Key Laboratory of Reproductive Medicine, Nanjing Maternity and Child Health Care Hospital Affiliated to Nanjing Medical University, Nanjing, Jiangsu 210029, P.R. China
| | - Ying Lin
- Department of Prenatal Diagnosis, State Key Laboratory of Reproductive Medicine, Nanjing Maternity and Child Health Care Hospital Affiliated to Nanjing Medical University, Nanjing, Jiangsu 210029, P.R. China
| | - Xiuqing Ji
- Department of Prenatal Diagnosis, State Key Laboratory of Reproductive Medicine, Nanjing Maternity and Child Health Care Hospital Affiliated to Nanjing Medical University, Nanjing, Jiangsu 210029, P.R. China
| | - Ping Hu
- Department of Prenatal Diagnosis, State Key Laboratory of Reproductive Medicine, Nanjing Maternity and Child Health Care Hospital Affiliated to Nanjing Medical University, Nanjing, Jiangsu 210029, P.R. China
| | - Zhengfeng Xu
- Department of Prenatal Diagnosis, State Key Laboratory of Reproductive Medicine, Nanjing Maternity and Child Health Care Hospital Affiliated to Nanjing Medical University, Nanjing, Jiangsu 210029, P.R. China
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47
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de Moraes VCS, Bernardinelli E, Zocal N, Fernandez JA, Nofziger C, Castilho AM, Sartorato EL, Paulmichl M, Dossena S. Reduction of Cellular Expression Levels Is a Common Feature of Functionally Affected Pendrin (SLC26A4) Protein Variants. Mol Med 2016; 22:41-53. [PMID: 26752218 DOI: 10.2119/molmed.2015.00226] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Accepted: 01/04/2016] [Indexed: 11/06/2022] Open
Abstract
Sequence alterations in the pendrin gene (SLC26A4) leading to functionally affected protein variants are frequently involved in the pathogenesis of syndromic and nonsyndromic deafness. Considering the high number of SLC26A4 sequence alterations reported to date, discriminating between functionally affected and unaffected pendrin protein variants is essential in contributing to determine the genetic cause of deafness in a given patient. In addition, identifying molecular features common to the functionally affected protein variants can be extremely useful to design future molecule-directed therapeutic approaches. Here we show the functional and molecular characterization of six previously uncharacterized pendrin protein variants found in a cohort of 58 Brazilian deaf patients. Two variants (p.T193I and p.L445W) were undetectable in the plasma membrane, completely retained in the endoplasmic reticulum and showed no transport function; four (p.P142L, p.G149R, p.C282Y and p.Q413R) showed reduced function and significant, although heterogeneous, expression levels in the plasma membrane. Importantly, total expression levels of all of the functionally affected protein variants were significantly reduced with respect to the wild-type and a fully functional variant (p.R776C), regardless of their subcellular localization. Interestingly, reduction of expression may also reduce the transport activity of variants with an intrinsic gain of function (p.Q413R). As reduction of overall cellular abundance was identified as a common molecular feature of pendrin variants with affected function, the identification of strategies to prevent reduction in expression levels may represent a crucial step of potential future therapeutic interventions aimed at restoring the transport activity of dysfunctional pendrin variants.
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Affiliation(s)
- Vanessa C S de Moraes
- Center of Molecular Biology and Genetic Engineering (CBMEG), Molecular Biology Laboratory, State University of Campinas, UNICAMP, Campinas/São Paulo, Brazil
| | - Emanuele Bernardinelli
- Institute of Pharmacology and Toxicology, Paracelsus Medical University, Salzburg, Austria
| | - Nathalia Zocal
- Center of Molecular Biology and Genetic Engineering (CBMEG), Molecular Biology Laboratory, State University of Campinas, UNICAMP, Campinas/São Paulo, Brazil
| | - Jhonathan A Fernandez
- Center of Molecular Biology and Genetic Engineering (CBMEG), Molecular Biology Laboratory, State University of Campinas, UNICAMP, Campinas/São Paulo, Brazil
| | - Charity Nofziger
- Institute of Pharmacology and Toxicology, Paracelsus Medical University, Salzburg, Austria
| | - Arthur M Castilho
- Otology, Audiology and Implantable Ear Prostheses, State University of Campinas, UNICAMP, Campinas/São Paulo, Brazil
| | - Edi L Sartorato
- Center of Molecular Biology and Genetic Engineering (CBMEG), Molecular Biology Laboratory, State University of Campinas, UNICAMP, Campinas/São Paulo, Brazil
| | - Markus Paulmichl
- Institute of Pharmacology and Toxicology, Paracelsus Medical University, Salzburg, Austria
| | - Silvia Dossena
- Institute of Pharmacology and Toxicology, Paracelsus Medical University, Salzburg, Austria
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Lu YJ, Yao J, Wei QJ, Xing GQ, Cao X. Diagnostic Value of SLC26A4 Mutation Status in Hereditary Hearing Loss With EVA: A PRISMA-Compliant Meta-Analysis. Medicine (Baltimore) 2015; 94:e2248. [PMID: 26683941 PMCID: PMC5058913 DOI: 10.1097/md.0000000000002248] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Many SLC26A4 mutations have been identified in patients with nonsyndromic enlarged vestibular aqueduct (EVA). However, the roles of SLC26A4 genotypes and phenotypes in hereditary deafness remain unexplained. This study aims to perform a meta-analysis based on the PRISMA statement to evaluate the diagnostic value of SLC26A4 mutant alleles and their correlations with multiethnic hearing phenotypes in EVA patients. The systematic literature search of the PubMed, Wiley Online Library, EMBASE, Web of Science, and Science Direct databases was conducted in English for articles published before July 15, 2015. Two investigators independently reviewed retrieved literature and evaluated eligibility. Discrepancy was resolved by discussion and a third investigator. Quality of included studies was evaluated using Newcastle-Ottawa Quality Assessment Scale. Data were synthesized using random-effect or fixed-effect models. The effect sizes were estimated by measuring odds ratios (ORs) with 95% confidence interval (CI). Twenty-five eligible studies involved 2294 cases with EVA data. A total of 272 SLC26A4 variations were found in deafness with EVA and 26 mutations of SCL26A4 had higher frequency. The overall OR was 646.71 (95% CI: 383.30-1091.15, P = 0.000). A total of 22 mutants were considered statistically significant in all ethnicities (ORs >1, P < 0.05). In particular, 8 mutants were specificity of EVA phenotypes in mutations of SLC26A4 for Asia deafness populations (ORs >1, P < 0.05), 4 mutants for Europe and North America (ORs >1, P < 0.05), and the IVS7-2A>G mutations in SLC26A4 were found to have the highest frequency in deafness individuals with EVA phenotype (62.42%). Moreover, subgroups for studies limited to cases with EVA phenotype, 11 mutants relevant risks (RRs) were P < 0.05, especially for IVS7-2A>G bi-allelic mutants assayed in a deafness population (RR = 0.880, P = 0.000). Diagnostic accuracy of SLC26A4 mutation results also identified the significant association of IVS7-2A>G (AUC = 0.99, 95% CI: 0.97-0.99) and p.H723R (AUC = 0.99, 95% CI: 0.98-1.00) detecting deafness with EVA. To conclude, the IVS7-2A>G and H723R in SLC26A4 present a significant predicting value and discriminatory ability for clinical use on diagnosis of EVA within a deafness population.
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Affiliation(s)
- Ya-Jie Lu
- From the Department of Biotechnology, School of Basic Medical Science, Nanjing Medical University (Y-JL, JY, Q-JW, XC,); Department of Otolaryngology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, P.R. China (G-Q X)
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Tsukada K, Nishio SY, Hattori M, Usami SI. Ethnic-specific spectrum of GJB2 and SLC26A4 mutations: their origin and a literature review. Ann Otol Rhinol Laryngol 2015; 124 Suppl 1:61S-76S. [PMID: 25999548 DOI: 10.1177/0003489415575060] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
OBJECTIVE The mutation spectrum of the GJB2 and SLC26A4 genes, the 2 most common genes causing deafness, are known to be ethnic specific. In this study, the spectrum of the reported GJB2 and SLC26A4 mutations in different populations are reviewed and considered from a human migration perspective. METHODS Fifty-two and 17 articles on GJB2 and SLC26A4 mutations, respectively, were reviewed through the PubMed database from April 1996 to September 2014. The 4 most prevalent mutations were selected and compared. A cluster analysis was subsequently performed for these selected mutations. RESULTS The present review of frequent mutations shows the ethnic-specific GJB2 and SLC26A4 gene mutation spectrum. A cluster analysis of the GJB2 and SLC26A4 genes revealed similarities between ethnic populations. CONCLUSION The mutation spectrum reviewed in this study clearly indicated that the frequent mutations in the GJB2 and SLC26A4 genes are consistent with the founder mutation hypothesis. A comparison with the Y-chromosome phylogenetic tree indicated that these mutations may have occurred during human migration.
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Affiliation(s)
- Keita Tsukada
- Department of Otorhinolaryngology, Shinshu University School of Medicine, Matsumoto, Japan
| | - Shin-Ya Nishio
- Department of Otorhinolaryngology, Shinshu University School of Medicine, Matsumoto, Japan Department of Hearing Implant Sciences, Shinshu University School of Medicine, Matsumoto, Japan
| | - Mitsuru Hattori
- Department of Otorhinolaryngology, Shinshu University School of Medicine, Matsumoto, Japan
| | - Shin-Ichi Usami
- Department of Otorhinolaryngology, Shinshu University School of Medicine, Matsumoto, Japan Department of Hearing Implant Sciences, Shinshu University School of Medicine, Matsumoto, Japan
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Jiang Y, Huang S, Deng T, Wu L, Chen J, Kang D, Xu X, Li R, Han D, Dai P. Mutation Spectrum of Common Deafness-Causing Genes in Patients with Non-Syndromic Deafness in the Xiamen Area, China. PLoS One 2015; 10:e0135088. [PMID: 26252218 PMCID: PMC4529078 DOI: 10.1371/journal.pone.0135088] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 07/16/2015] [Indexed: 11/19/2022] Open
Abstract
In China, approximately 30,000 babies are born with hearing impairment each year. However, the molecular factors causing congenital hearing impairment in the Xiamen area of Fujian province have not been evaluated. To provide accurate genetic testing and counseling in the Xiamen area, we investigated the molecular etiology of non-syndromic deafness in a deaf population from Xiamen. Unrelated students with hearing impairment (n = 155) who attended Xiamen Special Education School in Fujian Province were recruited for this study. Three common deafness-related genes, GJB2, SLC26A4, and mtDNA12SrRNA, were analyzed using all-exon sequencing. GJB2 mutations were detected in 27.1% (42/155) of the entire cohort. The non-syndromic hearing loss (NSHL) hotspot mutations c.109G>A (p.V37I) and c.235delC were found in this population, whereas the Caucasian hotspot mutation c.35delG was not. The allelic frequency of the c.109G>A mutation was 9.03% (28/310), slightly higher than that of c.235delC (8.39%, 26/310), which is the most common GJB2 mutation in most areas of China. The allelic frequency of the c.109G>A mutation was significantly higher in this Xiamen's deaf population than that in previously reported cohorts (P = 0.00). The SLC26A4 mutations were found in 16.77% (26/155) of this cohort. The most common pathogenic allele was c.IVS7-2A>G (6.13%, 19/310), and the second most common was the c.1079C>T (p.A360V) mutation (1.94%, 6/310) which has rarely been reported as a hotspot mutation in other studies. The mutation rate of mtDNA12SrRNA in this group was 3.87% (6/155), all being the m.A1555G mutation. These findings show the specificity of the common deaf gene-mutation spectrum in this area. According to this study, there were specific hotspot mutations in Xiamen deaf patients. Comprehensive sequencing analysis of the three common deaf genes can help portray the mutation spectrum and develop optimal testing strategies for deaf patients in this area.
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Affiliation(s)
- Yi Jiang
- Department of Otolaryngology, Head and Neck Surgery, PLA General Hospital, Beijing, P. R. China
- Fujian Medical University ShengLi clinical college, Fujian Provincial Hospital, Fuzhou, P. R. China
| | - Shasha Huang
- Department of Otolaryngology, Head and Neck Surgery, PLA General Hospital, Beijing, P. R. China
| | - Tao Deng
- Beijing Capital Bio Independent Clinical Laboratory, Beijing, P. R. China
| | - Lihua Wu
- Fujian Medical University ShengLi clinical college, Fujian Provincial Hospital, Fuzhou, P. R. China
| | - Juan Chen
- Fujian Medical University ShengLi clinical college, Fujian Provincial Hospital, Fuzhou, P. R. China
| | - Dongyang Kang
- Department of Otolaryngology, Head and Neck Surgery, PLA General Hospital, Beijing, P. R. China
| | - Xiufeng Xu
- Beijing Capital Bio Independent Clinical Laboratory, Beijing, P. R. China
| | - Ruiyu Li
- Fujian Medical University ShengLi clinical college, Fujian Provincial Hospital, Fuzhou, P. R. China
- * E-mail: (PD); (DYH); (RYL)
| | - Dongyi Han
- Department of Otolaryngology, Head and Neck Surgery, PLA General Hospital, Beijing, P. R. China
- * E-mail: (PD); (DYH); (RYL)
| | - Pu Dai
- Department of Otolaryngology, Head and Neck Surgery, PLA General Hospital, Beijing, P. R. China
- * E-mail: (PD); (DYH); (RYL)
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