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Duan S, Hou Y, Li Y, Guo Y. Mutation spectrum of GJB2, SLC26A4 and mtDNA12SrRNA genes in non-syndromic hearing loss patients from Gansu, China. Int J Pediatr Otorhinolaryngol 2025; 191:112298. [PMID: 40054393 DOI: 10.1016/j.ijporl.2025.112298] [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: 11/20/2024] [Revised: 02/08/2025] [Accepted: 03/03/2025] [Indexed: 03/16/2025]
Abstract
OBJECTIVE This study examined the mutation spectrum and frequency of three prevalent pathogenic genes in patients with non-syndromic hearing loss (NSHL) from Gansu Province, China. METHODS We analyzed 452 NSHL patients from five special education schools across several cities in Gansu Province using SNPscan technology to determine the mutation spectrum of mtDNA 12S rRNA, GJB2, and SLC26A4 genes. RESULTS Among the 452 patients evaluated, mutations in the GJB2 gene were observed in 91 cases (20.13 %), mutations in the SLC26A4 gene in 81 cases (17.92 %), and homoplasmic mutations in mtDNA 12S rRNA in 26 cases (5.75 %). Significant differences in GJB2 mutations were observed between Han patients and those of Hui, Tibetan and Mongolian ethnicity (χ2 = 4.554, p = 0.033; χ2 = 3.987, p = 0.046; χ2 = 4.041, p = 0.044), as well as in SLC26A4 gene mutations between Han patients and both Hui and Tu patients (χ2 = 4.247, p = 0.039; p = 0.035, two-sided). MT-RNR1 mutations were exclusively identified in Tibetans, Han, and Hui patients. CONCLUSION Our findings demonstrate variations in the mutation spectra of the GJB2, SLC26A4, and mtDNA 12S rRNA genes across different ethnic groups, highlighting ethnic variations in mutation prevalence. This study expands the understanding of the genetic mutation spectrum associated with deafness in Gansu and supports the enhancement of molecular diagnostic accuracy for diverse ethnic populations in the region.
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Affiliation(s)
- Shihong Duan
- Department of Otolaryngology-Head & Neck Surgery, Lanzhou University Second Hospital, Cuiyingmen RoadNo.82, Lanzhou, Gansu, People's Republic of China.
| | - Yuan Hou
- Department of Otolaryngology-Head & Neck Surgery, Lanzhou University Second Hospital, Cuiyingmen RoadNo.82, Lanzhou, Gansu, People's Republic of China.
| | - Yong Li
- Department of Otolaryngology-Head & Neck Surgery, Lanzhou University Second Hospital, Cuiyingmen RoadNo.82, Lanzhou, Gansu, People's Republic of China.
| | - Yufen Guo
- Department of Otolaryngology-Head & Neck Surgery, Lanzhou University Second Hospital, Cuiyingmen RoadNo.82, Lanzhou, Gansu, People's Republic of China.
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2
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Pshennikova VG, Teryutin FM, Cherdonova AM, Borisova TV, Solovyev AV, Romanov GP, Morozov IV, Bondar AA, Posukh OL, Fedorova SA, Barashkov NA. The GJB2 (Cx26) Gene Variants in Patients with Hearing Impairment in the Baikal Lake Region (Russia). Genes (Basel) 2023; 14:genes14051001. [PMID: 37239361 DOI: 10.3390/genes14051001] [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: 03/25/2023] [Revised: 04/22/2023] [Accepted: 04/25/2023] [Indexed: 05/28/2023] Open
Abstract
The GJB2 (Cx26) gene pathogenic variants are associated with autosomal recessive deafness type 1A (DFNB1A, OMIM #220290). Direct sequencing of the GJB2 gene among 165 hearing-impaired individuals living in the Baikal Lake region of Russia identified 14 allelic variants: pathogenic/likely pathogenic-nine variants, benign-three variants, unclassified-one variant, and one novel variant. The contribution of the GJB2 gene variants to the etiology of hearing impairment (HI) in the total sample of patients was 15.8% (26 out of 165) and significantly differed in patients of different ethnicity (5.1% in Buryat patients and 28.9% in Russian patients). In patients with DFNB1A (n = 26), HIs were congenital/early onset (92.3%), symmetric (88.5%), sensorineural (100.0%), and variable in severity (moderate-11.6%, severe-26.9% or profound-61.5%). The reconstruction of the SNP haplotypes with three frequent GJB2 pathogenic variants (c.-23+1G>A, c.35delG or c.235delC), in comparison with previously published data, supports a major role of the founder effect in the expansion of the c.-23+1G>A and c.35delG variants around the world. Comparative analysis of the haplotypes with c.235delC revealed one major haplotype G A C T (97.5%) in Eastern Asians (Chinese, Japanese and Korean patients) and two haplotypes, G A C T (71.4%) and G A C C (28.6%), in Northern Asians (Altaians, Buryats and Mongols). The variable structure of the c.235delC-haplotypes in Northern Asians requires more studies to expand our knowledge about the origin of this pathogenic variant.
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Affiliation(s)
- Vera G Pshennikova
- Laboratory of Molecular Genetics, Yakut Science Centre of Complex Medical Problems, Yaroslavskogo 6/3, 677019 Yakutsk, Russia
| | - Fedor M Teryutin
- Laboratory of Molecular Genetics, Yakut Science Centre of Complex Medical Problems, Yaroslavskogo 6/3, 677019 Yakutsk, Russia
| | - Alexandra M Cherdonova
- Laboratory of Molecular Biology, Institute of Natural Sciences, M.K. Ammosov North-Eastern Federal University, Kulakovskogo 46, 677010 Yakutsk, Russia
| | - Tuyara V Borisova
- Laboratory of Molecular Biology, Institute of Natural Sciences, M.K. Ammosov North-Eastern Federal University, Kulakovskogo 46, 677010 Yakutsk, Russia
| | - Aisen V Solovyev
- Laboratory of Molecular Biology, Institute of Natural Sciences, M.K. Ammosov North-Eastern Federal University, Kulakovskogo 46, 677010 Yakutsk, Russia
| | - Georgii P Romanov
- Laboratory of Molecular Biology, Institute of Natural Sciences, M.K. Ammosov North-Eastern Federal University, Kulakovskogo 46, 677010 Yakutsk, Russia
| | - Igor V Morozov
- Novosibirsk State University, 630090 Novosibirsk, Russia
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Alexander A Bondar
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Olga L Posukh
- Novosibirsk State University, 630090 Novosibirsk, Russia
- Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Sardana A Fedorova
- Laboratory of Molecular Genetics, Yakut Science Centre of Complex Medical Problems, Yaroslavskogo 6/3, 677019 Yakutsk, Russia
- Laboratory of Molecular Biology, Institute of Natural Sciences, M.K. Ammosov North-Eastern Federal University, Kulakovskogo 46, 677010 Yakutsk, Russia
| | - Nikolay A Barashkov
- Laboratory of Molecular Genetics, Yakut Science Centre of Complex Medical Problems, Yaroslavskogo 6/3, 677019 Yakutsk, Russia
- Laboratory of Molecular Biology, Institute of Natural Sciences, M.K. Ammosov North-Eastern Federal University, Kulakovskogo 46, 677010 Yakutsk, Russia
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Aboagye ET, Adadey SM, Wonkam-Tingang E, Amenga-Etego L, Awandare GA, Wonkam A. Global Distribution of Founder Variants Associated with Non-Syndromic Hearing Impairment. Genes (Basel) 2023; 14:399. [PMID: 36833326 PMCID: PMC9957346 DOI: 10.3390/genes14020399] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 01/28/2023] [Accepted: 01/30/2023] [Indexed: 02/05/2023] Open
Abstract
The genetic etiology of non-syndromic hearing impairment (NSHI) is highly heterogeneous with over 124 distinct genes identified. The wide spectrum of implicated genes has challenged the implementation of molecular diagnosis with equal clinical validity in all settings. Differential frequencies of allelic variants in the most common NSHI causal gene, gap junction beta 2 (GJB2), has been described as stemming from the segregation of a founder variant and/or spontaneous germline variant hot spots. We aimed to systematically review the global distribution and provenance of founder variants associated with NSHI. The study protocol was registered on PROSPERO, the International Prospective Register of Systematic Reviews, with the registration number "CRD42020198573". Data from 52 reports, involving 27,959 study participants from 24 countries, reporting 56 founder pathogenic or likely pathogenic (P/LP) variants in 14 genes (GJB2, GJB6, GSDME, TMC1, TMIE, TMPRSS3, KCNQ4, PJVK, OTOF, EYA4, MYO15A, PDZD7, CLDN14, and CDH23), were reviewed. Varied number short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs) were used for haplotype analysis to identify the shared ancestral informative markers in a linkage disequilibrium and variants' origins, age estimates, and common ancestry computations in the reviewed reports. Asia recorded the highest number of NSHI founder variants (85.7%; 48/56), with variants in all 14 genes, followed by Europe (16.1%; 9/56). GJB2 had the highest number of ethnic-specific P/LP founder variants. This review reports on the global distribution of NSHI founder variants and relates their evolution to population migration history, bottleneck events, and demographic changes in populations linked with the early evolution of deleterious founder alleles. International migration and regional and cultural intermarriage, coupled to rapid population growth, may have contributed to re-shaping the genetic architecture and structural dynamics of populations segregating these pathogenic founder variants. We have highlighted and showed the paucity of data on hearing impairment (HI) variants in Africa, establishing unexplored opportunities in genetic traits.
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Affiliation(s)
- Elvis Twumasi Aboagye
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra LG Box 54, Ghana
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Samuel Mawuli Adadey
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra LG Box 54, Ghana
| | - Edmond Wonkam-Tingang
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Lucas Amenga-Etego
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra LG Box 54, Ghana
| | - Gordon A. Awandare
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra LG Box 54, Ghana
| | - Ambroise Wonkam
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
- McKusick-Nathans Institute and Department of Genetic Medicine, John Hopkins University School of Medicine, Baltimore, MD 21205, USA
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4
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Jiang Y, Huang S, Zhang Y, Fang N, Liu Q, Liu Y, Bai L, Han D, Dai P. Evolutionary origin of pathogenic GJB2 alleles in China. Clin Genet 2022; 102:305-313. [PMID: 35841299 DOI: 10.1111/cge.14191] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 07/12/2022] [Accepted: 07/13/2022] [Indexed: 11/28/2022]
Abstract
The frequency of the pathogenic allele of the autosomal recessive deafness gene GJB2 varies among different populations in the world, and accumulates to a sufficiently high frequency in certain population. The purpose of this study is to investigate the origin and evolution of GJB2 pathogenic alleles in Chinese deaf patients. Children with non-syndromic hearing loss, and their parents, from 295 families were recruited. Customized capture probes targeted at 943 SNPs related to GJB2 gene were designed for sequencing of genomic DNA in blood samples. Haplotypes carrying pathogenic allele were analyzed through linkage disequilibrium block building, ancestry tracing, and extended haplotype heterozygosity calculation. Two pathogenic GJB2 alleles, c.235delC (18.41%) and c.109G>A (15.57%), were observed in 867 donors. For c.235delC allele, 3 different core haplotypes with one major haplotype (97.32%) were found, and their core SNPs were 100% conserved. For c.109G>A allele, 6 different haplotypes with one major haplotype (93.28%) were found and the major c.109G>A allele evolved from a specific ancestral haplotype. Geographical origins of donors carrying GJB2 c.109G>A and c.235delC core haplotypes centered between Qinghai and Neimenggu. GJB2 c.235delC has long-range linkage disequilibrium. No positive selection signature was found for GJB2 c.235delC or c.109G>A in the studied population. In conclusion, we discovered a single origin of GJB2 c.235delC allele and multiple independent origins of GJB2 c.109G>A allele. Alternative to positive selection or multiple independent recurrent mutation event, population bottleneck effect might account for the observed high population frequency of these pathogenic alleles.
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Affiliation(s)
- Yi Jiang
- Department of Otolaryngology-Head and Neck Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Ear Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases, Shanghai, China
| | - Shasha Huang
- Department of Otolaryngology, Head and Neck Surgery, Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, China.,National Clinical Research Center for Otolaryngologic Diseases, Beijing, China.,Key Lab of Hearing Impairment Science of Ministry of Education, Beijing, China.,Key Lab of Hearing Impairment Prevention and Treatment of Beijing, Beijing, China
| | - Yi Zhang
- Euler Technology, Beijing, China
| | - Nan Fang
- Beijing Scisoon Biotechnology Co., Ltd, Beijing, China
| | - Qian Liu
- Beijing Scisoon Biotechnology Co., Ltd, Beijing, China
| | - Yunchao Liu
- Beijing Scisoon Biotechnology Co., Ltd, Beijing, China
| | - Ling Bai
- Beijing Scisoon Biotechnology Co., Ltd, Beijing, China
| | - Dongyi Han
- Department of Otolaryngology, Head and Neck Surgery, Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, China.,National Clinical Research Center for Otolaryngologic Diseases, Beijing, China.,Key Lab of Hearing Impairment Science of Ministry of Education, Beijing, China.,Key Lab of Hearing Impairment Prevention and Treatment of Beijing, Beijing, China
| | - Pu Dai
- Department of Otolaryngology, Head and Neck Surgery, Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, China.,National Clinical Research Center for Otolaryngologic Diseases, Beijing, China.,Key Lab of Hearing Impairment Science of Ministry of Education, Beijing, China.,Key Lab of Hearing Impairment Prevention and Treatment of Beijing, Beijing, China
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Agent-Based Modeling of Autosomal Recessive Deafness 1A (DFNB1A) Prevalence with Regard to Intensity of Selection Pressure in Isolated Human Population. BIOLOGY 2022; 11:biology11020257. [PMID: 35205123 PMCID: PMC8869167 DOI: 10.3390/biology11020257] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/28/2022] [Accepted: 02/03/2022] [Indexed: 01/09/2023]
Abstract
An increase in the prevalence of autosomal recessive deafness 1A (DFNB1A) in populations of European descent was shown to be promoted by assortative marriages among deaf people. Assortative marriages became possible with the widespread introduction of sign language, resulting in increased genetic fitness of deaf individuals and, thereby, relaxing selection against deafness. However, the effect of this phenomenon was not previously studied in populations with different genetic structures. We developed an agent-based computer model for the analysis of the spread of DFNB1A. Using this model, we tested the impact of different intensities of selection pressure against deafness in an isolated human population over 400 years. Modeling of the "purifying" selection pressure on deafness ("No deaf mating" scenario) resulted in a decrease in the proportion of deaf individuals and the pathogenic allele frequency. Modeling of the "relaxed" selection ("Assortative mating" scenario) resulted in an increase in the proportion of deaf individuals in the first four generations, which then quickly plateaued with a subsequent decline and a decrease in the pathogenic allele frequency. The results of neutral selection pressure modeling ("Random mating" scenario) showed no significant changes in the proportion of deaf individuals or the pathogenic allele frequency after 400 years.
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6
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A common founder effect of the splice site variant c.-23 + 1G > A in GJB2 gene causing autosomal recessive deafness 1A (DFNB1A) in Eurasia. Hum Genet 2021; 141:697-707. [PMID: 34839402 DOI: 10.1007/s00439-021-02405-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 11/21/2021] [Indexed: 10/19/2022]
Abstract
Mutations in the GJB2 gene are known to be a major cause of autosomal recessive deafness 1A (OMIM 220290). The most common pathogenic variants of the GJB2 gene have a high ethno-geographic specificity in their distribution, being attributed to a founder effect related to the Neolithic migration routes of Homo sapiens. The c.-23 + 1G > A splice site variant is frequently found among deaf patients of both Caucasian and Asian origins. It is currently unknown whether the spread of this mutation across Eurasia is a result of the founder effect or if it could have multiple local centers of origin. To determine the origin of c.-23 + 1G > A, we reconstructed haplotypes by genotyping SNPs on an Illumina OmniExpress 730 K platform of 23 deaf individuals homozygous for this variant from different populations of Eurasia. The analyses revealed the presence of common regions of homozygosity in different individual genomes in the sample. These data support the hypothesis of the common founder effect in the distribution of the c.-23 + 1G > A variant of the GJB2 gene. Based on the published data on the c.-23 + 1G > A prevalence among 16,177 deaf people and the calculation of the TMRCA of the modified f2-haplotypes carrying this variant, we reconstructed the potential migration routes of the carriers of this mutation around the world. This analysis indicates that the c.-23 + 1G > A variant in the GJB2 gene may have originated approximately 6000 years ago in the territory of the Caucasus or the Middle East then spread throughout Europe, South and Central Asia and other regions of the world.
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7
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Posukh OL. Genetic etiology of hearing loss in Russia. Hum Genet 2021; 141:649-663. [PMID: 34363095 DOI: 10.1007/s00439-021-02327-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 07/28/2021] [Indexed: 10/20/2022]
Abstract
Prevalence and locus/allelic heterogeneity of the hereditary hearing loss (HL) vary significantly in different human populations. Investigation of the hereditary HL diversity and the evaluation of the factors determining the region-specific landscapes of genetic HL are important for local healthcare and medical genetic services. This review presents the summarized data from the published studies concerning the genetic etiology of HL in different populations of Russia. Multiethnic population of Russia (in total, about 146 million on 2021) includes over 180 different ethnic groups, the number of which varies from millions to just several thousand people. Among them, Russians are the largest group (about 111 million). The contribution of GJB2 gene in the HL etiology in patients of different ethnicities and ethnic-specific prevalence of the GJB2 pathogenic variants were studied in many local populations of Russia. However, the investigation of other "deafness" genes is still limited to a relatively small number of studies on patients with HL of unsolved etiology.
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Affiliation(s)
- Olga L Posukh
- Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia, 630090. .,Novosibirsk State University, Novosibirsk, Russia, 630090.
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Novel Variants in Hearing Loss Genes and Associations With Audiometric Thresholds in a Multi-ethnic Cohort of US Patients With Cochlear Implants. Otol Neurotol 2021; 41:978-985. [PMID: 32658404 DOI: 10.1097/mao.0000000000002671] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
OBJECTIVES To investigate novel variants in hearing loss genes and clinical factors affecting audiometric outcomes of cochlear implant (CI) patients. BACKGROUND Approximately 50% of hearing loss has a genetic etiology, with certain genetic variants more prevalent in specific ethnic groups. Different variants and some clinical variables including inner ear malformations result in different prognoses or clinical outcomes after CI. METHODS Medical and genetic testing records of pediatric CI patients were reviewed for clinical variables. Minor allele frequencies of variants were obtained from Genome Aggregation Database (gnomAD) and variants were classified for pathogenicity. Standard statistical testing was done using Fisher's exact, Wilcoxon, and Spearman correlation tests. RESULTS Eighteen CI patients with genetic test results had pathogenic variants, including six patients with syndromic hearing loss and six patients with known GJB2 variants. Novel pathogenic variants were noted in CHD7, ADGRV1, and ARID1B, with variants in the latter two genes identified in Hispanic patients. Overall, carriage of genetic variants was associated with better pre-CI audiometric thresholds at 2000 Hz (p = 0.048). On the other hand, post-CI thresholds were significantly worse in patients with inner ear malformations, particularly in patients with atretic cochlear nerve canals. CONCLUSION Four novel pathogenic variants were identified, which contributes to knowledge of allelic spectrum for hearing loss especially in Hispanic patients. In this cohort, carriage of pathogenic variants particularly of GJB2 variants was associated with better pre-CI audiometric thresholds, while patients with inner ear malformations had worse post-CI audiometric thresholds.
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Wang H, Gao Y, Guan J, Lan L, Yang J, Xiong W, Zhao C, Xie L, Yu L, Wang D, Wang Q. Phenotypic Heterogeneity of Post-lingual and/or Milder Hearing Loss for the Patients With the GJB2 c.235delC Homozygous Mutation. Front Cell Dev Biol 2021; 9:647240. [PMID: 33718389 PMCID: PMC7953049 DOI: 10.3389/fcell.2021.647240] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 02/08/2021] [Indexed: 01/01/2023] Open
Abstract
Objective To report the phenotypic heterogeneity of GJB2 c.235delC homozygotes associated with post-lingual and/or milder hearing loss, and explore the possible mechanism of these unconditional phenotypes. Methods Mutation screening of GJB2 was performed on all ascertained members from Family 1006983 and three sporadic patients by polymerase chain reaction (PCR) amplification and Sanger sequencing. Next generation sequencing (NGS) was successively performed on some of the affected members and normal controls from Family 1006983 to explore additional possible genetic codes. Reverse transcriptase–quantitative PCR was conducted to test the expression of Connexin30. Results We identified a Chinese autosomal recessive hearing loss family with the GJB2 c.235delC homozygous mutation, affected members from which had post-lingual moderate to profound hearing impairment, and three sporadic patients with post-lingual moderate hearing impairment, instead of congenital profound hearing loss. NGS showed no other particular variants. Overexpression of Connexin30 in some of these cases was verified. Conclusion Post-lingual and/or moderate hearing impairment phenotypes of GJB2 c.235delC homozygotes are not the most common phenotype, revealing the heterogeneity of GJB2 pathogenic mutations. To determine the possible mechanism that rescues part of the hearing or postpones onset age of these cases, more cases are required to confirm both Connexin30 overexpression and the existence of modifier genes.
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Affiliation(s)
- Hongyang Wang
- College of Otolaryngology, Head and Neck Surgery, Chinese People's Liberation Army (PLA) Institute of Otolaryngology, Chinese People's Liberation Army (PLA) General Hospital, Beijing, China
| | - Yun Gao
- College of Otolaryngology, Head and Neck Surgery, Chinese People's Liberation Army (PLA) Institute of Otolaryngology, Chinese People's Liberation Army (PLA) General Hospital, Beijing, China.,National Clinical Research Center for Otolaryngologic Diseases, Beijing, China.,Key Lab of Hearing Impairment Science of Ministry of Education, Beijing, China.,Key Lab of Hearing Impairment Prevention and Treatment of Beijing, Beijing, China
| | - Jing Guan
- College of Otolaryngology, Head and Neck Surgery, Chinese People's Liberation Army (PLA) Institute of Otolaryngology, Chinese People's Liberation Army (PLA) General Hospital, Beijing, China.,National Clinical Research Center for Otolaryngologic Diseases, Beijing, China.,Key Lab of Hearing Impairment Science of Ministry of Education, Beijing, China.,Key Lab of Hearing Impairment Prevention and Treatment of Beijing, Beijing, China
| | - Lan Lan
- College of Otolaryngology, Head and Neck Surgery, Chinese People's Liberation Army (PLA) Institute of Otolaryngology, Chinese People's Liberation Army (PLA) General Hospital, Beijing, China.,National Clinical Research Center for Otolaryngologic Diseases, Beijing, China.,Key Lab of Hearing Impairment Science of Ministry of Education, Beijing, China.,Key Lab of Hearing Impairment Prevention and Treatment of Beijing, Beijing, China
| | - Ju Yang
- College of Otolaryngology, Head and Neck Surgery, Chinese People's Liberation Army (PLA) Institute of Otolaryngology, Chinese People's Liberation Army (PLA) General Hospital, Beijing, China.,National Clinical Research Center for Otolaryngologic Diseases, Beijing, China.,Key Lab of Hearing Impairment Science of Ministry of Education, Beijing, China.,Key Lab of Hearing Impairment Prevention and Treatment of Beijing, Beijing, China
| | - Wenping Xiong
- College of Otolaryngology, Head and Neck Surgery, Chinese People's Liberation Army (PLA) Institute of Otolaryngology, Chinese People's Liberation Army (PLA) General Hospital, Beijing, China.,National Clinical Research Center for Otolaryngologic Diseases, Beijing, China.,Key Lab of Hearing Impairment Science of Ministry of Education, Beijing, China.,Key Lab of Hearing Impairment Prevention and Treatment of Beijing, Beijing, China
| | - Cui Zhao
- College of Otolaryngology, Head and Neck Surgery, Chinese People's Liberation Army (PLA) Institute of Otolaryngology, Chinese People's Liberation Army (PLA) General Hospital, Beijing, China.,National Clinical Research Center for Otolaryngologic Diseases, Beijing, China.,Key Lab of Hearing Impairment Science of Ministry of Education, Beijing, China.,Key Lab of Hearing Impairment Prevention and Treatment of Beijing, Beijing, China
| | - Linyi Xie
- College of Otolaryngology, Head and Neck Surgery, Chinese People's Liberation Army (PLA) Institute of Otolaryngology, Chinese People's Liberation Army (PLA) General Hospital, Beijing, China.,National Clinical Research Center for Otolaryngologic Diseases, Beijing, China.,Key Lab of Hearing Impairment Science of Ministry of Education, Beijing, China.,Key Lab of Hearing Impairment Prevention and Treatment of Beijing, Beijing, China
| | - Lan Yu
- College of Otolaryngology, Head and Neck Surgery, Chinese People's Liberation Army (PLA) Institute of Otolaryngology, Chinese People's Liberation Army (PLA) General Hospital, Beijing, China.,National Clinical Research Center for Otolaryngologic Diseases, Beijing, China.,Key Lab of Hearing Impairment Science of Ministry of Education, Beijing, China.,Key Lab of Hearing Impairment Prevention and Treatment of Beijing, Beijing, China
| | - Dayong Wang
- College of Otolaryngology, Head and Neck Surgery, Chinese People's Liberation Army (PLA) Institute of Otolaryngology, Chinese People's Liberation Army (PLA) General Hospital, Beijing, China.,National Clinical Research Center for Otolaryngologic Diseases, Beijing, China.,Key Lab of Hearing Impairment Science of Ministry of Education, Beijing, China.,Key Lab of Hearing Impairment Prevention and Treatment of Beijing, Beijing, China
| | - Qiuju Wang
- College of Otolaryngology, Head and Neck Surgery, Chinese People's Liberation Army (PLA) Institute of Otolaryngology, Chinese People's Liberation Army (PLA) General Hospital, Beijing, China.,National Clinical Research Center for Otolaryngologic Diseases, Beijing, China.,Key Lab of Hearing Impairment Science of Ministry of Education, Beijing, China.,Key Lab of Hearing Impairment Prevention and Treatment of Beijing, Beijing, China
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Braun DC, Jain S, Epstein E, Greenwald BH, Herold B, Gray M. Deaf intermarriage has limited effect on the prevalence of recessive deafness and no effect on underlying allelic frequency. PLoS One 2020; 15:e0241609. [PMID: 33147256 PMCID: PMC7641374 DOI: 10.1371/journal.pone.0241609] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 10/16/2020] [Indexed: 11/19/2022] Open
Abstract
The idea that deaf intermarriage increases the prevalence of deafness was forcefully pushed in the late 19th century by Alexander Graham Bell, in proceedings published by the National Academy of Science. Bell's hypothesis was not supported by a 19th century study by Edward Allen Fay, which was funded by Bell's own organization, the Volta Bureau. The Fay study showed through an analysis of 4,471 deaf marriages that the chances of having deaf children did not increase significantly when both parents were deaf. In light of an apparent increase in non-complementary pairings when a modern dataset of Gallaudet alumni was compared with the 19th century Fay dataset, Bell's argument has been resurrected. This hypothesis is that residential schools for the deaf, which concentrate signing deaf individuals together, have promoted assortative mating, which in turn has increased the prevalence of recessive deafness and also the commonest underlying deafness allele. Because this hypothesis persists, even though it contradicts classical models of assortative mating, it is critically important that it be thoroughly investigated. In this study, we used an established forward-time genetics simulator with parameters and measurements collected from the published literature. Compared to mathematical equations, simulations allowed for more complex modeling, operated without assumptions of parametricity, and captured ending distributions and variances. Our simulation results affirm predictions from classical equations and show that intense assortative mating only modestly increases the prevalence of deafness, with this effect mostly completed by the third generation. More importantly, our data show that even intense assortative mating does not affect the frequency of the underlying alleles under reported conditions. These results are not locus-specific and are generalizable to other forms of recessive deafness. We explain the higher rate of non-complementary pairings measured in the contemporary Gallaudet alumni sample as compared to the Fay dataset.
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Affiliation(s)
- Derek C. Braun
- Department of Science, Technology, and Mathematics, Gallaudet University, Washington, D.C., United States of America
- * E-mail:
| | - Samir Jain
- Department of Science, Technology, and Mathematics, Gallaudet University, Washington, D.C., United States of America
| | - Eric Epstein
- Department of Science, Technology, and Mathematics, Gallaudet University, Washington, D.C., United States of America
| | - Brian H. Greenwald
- Department of History, Philosophy, Religion, and Sociology, Gallaudet University, Washington, D.C., United States of America
| | - Brienna Herold
- Department of Science, Technology, and Mathematics, Gallaudet University, Washington, D.C., United States of America
| | - Margaret Gray
- Department of Science, Technology, and Mathematics, Gallaudet University, Washington, D.C., United States of America
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11
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High Rates of Three Common GJB2 Mutations c.516G>C, c.-23+1G>A, c.235delC in Deaf Patients from Southern Siberia Are Due to the Founder Effect. Genes (Basel) 2020; 11:genes11070833. [PMID: 32708339 PMCID: PMC7397271 DOI: 10.3390/genes11070833] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 07/10/2020] [Accepted: 07/17/2020] [Indexed: 11/17/2022] Open
Abstract
The mutations in the GJB2 gene (13q12.11, MIM 121011) encoding transmembrane protein connexin 26 (Cx26) account for a significant portion of hereditary hearing loss worldwide. Earlier we found a high prevalence of recessive GJB2 mutations c.516G>C, c.-23+1G>A, c.235delC in indigenous Turkic-speaking Siberian peoples (Tuvinians and Altaians) from the Tyva Republic and Altai Republic (Southern Siberia, Russia) and proposed the founder effect as a cause for their high rates in these populations. To reconstruct the haplotypes associated with each of these mutations, the genotyping of polymorphic genetic markers both within and flanking the GJB2 gene was performed in 28 unrelated individuals homozygous for c.516G>C (n = 18), c.-23+1G>A (n = 6), or c.235delC (n = 4) as well as in the ethnically matched controls (62 Tuvinians and 55 Altaians) without these mutations. The common haplotypes specific for mutations c.516G>C, c.-23+1G>A, or c.235delC were revealed implying a single origin of each of these mutations. The age of mutations estimated by the DMLE+ v2.3 software and the single marker method is discussed in relation to ethnic history of Tuvinians and Altaians. The data obtained in this study support a crucial role of the founder effect in the high prevalence of GJB2 mutations c.516G>C, c.-23+1G>A, c.235delC in indigenous populations of Southern Siberia.
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12
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Shinagawa J, Moteki H, Nishio SY, Noguchi Y, Usami SI. Haplotype Analysis of GJB2 Mutations: Founder Effect or Mutational Hot Spot? Genes (Basel) 2020; 11:E250. [PMID: 32120898 PMCID: PMC7140863 DOI: 10.3390/genes11030250] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 02/25/2020] [Accepted: 02/25/2020] [Indexed: 01/29/2023] Open
Abstract
The GJB2 gene is the most frequent cause of congenital or early onset hearing loss worldwide. In this study, we investigated the haplotypes of six GJB2 mutations frequently observed in Japanese hearing loss patients (i.e., c.235delC, p.V37I, p.[G45E; Y136X], p.R143W, c.176_191del, and c.299_300delAT) and analyzed whether the recurring mechanisms for each mutation are due to founder effects or mutational hot spots. Furthermore, regarding the mutations considered to be caused by founder effects, we also calculated the age at which each mutation occurred using the principle of genetic clock analysis. As a result, all six mutations were observed in a specific haplotype and were estimated to derive from founder effects. Our haplotype data together with their distribution patterns indicated that p.R143W and p.V37I may have occurred as multiple events, and suggested that both a founder effect and hot spot may be involved in some mutations. With regard to the founders' age of frequent GJB2 mutations, each mutation may have occurred at a different time, with the oldest, p.V37I, considered to have occurred around 14,500 years ago, and the most recent, c.176_191del, considered to have occurred around 4000 years ago.
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Affiliation(s)
- Jun Shinagawa
- Department of Otorhinolaryngology, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, Nagano 390-8621, Japan; (J.S.); (H.M.)
| | - Hideaki Moteki
- Department of Otorhinolaryngology, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, Nagano 390-8621, Japan; (J.S.); (H.M.)
- Department of Hearing Implant Sciences, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, Nagano 390-8621, Japan; (S.-y.N.); (Y.N.)
| | - Shin-ya Nishio
- Department of Hearing Implant Sciences, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, Nagano 390-8621, Japan; (S.-y.N.); (Y.N.)
| | - Yoshihiro Noguchi
- Department of Hearing Implant Sciences, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, Nagano 390-8621, Japan; (S.-y.N.); (Y.N.)
- Department of Otorhinolaryngology, International University of Health and Welfare, Mita Hospital, 1-4-3 Mita, Minato-ku, Tokyo 108-8329, Japan
| | - Shin-ichi Usami
- Department of Otorhinolaryngology, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, Nagano 390-8621, Japan; (J.S.); (H.M.)
- Department of Hearing Implant Sciences, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, Nagano 390-8621, Japan; (S.-y.N.); (Y.N.)
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13
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Esperón-Moldes U, Ginarte-Val M, Rodríguez-Pazos L, Fachal L, Martín-Santiago A, Vicente A, Jiménez-Gallo D, Guillén-Navarro E, Sampol LM, González-Enseñat MA, Vega A. Novel CYP4F22 mutations associated with autosomal recessive congenital ichthyosis (ARCI). Study of the CYP4F22 c.1303C>T founder mutation. PLoS One 2020; 15:e0229025. [PMID: 32069299 PMCID: PMC7028276 DOI: 10.1371/journal.pone.0229025] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Accepted: 01/28/2020] [Indexed: 11/18/2022] Open
Abstract
Mutations in CYP4F22 cause autosomal recessive congenital ichthyosis (ARCI). However, less than 10% of all ARCI patients carry a mutation in CYP4F22. In order to identify the molecular basis of ARCI among our patients (a cohort of ninety-two Spanish individuals) we performed a mutational analysis using direct Sanger sequencing in combination with a multigene targeted NGS panel. From these, eight ARCI families (three of them with Moroccan origin) were found to carry five different CYP4F22 mutations, of which two were novel. Computational analysis showed that the mutations found were present in highly conserved residues of the protein and may affect its structure and function. Seven of the eight families were carriers of a highly recurrent CYP4F22 variant, c.1303C>T; p.(His435Tyr). A 12Mb haplotype was reconstructed in all c.1303C>T carriers by genotyping ten microsatellite markers flanking the CYP4F22 gene. A prevalent 2.52Mb haplotype was observed among Spanish carrier patients suggesting a recent common ancestor. A smaller core haplotype of 1.2Mb was shared by Spanish and Moroccan families. Different approaches were applied to estimate the time to the most recent common ancestor (TMRCA) of carrier patients with Spanish origin. The age of the mutation was calculated by using DMLE and BDMC2. The algorithms estimated that the c.1303C>T variant arose approximately 2925 to 4925 years ago, while Spanish carrier families derived from a common ancestor who lived in the XIII century. The present study reports five CYP4F22 mutations, two of them novel, increasing the number of CYP4F22 mutations currently listed. Additionally, our results suggest that the recurrent c.1303C>T change has a founder effect in Spanish population and c.1303C>T carrier families originated from a single ancestor with probable African ancestry.
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Affiliation(s)
- Uxia Esperón-Moldes
- Fundación Pública Galega de Medicina Xenómica-SERGAS, Grupo de Medicina Xenómica-USC, CIBERER, IDIS, Santiago de Compostela, Spain
- Departamento de Ciencias Forenses, Anatomía Patolóxica, Xinecoloxía, Obstetricia e Pediatría, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Manuel Ginarte-Val
- Dermatology Service of Complexo Hospitalario Universitario de Santiago, Santiago de Compostela, Spain
| | | | - Laura Fachal
- Fundación Pública Galega de Medicina Xenómica-SERGAS, Grupo de Medicina Xenómica-USC, CIBERER, IDIS, Santiago de Compostela, Spain
| | - Ana Martín-Santiago
- Dermatology Service of Hospital Universitari Son Espases, Palma de Mallorca, Spain
| | - Asunción Vicente
- Dermatology Service of Hospital Sant Joan de Déu, Barcelona, Spain
| | | | | | | | | | - Ana Vega
- Fundación Pública Galega de Medicina Xenómica-SERGAS, Grupo de Medicina Xenómica-USC, CIBERER, IDIS, Santiago de Compostela, Spain
- * E-mail:
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14
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Zhang M, Han Y, Zhang F, Bai X, Wang H. Mutation spectrum and hotspots of the common deafness genes in 314 patients with nonsyndromic hearing loss in Heze area, China. Acta Otolaryngol 2019; 139:612-617. [PMID: 31107121 DOI: 10.1080/00016489.2019.1609699] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Background: Although, half of the childhood deafness is genetically related, the molecular etiology of hearing impairment has not been demonstrated explicitly. In addition, the mutation spectrums of deafness genes vary among different areas and ethnics. Objectives: To know more about the mutation spectrums of deafness genes in China, we tested the mutations of three common deafness genes (GJB2, SLC26A4, and mtDNA12SrRNA) in a particular deafness population from Heze area. Materials and methods: SNPscan technology was utilized to perform mutation screening for these three common deafness genes in 314 nonsyndromic deaf patients from Heze area. Results: 38.21% (120/314) of these 314 patients with nonsyndromic hearing loss from Heze area were related to the genetic defects in these three deafness genes, including 20.06% (63/314) for GJB2, 15.29% (48/314) for SLC26A4, and 2.87% (9/314) for mtDNA12SrRNA. Furthermore, the mutation hotspots in three deaf genes were GJB2 235delC, SLC26A4 c.919-2A > G, and mtDNA12SrRNA 1555A > G, respectively, distinct from hotspots reported in other regions worldwide. Conclusion: Our results disclosed a special and unique mutation spectrum of these three common deaf genes in Heze deaf population.
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Affiliation(s)
- Meng Zhang
- Department of Otolaryngology-Head and Neck Surgery, Shandong Provincial ENT Hospital, Shandong Provincial ENT Hospital Affiliated to Shandong University, Jinan, P.R. China
- Key Laboratory of Otorhinolaryngology, National Health Commission (Shandong University), Jinan, P.R. China
- Shandong Provincial Key Laboratory of Otology, Jinan, P.R. China
- Shandong Institute of Otolaryngology, Jinan, P.R. China
| | - Yuechen Han
- Department of Otolaryngology-Head and Neck Surgery, Shandong Provincial ENT Hospital, Shandong Provincial ENT Hospital Affiliated to Shandong University, Jinan, P.R. China
- Key Laboratory of Otorhinolaryngology, National Health Commission (Shandong University), Jinan, P.R. China
- Shandong Provincial Key Laboratory of Otology, Jinan, P.R. China
- Shandong Institute of Otolaryngology, Jinan, P.R. China
| | - Fengguo Zhang
- Department of Otolaryngology-Head and Neck Surgery, Shandong Provincial ENT Hospital, Shandong Provincial ENT Hospital Affiliated to Shandong University, Jinan, P.R. China
- Key Laboratory of Otorhinolaryngology, National Health Commission (Shandong University), Jinan, P.R. China
- Shandong Provincial Key Laboratory of Otology, Jinan, P.R. China
- Shandong Institute of Otolaryngology, Jinan, P.R. China
| | - Xiaohui Bai
- Department of Otolaryngology-Head and Neck Surgery, Shandong Provincial ENT Hospital, Shandong Provincial ENT Hospital Affiliated to Shandong University, Jinan, P.R. China
- Key Laboratory of Otorhinolaryngology, National Health Commission (Shandong University), Jinan, P.R. China
- Shandong Provincial Key Laboratory of Otology, Jinan, P.R. China
- Shandong Institute of Otolaryngology, Jinan, P.R. China
| | - Haibo Wang
- Department of Otolaryngology-Head and Neck Surgery, Shandong Provincial ENT Hospital, Shandong Provincial ENT Hospital Affiliated to Shandong University, Jinan, P.R. China
- Key Laboratory of Otorhinolaryngology, National Health Commission (Shandong University), Jinan, P.R. China
- Shandong Provincial Key Laboratory of Otology, Jinan, P.R. China
- Shandong Institute of Otolaryngology, Jinan, P.R. China
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15
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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: 2.0] [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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Fu Y, Zha S, Lü N, Xu H, Zhang X, Shi W, Zha J. Carrier frequencies of hearing loss variants in newborns of China: A meta-analysis. J Evid Based Med 2019; 12:40-50. [PMID: 29968368 DOI: 10.1111/jebm.12305] [Citation(s) in RCA: 17] [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: 11/28/2017] [Accepted: 05/28/2018] [Indexed: 01/11/2023]
Abstract
OBJECTIVE The objective of this study was to review the carrier frequencies of hearing loss gene variants, such as GJB2, SLC26A4, and MT-RNR1 in newborns of China. DESIGN PubMed, Embase, BioCentral, CNKI, WanFang, and VIP databases were used for searching relevant literature studies published during the period of January 2007 and January 2016. Meta-analysis was performed by using the R software. The estimated rate and its 95% confidence intervals (CI) of the relevant indexes in newborns were collected and calculated using a fixed-effects model or a random-effects model when appropriate. RESULTS In total, 35 of 958 published literature studies in Chinese and English were selected. The overall results showed that in newborns of China, the carrier frequencies of GJB2 variants (235 delC, 299 delAT) were 1.64% (95% CI 1.52% to 1.77%) and 0.33% (95% CI 0.19% to 0.51%); SLC26A4 variants (IVS7-2 A > G, 2168 A > G) were 1.02% (95% CI 0.91% to 1.15%) and 0.14% (95% CI 0.06% to 0.25%); MT-RNR1 variants (1555 A > G, 1449 C > T) were 0.20% (95% CI 0.17% to 0.23%) and 0.03% (95% CI 0.02% to 0.05%). CONCLUSIONS There are high carrier frequencies of GJB2 variants among newborns in China, followed by SLC26A4 and MT-RNR1 variants. In order to achieve "early detection, early diagnosis and early treatment" and reduce the incidence of hereditary hearing loss in offspring, a comprehensive combination of neonatal hearing screening and deafness gene detection should be recommended and implemented in China.
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Affiliation(s)
- Yali Fu
- Jiangsu Family Planning Research Institute, Nanjing, P. R. China
| | - Shuwei Zha
- Jiangsu Family Planning Research Institute, Nanjing, P. R. China
| | - Nianqing Lü
- Jiangsu Family Planning Research Institute, Nanjing, P. R. China
| | - Haoqin Xu
- Jiangsu Family Planning Research Institute, Nanjing, P. R. China
| | - Xuening Zhang
- Jiangsu Family Planning Research Institute, Nanjing, P. R. China
| | - Wenhui Shi
- Jiangsu Family Planning Research Institute, Nanjing, P. R. China
| | - Ji Zha
- Children's Hospital of Philadelphia, Philadelphia, PA, USA
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Erdenechuluun J, Lin YH, Ganbat K, Bataakhuu D, Makhbal Z, Tsai CY, Lin YH, Chan YH, Hsu CJ, Hsu WC, Chen PL, Wu CC. Unique spectra of deafness-associated mutations in Mongolians provide insights into the genetic relationships among Eurasian populations. PLoS One 2018; 13:e0209797. [PMID: 30576380 PMCID: PMC6303056 DOI: 10.1371/journal.pone.0209797] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Accepted: 12/11/2018] [Indexed: 02/07/2023] Open
Abstract
Genetic factors are an important cause of idiopathic sensorineural hearing impairment (SNHI). From the epidemiological perspective, mutations of three deafness genes: GJB2, SLC26A4, and MT-RNR1, are much more prevalent than those of other genes worldwide. However, mutation spectra of common deafness genes differ remarkably across different populations. Here, we performed comprehensive genetic examination and haplotype analyses in 188 unrelated Mongolian families with idiopathic SNHI, and compared their mutation spectra and haplotypes to those of other European and Asian cohorts. We confirmed genetic diagnoses in 18 (9.6%) of the 188 families, including 13 with bi-allelic GJB2 mutations, three with bi-allelic SLC26A4 mutations, and two with homoplasmic MT-RNR1 m.1555A>G mutation. Moreover, mono-allelic mutations were identified in 17 families (9.0%), including 14 with mono-allelic GJB2 mutations and three with mono-allelic SLC26A4 mutations. Interestingly, three GJB2 mutations prevalent in other populations, including c.35delG in Caucasians, c.235delC in East Asians, and c.-23+1G>A in Southwest and South Asians, were simultaneously detected in Mongolian patients. Haplotype analyses further confirmed founder effects for each of the three mutations, indicating that each mutation derived from its ancestral origin independently. By demonstrating the unique spectra of deafness-associated mutations, our findings may have important clinical and scientific implications for refining the molecular diagnostics of SNHI in Mongolian patients, and for elucidating the genetic relationships among Eurasian populations.
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Affiliation(s)
- Jargalkhuu Erdenechuluun
- Department of Otolaryngology, Mongolian National University of Medical Sciences, Ulaanbaatar, Mongolia
- The EMJJ Otolaryngology Hospital, Ulaanbaatar, Mongolia
| | - Yin-Hung Lin
- Department of Otolaryngology, National Taiwan University Hospital, Taipei, Taiwan
- Graduate Institute of Medical Genomics and Proteomics, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Khongorzul Ganbat
- The EMJJ Otolaryngology Hospital, Ulaanbaatar, Mongolia
- Department of Otolaryngology, National Center for Maternal and Child Health, Ulaanbaatar, Mongolia
| | - Delgermaa Bataakhuu
- Department of Otolaryngology, National Center for Maternal and Child Health, Ulaanbaatar, Mongolia
| | - Zaya Makhbal
- Department of Otolaryngology, National Center for Maternal and Child Health, Ulaanbaatar, Mongolia
| | - Cheng-Yu Tsai
- Department of Otolaryngology, National Taiwan University Hospital, Taipei, Taiwan
- Graduate Institute of Medical Genomics and Proteomics, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Yi-Hsin Lin
- Department of Otolaryngology, National Taiwan University Hospital, Taipei, Taiwan
| | - Yen-Hui Chan
- Department of Otolaryngology, National Taiwan University Hospital, Taipei, Taiwan
| | - Chuan-Jen Hsu
- Department of Otolaryngology, National Taiwan University Hospital, Taipei, Taiwan
| | - Wei-Chung Hsu
- Department of Otolaryngology, National Taiwan University Hospital, Taipei, Taiwan
| | - Pei-Lung Chen
- Graduate Institute of Medical Genomics and Proteomics, National Taiwan University College of Medicine, Taipei, Taiwan
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
| | - Chen-Chi Wu
- Department of Otolaryngology, National Taiwan University Hospital, Taipei, Taiwan
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
- * E-mail:
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Romanov GP, Barashkov NA, Teryutin FM, Lashin SA, Solovyev AV, Pshennikova VG, Bondar AA, Morozov IV, Sazonov NN, Tomsky MI, Dzhemileva LU, Khusnutdinova EK, Posukh OL, Fedorova SA. Marital Structure, Genetic Fitness, and the GJB2 Gene Mutations among Deaf People in Yakutia (Eastern Siberia, Russia). RUSS J GENET+ 2018. [DOI: 10.1134/s1022795418050071] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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19
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Yuan EF, Xia W, Huang JT, Hu L, Liao X, Dai X, Liu SM. A sensitive and convenient method for clinical detection of non-syndromic hearing loss-associated common mutations. Gene 2017; 628:322-328. [PMID: 28734895 DOI: 10.1016/j.gene.2017.07.045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2017] [Revised: 06/21/2017] [Accepted: 07/13/2017] [Indexed: 12/25/2022]
Abstract
BACKGROUND The majority of non-syndromic hearing loss (NSHL) patients result from causative mutations in GJB2, SLC26A4 and mitochondrial 12S rRNA genes. Accurate detection of these genetic mutations is increasingly recognized for its clinical significance to reduce incidence and guide individual treatment of NSHL. Current methods for clinical practice are labor intensive, expensive or of low sensitivity. METHODS Genomic DNA from 7 newborns not passing the hearing screening and 94 newborns passing the hearing screening were analyzed for the common mutations using high resolution melting analysis (HRMA) and Sanger sequencing. RESULTS Our newly developed HRMA allowed the hot-spot mutations of GJB2 c.176_191del16 and c.235delC, SLC26A4 IVS7-2A>G and mitochondrial 12S rRNA 1494C>T and 1555A>G to be detected by melting profiles based on small amplicons. HRMA can distinguish different content mutant DNA from wildtype DNA, with a detection limit of 5%. Moreover, the results were highly concordant between HRMA and Sanger sequencing. CONCLUSIONS These results indicate that HRMA could be used as a routine clinical method for prenatal diagnosis and newborn genetic screening due to its accuracy, sensitivity, and rapid, low-cost and less laborious workflows.
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Affiliation(s)
- Er-Feng Yuan
- Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University, Donghu Road 169#, Wuhan 430071, China
| | - Wei Xia
- Department of Clinical Laboratory, Wuhan Children's Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science & Technology, Wuhan 430016, China
| | - Jing-Tao Huang
- Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University, Donghu Road 169#, Wuhan 430071, China
| | - Ling Hu
- Department of Neurology, Wuhan Children's Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science & Technology, Wuhan 430016, China
| | - Xing Liao
- Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University, Donghu Road 169#, Wuhan 430071, China
| | - Xiang Dai
- Laboratory of Reproductive Medicine, Wuhan Children's Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science & Technology, Wuhan 430016, China
| | - Song-Mei Liu
- Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University, Donghu Road 169#, Wuhan 430071, China.
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Solovyev AV, Barashkov NA, Bady-Khoo MS, Zytsar MV, Posukh OL, Romanov GP, Rafailov AM, Sazonov NN, Alexeev AN, Dzhemileva LU, Khusnutdinova EK, Fedorova SA. Reconstruction of SNP haplotypes with mutation c.-23+1G>A in human gene GJB2 (Chromosome 13) in some populations of Eurasia. RUSS J GENET+ 2017. [DOI: 10.1134/s1022795417080099] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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21
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Adhikary B, Bankura B, Biswas S, Paul S, Das M. Absence of KCNQ4 mutation in Bengali families with ADNSHL originated from West Bengal, India. Int J Pediatr Otorhinolaryngol 2017; 100:35-38. [PMID: 28802383 DOI: 10.1016/j.ijporl.2017.06.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 06/06/2017] [Accepted: 06/09/2017] [Indexed: 10/19/2022]
Abstract
OBJECTIVE Autosomal Dominant Non-Syndromic Hearing Loss (ADNSHL) is extremely heterogeneous in nature. More than 60 loci with 30 different genes have been identified linked to ADNSHL. Mutation in KCNQ4 is considered as one of the most common causative factor responsible for ADNSHL. No study focused on the genetic alteration of KCNQ4 gene among hearing loss patients in India. The present study for the first time was carried out to determine the mutation spectrum of KCNQ4 gene in ADNSHL patients of West Bengal state, India. METHOD Twenty nine individuals from 10 independent ADNSHL family (with two or more generation affected) were studied both clinically and genetically. Most of the patients showed moderate progressive sensorineural hearing loss. Mutation analysis was conducted for KCNQ4 gene using polymerase chain reaction followed by direct sequencing. RESULTS Neither any reported nor a novel pathogenic mutation in KCNQ4was detected in our studied group, in contrast to the findings among East Asians. CONCLUSION The result of the present study suggests that mutations in KCNQ4 gene are unlikely to be a major causative factor of ADNSHL in our studied patients from West Bengal, India, pointing to other genes might be responsible for ADNSHL in our studied patients.
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Affiliation(s)
- Bidisha Adhikary
- Department of Zoology, University of Calcutta, 35 Ballygunge Circular Road, Kolkata 700019, West Bengal, India
| | - Biswabandhu Bankura
- Department of Zoology, University of Calcutta, 35 Ballygunge Circular Road, Kolkata 700019, West Bengal, India
| | - Subhradev Biswas
- Department of E.N.T, Institute of Post Graduate Medical Education & Research, 244 A J C Bose Road, Kolkata 700020, West Bengal, India
| | - Silpita Paul
- Department of Zoology, University of Calcutta, 35 Ballygunge Circular Road, Kolkata 700019, West Bengal, India
| | - Madhusudan Das
- Department of Zoology, University of Calcutta, 35 Ballygunge Circular Road, Kolkata 700019, West Bengal, India.
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Rudman JR, Kabahuma RI, Bressler SE, Feng Y, Blanton SH, Yan D, Liu XZ. The genetic basis of deafness in populations of African descent. J Genet Genomics 2017; 44:285-294. [PMID: 28642064 DOI: 10.1016/j.jgg.2017.03.008] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 02/03/2017] [Accepted: 03/24/2017] [Indexed: 11/24/2022]
Abstract
Hearing loss is the most common sensorineural disorder worldwide and is associated with more than 1000 mutations in more than 90 genes. While mutations in genes such as GJB2 (gap-junction protein β 2) and GJB6 (gap-junction protein β 6) are highly prevalent in Caucasian, Asian, and Middle Eastern populations, they are rare in both native African populations and those of African descent. The objective of this paper is to review the current knowledge regarding the epidemiology and genetics of hearing loss in African populations with a focus on native sub-Saharan African populations. Environmental etiologies related to poor access to healthcare and perinatal care account for the majority of cases. Syndromic etiologies including Waardenburg, Pendred and Usher syndromes are uncommon causes of hearing loss in these populations. Of the non-syndromic causes, common mutations in GJB2 and GJB6 are rarely implicated in populations of African descent. Recent use of next-generation sequencing (NGS) has identified several candidate deafness genes in African populations from Nigeria and South Africa that are unique when compared to common causative mutations worldwide. Researchers also recently described a dominant mutation in MYO3a in an African American family with non-syndromic hearing loss. The use of NGS and specialized panels will aid in identifying rare and novel mutations in a more cost- and time-effective manner. The identification of common hearing loss mutations in indigenous African populations will pave the way for translation into genetic deafness research in populations of African descent worldwide.
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Affiliation(s)
- Jason R Rudman
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Rosemary I Kabahuma
- Department of Otorhinolaryngology, Steve Biko Academic Hospital, University of Pretoria, Pretoria 0001, South Africa.
| | - Sara E Bressler
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Yong Feng
- Department of Otolaryngology, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Susan H Blanton
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL 33136, USA; John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Denise Yan
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Xue-Zhong Liu
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Department of Otolaryngology, Xiangya Hospital, Central South University, Changsha 410008, China; Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL 33136, USA; John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136, USA.
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Kumar Swain S, Sahu MC, Baisakh MR. WITHDRAWN: Early detection of hearing loss with Connexin 26 gene assessment – A review. APOLLO MEDICINE 2017. [DOI: 10.1016/j.apme.2017.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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24
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Yan D, Xiang G, Chai X, Qing J, Shang H, Zou B, Mittal R, Shen J, Smith RJH, Fan YS, Blanton SH, Tekin M, Morton C, Xing W, Cheng J, Liu XZ. Screening of deafness-causing DNA variants that are common in patients of European ancestry using a microarray-based approach. PLoS One 2017; 12:e0169219. [PMID: 28273078 PMCID: PMC5342170 DOI: 10.1371/journal.pone.0169219] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 12/04/2016] [Indexed: 12/12/2022] Open
Abstract
The unparalleled heterogeneity in genetic causes of hearing loss along with remarkable differences in prevalence of causative variants among ethnic groups makes single gene tests technically inefficient. Although hundreds of genes have been reported to be associated with nonsyndromic hearing loss (NSHL), GJB2, GJB6, SLC26A4, and mitochondrial (mt) MT-RNR1 and MTTS are the major contributors. In order to provide a faster, more comprehensive and cost effective assay, we constructed a DNA fluidic array, CapitalBioMiamiOtoArray, for the detection of sequence variants in five genes that are common in most populations of European descent. They consist of c.35delG, p.W44C, p.L90P, c.167delT (GJB2); 309kb deletion (GJB6); p.L236P, p.T416P (SLC26A4); and m.1555A>G, m.7444G>A (mtDNA). We have validated our hearing loss array by analyzing a total of 160 DNAs samples. Our results show 100% concordance between the fluidic array biochip-based approach and the established Sanger sequencing method, thus proving its robustness and reliability at a relatively low cost.
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Affiliation(s)
- Denise Yan
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, Florida, United States of America
| | - Guangxin Xiang
- National Engineering Research Center for Beijing Biochip Technology, Beijing, China
| | - Xingping Chai
- National Engineering Research Center for Beijing Biochip Technology, Beijing, China
- Tsinghua University School of Medicine, Beijing, China
| | - Jie Qing
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, Florida, United States of America
| | - Haiqiong Shang
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, Florida, United States of America
| | - Bing Zou
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, Florida, United States of America
| | - Rahul Mittal
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, Florida, United States of America
| | - Jun Shen
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- Laboratory for Molecular Medicine, Partners Personalized Medicine, Cambridge, Massachusetts, United States of America
| | - Richard J. H. Smith
- Department of Otolaryngology - Head and Neck Surgery, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Yao-Shan Fan
- Department of Pathology, University of Miami Miller School of Medicine, Miami, Florida, United States of America
- Dr. John T. Macdonald Department of Human Genetics and John P.Hussman Institute for Human Genetics, University of Miami Miller School of Medicine, Miami, Florida, United States of America
| | - Susan H. Blanton
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, Florida, United States of America
- Department of Pathology, University of Miami Miller School of Medicine, Miami, Florida, United States of America
| | - Mustafa Tekin
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, Florida, United States of America
- Department of Pathology, University of Miami Miller School of Medicine, Miami, Florida, United States of America
| | - Cynthia Morton
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Evolution and Genomic Science, School of Biological Sciences, Manchester Academic Health Science Center, University of Manchester, United Kingdom
| | - Wanli Xing
- National Engineering Research Center for Beijing Biochip Technology, Beijing, China
- Tsinghua University School of Medicine, Beijing, China
| | - Jing Cheng
- National Engineering Research Center for Beijing Biochip Technology, Beijing, China
- Tsinghua University School of Medicine, Beijing, China
| | - Xue Zhong Liu
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, Florida, United States of America
- Tsinghua University School of Medicine, Beijing, China
- Dr. John T. Macdonald Department of Human Genetics and John P.Hussman Institute for Human Genetics, University of Miami Miller School of Medicine, Miami, Florida, United States of America
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25
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Barashkov NA, Pshennikova VG, Posukh OL, Teryutin FM, Solovyev AV, Klarov LA, Romanov GP, Gotovtsev NN, Kozhevnikov AA, Kirillina EV, Sidorova OG, Vasilyevа LM, Fedotova EE, Morozov IV, Bondar AA, Solovyevа NA, Kononova SK, Rafailov AM, Sazonov NN, Alekseev AN, Tomsky MI, Dzhemileva LU, Khusnutdinova EK, Fedorova SA. Spectrum and Frequency of the GJB2 Gene Pathogenic Variants in a Large Cohort of Patients with Hearing Impairment Living in a Subarctic Region of Russia (the Sakha Republic). PLoS One 2016; 11:e0156300. [PMID: 27224056 PMCID: PMC4880331 DOI: 10.1371/journal.pone.0156300] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 05/12/2016] [Indexed: 11/29/2022] Open
Abstract
Pathogenic variants in the GJB2 gene, encoding connexin 26, are known to be a major cause of hearing impairment (HI). More than 300 allelic variants have been identified in the GJB2 gene. Spectrum and allelic frequencies of the GJB2 gene vary significantly among different ethnic groups worldwide. Until now, the spectrum and frequency of the pathogenic variants in exon 1, exon 2 and the flanking intronic regions of the GJB2 gene have not been described thoroughly in the Sakha Republic (Yakutia), which is located in a subarctic region in Russia. The complete sequencing of the non-coding and coding regions of the GJB2 gene was performed in 393 patients with HI (Yakuts—296, Russians—51, mixed and other ethnicities—46) and in 187 normal hearing individuals of Yakut (n = 107) and Russian (n = 80) populations. In the total sample (n = 580), we revealed 12 allelic variants of the GJB2 gene, 8 of which were recessive pathogenic variants. Ten genotypes with biallelic recessive pathogenic variants in the GJB2 gene (in a homozygous or a compound heterozygous state) were found in 192 out of 393 patients (48.85%). We found that the most frequent GJB2 pathogenic variant in the Yakut patients was c.-23+1G>A (51.82%) and that the second most frequent was c.109G>A (2.37%), followed by c.35delG (1.64%). Pathogenic variants с.35delG (22.34%), c.-23+1G>A (5.31%), and c.313_326del14 (2.12%) were found to be the most frequent among the Russian patients. The carrier frequencies of the c.-23+1G>A and с.109G>A pathogenic variants in the Yakut control group were 10.20% and 2.80%, respectively. The carrier frequencies of с.35delG and c.101T>C were identical (2.5%) in the Russian control group. We found that the contribution of the GJB2 gene pathogenic variants in HI in the population of the Sakha Republic (48.85%) was the highest among all of the previously studied regions of Asia. We suggest that extensive accumulation of the c.-23+1G>A pathogenic variant in the indigenous Yakut population (92.20% of all mutant chromosomes in patients) and an extremely high (10.20%) carrier frequency in the control group may indicate a possible selective advantage for the c.-23+1G>A carriers living in subarctic climate.
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Affiliation(s)
- Nikolay A. Barashkov
- Department of Molecular Genetics, Federal State Budgetary Scientific Institution “Yakut Science Centre of Complex Medical Problems,” Yakutsk, Russian Federation
- Laboratory of Molecular Biology, Institute of Natural Sciences, M.K. Ammosov North-Eastern Federal University, Yakutsk, Russian Federation
- * E-mail:
| | - Vera G. Pshennikova
- Department of Molecular Genetics, Federal State Budgetary Scientific Institution “Yakut Science Centre of Complex Medical Problems,” Yakutsk, Russian Federation
- Laboratory of Molecular Biology, Institute of Natural Sciences, M.K. Ammosov North-Eastern Federal University, Yakutsk, Russian Federation
| | - Olga L. Posukh
- Laboratory of Human Molecular Genetics, Federal Research Center, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation
- Novosibirsk State University, Novosibirsk, Russian Federation
| | - Fedor M. Teryutin
- Department of Molecular Genetics, Federal State Budgetary Scientific Institution “Yakut Science Centre of Complex Medical Problems,” Yakutsk, Russian Federation
- Laboratory of Molecular Biology, Institute of Natural Sciences, M.K. Ammosov North-Eastern Federal University, Yakutsk, Russian Federation
| | - Aisen V. Solovyev
- Department of Molecular Genetics, Federal State Budgetary Scientific Institution “Yakut Science Centre of Complex Medical Problems,” Yakutsk, Russian Federation
- Laboratory of Molecular Biology, Institute of Natural Sciences, M.K. Ammosov North-Eastern Federal University, Yakutsk, Russian Federation
| | - Leonid A. Klarov
- Department of Molecular Genetics, Federal State Budgetary Scientific Institution “Yakut Science Centre of Complex Medical Problems,” Yakutsk, Russian Federation
- Department of Radiology, Republican Hospital # 2 –Center of Emergency Medicine, Ministry of Public Health of the Sakha Republic, Yakutsk, Russian Federation
| | - Georgii P. Romanov
- Department of Molecular Genetics, Federal State Budgetary Scientific Institution “Yakut Science Centre of Complex Medical Problems,” Yakutsk, Russian Federation
- Laboratory of Molecular Biology, Institute of Natural Sciences, M.K. Ammosov North-Eastern Federal University, Yakutsk, Russian Federation
| | - Nyurgun N. Gotovtsev
- Department of Molecular Genetics, Federal State Budgetary Scientific Institution “Yakut Science Centre of Complex Medical Problems,” Yakutsk, Russian Federation
- Laboratory of Molecular Biology, Institute of Natural Sciences, M.K. Ammosov North-Eastern Federal University, Yakutsk, Russian Federation
| | - Andrey A. Kozhevnikov
- Republican Centre of Professional Pathology, Republican Hospital # 2 –Center of Emergency Medicine, Ministry of Public Health of the Sakha Republic, Yakutsk, Russian Federation
| | - Elena V. Kirillina
- Institute of Foreign Philology and Regional Studies, M.K. Ammosov North-Eastern Federal University, Yakutsk, Russian Federation
| | - Oksana G. Sidorova
- Department of Molecular Genetics, Federal State Budgetary Scientific Institution “Yakut Science Centre of Complex Medical Problems,” Yakutsk, Russian Federation
| | - Lena M. Vasilyevа
- Audiology-Logopaedic Centre, Republican Hospital #1– National Medical Centre, Ministry of Public Health of the Sakha Republic, Yakutsk, Russian Federation
| | - Elvira E. Fedotova
- Audiology-Logopaedic Centre, Republican Hospital #1– National Medical Centre, Ministry of Public Health of the Sakha Republic, Yakutsk, Russian Federation
| | - Igor V. Morozov
- Novosibirsk State University, Novosibirsk, Russian Federation
- SB RAS Genomics Core Facility, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation
| | - Alexander A. Bondar
- SB RAS Genomics Core Facility, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation
| | - Natalya A. Solovyevа
- Department of Molecular Genetics, Federal State Budgetary Scientific Institution “Yakut Science Centre of Complex Medical Problems,” Yakutsk, Russian Federation
- Laboratory of Molecular Biology, Institute of Natural Sciences, M.K. Ammosov North-Eastern Federal University, Yakutsk, Russian Federation
| | - Sardana K. Kononova
- Department of Molecular Genetics, Federal State Budgetary Scientific Institution “Yakut Science Centre of Complex Medical Problems,” Yakutsk, Russian Federation
- Laboratory of Molecular Biology, Institute of Natural Sciences, M.K. Ammosov North-Eastern Federal University, Yakutsk, Russian Federation
| | - Adyum M. Rafailov
- Laboratory of Molecular Biology, Institute of Natural Sciences, M.K. Ammosov North-Eastern Federal University, Yakutsk, Russian Federation
| | - Nikolay N. Sazonov
- Department of Biochemistry and Biotechnology, Institute of Natural Sciences, M.K. Ammosov North-Eastern Federal University, Yakutsk, Russian Federation
| | - Anatoliy N. Alekseev
- Institute of Humanitarian Research and Indigenous Peoples of the North, Siberian Branch of the Russian Academy of Sciences, Yakutsk, Russian Federation
| | - Mikhail I. Tomsky
- Department of Molecular Genetics, Federal State Budgetary Scientific Institution “Yakut Science Centre of Complex Medical Problems,” Yakutsk, Russian Federation
| | - Lilya U. Dzhemileva
- Laboratory of Human Molecular Genetics, Institute of Biochemistry and Genetics, Ufa Scientific Centre, Russian Academy of Sciences, Ufa, Russian Federation
- Department of Immunology and Human Reproductive Health, Bashkir State Medical University, Ufa, Russian Federation
| | - Elza K. Khusnutdinova
- Laboratory of Human Molecular Genetics, Institute of Biochemistry and Genetics, Ufa Scientific Centre, Russian Academy of Sciences, Ufa, Russian Federation
- Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa, Russian Federation
| | - Sardana A. Fedorova
- Department of Molecular Genetics, Federal State Budgetary Scientific Institution “Yakut Science Centre of Complex Medical Problems,” Yakutsk, Russian Federation
- Laboratory of Molecular Biology, Institute of Natural Sciences, M.K. Ammosov North-Eastern Federal University, Yakutsk, Russian Federation
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26
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Tekin D, Yan D, Bademci G, Feng Y, Guo S, Foster J, Blanton S, Tekin M, Liu X. A next-generation sequencing gene panel (MiamiOtoGenes) for comprehensive analysis of deafness genes. Hear Res 2016; 333:179-184. [PMID: 26850479 DOI: 10.1016/j.heares.2016.01.018] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Revised: 11/06/2015] [Accepted: 01/31/2016] [Indexed: 12/30/2022]
Abstract
Extreme genetic heterogeneity along with remarkable variation in the distribution of causative variants across in different ethnicities makes single gene testing inefficient for hearing loss. We developed a custom capture/next-generation sequencing gene panel of 146 known deafness genes with a total target size of approximately 1 MB. The genes were identified by searching databases including Hereditary Hearing Loss Homepage, the Human Genome Mutation Database (HGMD), Online Mendelian Inheritance in Man (OMIM) and most recent peer-reviewed publications related to the genetics of deafness. The design covered all coding exons, UTRs and 25 bases of intronic flanking sequences for each exon. To validate our panel, we used 6 positive controls with variants in known deafness genes and 8 unsolved samples from individuals with hearing loss. Mean coverage of the targeted exons was 697X. On average, each sample had 99.8%, 96.2% and 92.7% of the targeted region coverage of 1X, 50X and 100X reads, respectively. Analysis detected all known variants in nuclear genes. These results prove the accuracy and reliability of the custom capture experiment.
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Affiliation(s)
- Demet Tekin
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Denise Yan
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Guney Bademci
- Dr. John T. Macdonald Foundation Department of Human Genetics, and John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL 33136, USA
| | - Yong Feng
- Department of Otolaryngology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Shengru Guo
- Dr. John T. Macdonald Foundation Department of Human Genetics, and John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL 33136, USA
| | - Joseph Foster
- Dr. John T. Macdonald Foundation Department of Human Genetics, and John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL 33136, USA
| | - Susan Blanton
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL 33136, USA.,Dr. John T. Macdonald Foundation Department of Human Genetics, and John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL 33136, USA
| | - Mustafa Tekin
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL 33136, USA.,Dr. John T. Macdonald Foundation Department of Human Genetics, and John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL 33136, USA
| | - Xuezhong Liu
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL 33136, USA.,Dr. John T. Macdonald Foundation Department of Human Genetics, and John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL 33136, USA.,Department of Otolaryngology, Xiangya Hospital, Central South University, Changsha, Hunan, China
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27
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Jin X, Fu R, Zhu W, Liu Z, Gu T, Jiao G, Yang H, Zhou Q, Gao Z, Zhao XY. Derivation of non-integration induced pluripotent stem cells from fibroblast of severe deafness patients with GJB2 mutation. J Genet Genomics 2015; 42:455-8. [PMID: 26336802 DOI: 10.1016/j.jgg.2015.06.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Revised: 06/04/2015] [Accepted: 06/05/2015] [Indexed: 10/23/2022]
Affiliation(s)
- Xiaofeng Jin
- Department of Otolaryngology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Rui Fu
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Wanwan Zhu
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhengxin Liu
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Tiantian Gu
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Guanyi Jiao
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Hua Yang
- Department of Otolaryngology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Qi Zhou
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhiqiang Gao
- Department of Otolaryngology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China.
| | - Xiao-Yang Zhao
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
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28
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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: 87] [Impact Index Per Article: 8.7] [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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29
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Kim SY, Kim AR, Kim NKD, Kim MY, Jeon EH, Kim BJ, Han YE, Chang MY, Park WY, Choi BY. Strong founder effect of p.P240L in CDH23 in Koreans and its significant contribution to severe-to-profound nonsyndromic hearing loss in a Korean pediatric population. J Transl Med 2015; 13:263. [PMID: 26264712 PMCID: PMC4534105 DOI: 10.1186/s12967-015-0624-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 07/30/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Despite the prevalence of CDH23 mutations in East Asians, its large size hinders investigation. The pathologic mutation p.P240L in CDH23 is common in East Asians. However, whether this mutation represents a common founder or a mutational hot spot is unclear. The prevalence of CDH23 mutations with prelingual severe-to-profound sporadic or autosomal recessive sensorineural hearing loss (arSNHL) is unknown in Koreans. METHODS From September 2010 to October 2014, children with severe-to-profound sporadic or arSNHL without phenotypic markers, and their families, were tested for mutations in connexins GJB2, GJB6 and GJB3. Sanger sequencing of CDH23 p.P240L was performed on connexin-negative samples without enlarged vestibular aqueducts (EVA), followed by targeted resequencing of 129 deafness genes, including CDH23, unless p.P240L homozygotes were detected in the first screening. Four p.P240L-allele-linked STR markers were genotyped in 40 normal-hearing control subjects, and the p.P240L carriers in the hearing-impaired cohort, to identify the haplotypes. RESULTS Four (3.1 %) of 128 children carried two CDH23 mutant alleles, and SLC26A4 and GJB2 accounted for 18.0 and 17.2 %, respectively. All four children showed profound nonsyndromic SNHL with minimal residual hearing. Interestingly, all had at least one p.P240L mutant allele. Analysis of p.P240L-linked STR markers in these children and other postlingual hearing-impaired adults carrying p.P240L revealed that p.P240L was mainly carried on a single haplotype. CONCLUSIONS p.P240L contributed significantly to Korean pediatric severe arSNHL with a strong founder effect, with implications for future phylogenetic studies. Screening for p.P240L as a first step in GJB2-negative arSNHL Koreans without EVA is recommended.
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Affiliation(s)
- So Young Kim
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea.
| | - Ah Reum Kim
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea.
| | - Nayoung K D Kim
- Samsung Genome Institute, Samsung Medical Center, Seoul, Korea.
| | - Min Young Kim
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Bundang Hospital, Seoul National University College of Medicine, 300 Gumi-dong, Bundang-gu, Seongnam, 463-707, Korea.
| | - Eun-Hee Jeon
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Bundang Hospital, Seoul National University College of Medicine, 300 Gumi-dong, Bundang-gu, Seongnam, 463-707, Korea.
| | - Bong Jik Kim
- Department of Otorhinolaryngology-Head and Neck Surgery, Dankook University Hospital, Cheonan, Korea.
| | - Young Eun Han
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea.
| | - Mun Young Chang
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea.
| | - Woong-Yang Park
- Samsung Genome Institute, Samsung Medical Center, Seoul, Korea. .,Department of Molecular Cell Biology, School of Medicine, Sungkyunkwan University, Seoul, Korea.
| | - Byung Yoon Choi
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Bundang Hospital, Seoul National University College of Medicine, 300 Gumi-dong, Bundang-gu, Seongnam, 463-707, Korea. .,Sensory Organ Research Institute, Seoul National University Medical Research Center, Seoul, Korea.
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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: 2.6] [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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Li H, Wang B, Liu D, Wang T, Li Q, Wang W, Li H. SNPscan as a high-performance screening tool for mutation hotspots of hearing loss-associated genes. Genomics 2015; 106:83-7. [DOI: 10.1016/j.ygeno.2015.05.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Revised: 05/15/2015] [Accepted: 05/17/2015] [Indexed: 11/16/2022]
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Yan D, Kannan-Sundhari A, Vishwanath S, Qing J, Mittal R, Kameswaran M, Liu XZ. The Genetic Basis of Nonsyndromic Hearing Loss in Indian and Pakistani Populations. Genet Test Mol Biomarkers 2015; 19:512-27. [PMID: 26186295 DOI: 10.1089/gtmb.2015.0023] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Deafness encompasses a series of etiologically heterogeneous disorders with mutations in more than 400 independent genes. However, several studies indicate that a large proportion of both syndromic and nonsyndromic forms of deafness in the racially diverse Indian and Pakistani populations are caused by defects in just a few genes. In these countries, there is a strong cultural preference for consanguineous marriage and an associated relatively high prevalence of genetic disorders. The current Indian population is approximately 1.2 billion and it is estimated that 30,000 infants are born with congenital sensorineural hearing loss (HL) each year. The estimated rate of profound bilateral HL is 1.6 per 1000 in Pakistan and 70% of this HL arises in consanguineous families. Knowledge of the genetic cause of deafness within a distinct population is important for accurate genetic counseling and early diagnosis for timely intervention and treatment options. Many sources and technologies are now available for the testing of hearing efficiency. Population-based screening has been proposed as one of the major strategies for translating genetic and genomic advances into population health gains. This review of the genetics of deafness in Indian and Pakistani populations deals with the major causes of deafness in these countries and prospectives for reducing the incidence of inherited deafness.
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Affiliation(s)
- Denise Yan
- 1 Departments of Otolaryngology-Head and Neck Surgery, Leonard M. Miller School of Medicine, University of Miami , Miami, Florida
| | - Abhiraami Kannan-Sundhari
- 1 Departments of Otolaryngology-Head and Neck Surgery, Leonard M. Miller School of Medicine, University of Miami , Miami, Florida.,2 SRM University , SRM Nagar, Chennai, India
| | - Subramanian Vishwanath
- 1 Departments of Otolaryngology-Head and Neck Surgery, Leonard M. Miller School of Medicine, University of Miami , Miami, Florida.,2 SRM University , SRM Nagar, Chennai, India
| | - Jie Qing
- 1 Departments of Otolaryngology-Head and Neck Surgery, Leonard M. Miller School of Medicine, University of Miami , Miami, Florida
| | - Rahul Mittal
- 1 Departments of Otolaryngology-Head and Neck Surgery, Leonard M. Miller School of Medicine, University of Miami , Miami, Florida
| | | | - Xue Zhong Liu
- 1 Departments of Otolaryngology-Head and Neck Surgery, Leonard M. Miller School of Medicine, University of Miami , Miami, Florida
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Kim SY, Kim AR, Han KH, Kim MY, Jeon EH, Koo JW, Oh SH, Choi BY. Residual Hearing in DFNB1 Deafness and Its Clinical Implication in a Korean Population. PLoS One 2015; 10:e0125416. [PMID: 26061264 PMCID: PMC4464755 DOI: 10.1371/journal.pone.0125416] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Accepted: 03/23/2015] [Indexed: 11/19/2022] Open
Abstract
Introduction The contribution of Gap junction beta-2 protein (GJB2) to the genetic load of deafness and its mutation spectra vary among different ethnic groups. Objective In this study, the mutation spectrum and audiologic features of patients with GJB2 mutations were evaluated with a specific focus on residual hearing. Methods An initial cohort of 588 subjects from 304 families with varying degrees of hearing loss were collected at the otolaryngology clinics of Seoul National University Hospital and Seoul National University Bundang Hospital from September 2010 through January 2014. GJB2 sequencing was carried out for 130 probands with sporadic or autosomal recessive non syndromic hearing loss. The audiograms were evaluated in the GJB2 mutants. Results Of the 130 subjects, 22 (16.9%) were found to carry at least one mutant allele of GJB2. The c.235delC mutation was shown to have the most common allele frequency (39.0%) among GJB2 mutations, followed by p.R143W (26.8%) and p.V37I (9.8%). Among those probands without the p.V37I allele in a trans configuration who showed some degree of residual hearing, the mean air conduction thresholds at 250 and 500 Hz were 57 dB HL and 77.8 dB HL, respectively. The c.235delC mutation showed a particularly wide spectrum of hearing loss, from mild to profound and significantly better hearing thresholds at 250 Hz and 2k Hz than in the non-p.V37I and non-235delC nonsyndromic hearing loss and deafness 1(DFNB1) subjects. Conclusion Despite its reputation as the cause of severe to profound deafness, c.235delC, the most frequent DFNB1 mutation in our cohort, caused a wide range of hearing loss with some residual hearing in low frequencies. This finding can be of paramount help for prediction of low frequency hearing thresholds in very young DFNB1 patients and highlights the importance of soft surgery for cochlear implantation in these patients.
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Affiliation(s)
- So Young Kim
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Ah Reum Kim
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Kyu Hee Han
- Department of Otorhinolaryngology-Head and Neck Surgery, National Medical Center, Seoul, Korea
| | - Min Young Kim
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, Korea
| | - Eun-Hee Jeon
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, Korea
| | - Ja-Won Koo
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, Korea
- Sensory Organ Research Institute, Seoul National University Medical Research Center, Seoul, Korea
| | - Seung Ha Oh
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
- Sensory Organ Research Institute, Seoul National University Medical Research Center, Seoul, Korea
| | - Byung Yoon Choi
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, Korea
- Sensory Organ Research Institute, Seoul National University Medical Research Center, Seoul, Korea
- * E-mail:
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Zheng J, Ying Z, Cai Z, Sun D, He Z, Gao Y, Zhang T, Zhu Y, Chen Y, Guan MX. GJB2 Mutation Spectrum and Genotype-Phenotype Correlation in 1067 Han Chinese Subjects with Non-Syndromic Hearing Loss. PLoS One 2015; 10:e0128691. [PMID: 26043044 PMCID: PMC4456361 DOI: 10.1371/journal.pone.0128691] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 04/29/2015] [Indexed: 11/17/2022] Open
Abstract
Mutations in Gap Junction Beta 2 (GJB2) have been reported to be a major cause of non-syndromic hearing loss in many populations worldwide. The spectrums and frequencies of GJB2 variants vary substantially among different ethnic groups, and the genotypes among these populations remain poorly understood. In the present study, we carried out a systematic and extended mutational screening of GJB2 gene in 1067 Han Chinese subjects with non-syndromic hearing loss, and the resultant GJB2 variants were evaluated by phylogenetic, structural and bioinformatic analysis. A total of 25 (23 known and 2 novel) GJB2 variants were identified, including 6 frameshift mutations, 1 nonsense mutation, 16 missense mutations and 2 silent mutations. In this cohort, c.235delC is the most frequently observed pathogenic mutation. The phylogenetic, structural and bioinformatic analysis showed that 2 novel variants c.127G>T (p.V43L), c.293G>C (p.R98P) and 2 known variants c. 107T>C (p.L36P) and c.187G>T (p.V63L) are localized at highly conserved amino acids. In addition, these 4 mutations are absent in 203 healthy individuals, therefore, they are probably the most likely candidate pathogenic mutations. In addition, 66 (24 novel and 42 known) genotypes were identified, including 6 homozygotes, 20 compound heterozygotes, 18 single heterozygotes, 21 genotypes harboring only polymorphism(s) and the wild type genotype. Among these, 153 (14.34%) subjects were homozygous for pathogenic mutations, 63 (5.91%) were compound heterozygotes, and 157 (14.71%) carried single heterozygous mutation. Furthermore, 65.28% (141/216) of these cases with two pathogenic mutations exhibited profound hearing loss. These data suggested that mutations in GJB2 gene are responsible for approximately 34.96% of non-syndromic hearing loss in Han Chinese population from Zhejiang Province in eastern China. In addition, our results also strongly supported the idea that other factors such as alterations in regulatory regions, additional genes, and environmental factors may contribute to the clinical manifestation of deafness.
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Affiliation(s)
- Jing Zheng
- Institute of Genetics, School of Medicine, Zhejiang University, Hangzhou, China
| | - Zhengbiao Ying
- Department of Otolaryngology, Wenling People’s Hospital, Wenzhou Medical University, Taizhou, China
| | - Zhaoyang Cai
- Department of Otolaryngology, Wenling People’s Hospital, Wenzhou Medical University, Taizhou, China
| | - Dongmei Sun
- Department of Laboratory Medicine, Jinhua Municipal Central Hospital, Jinhua, China
| | - Zheyun He
- Attardi Institute of Mitochondrial Biomedicine, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Yinglong Gao
- Attardi Institute of Mitochondrial Biomedicine, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Ting Zhang
- Department of Otolaryngology, Wenling People’s Hospital, Wenzhou Medical University, Taizhou, China
| | - Yi Zhu
- Department of Otolaryngology, the First Affiliated Hospital, Wenzhou Medical University, Wenzhou, China
| | - Ye Chen
- Institute of Genetics, School of Medicine, Zhejiang University, Hangzhou, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou, China
| | - Min-Xin Guan
- Institute of Genetics, School of Medicine, Zhejiang University, Hangzhou, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou, China
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Bosch J, Noubiap JJN, Dandara C, Makubalo N, Wright G, Entfellner JBD, Tiffin N, Wonkam A. Sequencing of GJB2 in Cameroonians and Black South Africans and comparison to 1000 Genomes Project Data Support Need to Revise Strategy for Discovery of Nonsyndromic Deafness Genes in Africans. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2014; 18:705-10. [PMID: 25162826 DOI: 10.1089/omi.2014.0063] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Mutations in the GJB2 gene, encoding connexin 26, could account for 50% of congenital, nonsyndromic, recessive deafness cases in some Caucasian/Asian populations. There is a scarcity of published data in sub-Saharan Africans. We Sanger sequenced the coding region of the GJB2 gene in 205 Cameroonian and Xhosa South Africans with congenital, nonsyndromic deafness; and performed bioinformatic analysis of variations in the GJB2 gene, incorporating data from the 1000 Genomes Project. Amongst Cameroonian patients, 26.1% were familial. The majority of patients (70%) suffered from sensorineural hearing loss. Ten GJB2 genetic variants were detected by sequencing. A previously reported pathogenic mutation, g.3741_3743delTTC (p.F142del), and a putative pathogenic mutation, g.3816G>A (p.V167M), were identified in single heterozygous samples. Amongst eight the remaining variants, two novel variants, g.3318-41G>A and g.3332G>A, were reported. There were no statistically significant differences in allele frequencies between cases and controls. Principal Components Analyses differentiated between Africans, Asians, and Europeans, but only explained 40% of the variation. The present study is the first to compare African GJB2 sequences with the data from the 1000 Genomes Project and have revealed the low variation between population groups. This finding has emphasized the hypothesis that the prevalence of mutations in GJB2 in nonsyndromic deafness amongst European and Asian populations is due to founder effects arising after these individuals migrated out of Africa, and not to a putative "protective" variant in the genomic structure of GJB2 in Africans. Our results confirm that mutations in GJB2 are not associated with nonsyndromic deafness in Africans.
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Affiliation(s)
- Jason Bosch
- 1 Division of Human Genetics, Faculty of Health Sciences, University of Cape Town , Cape Town, South Africa
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Chun JY, Shin SK, Min KT, Cho W, Kim J, Kim SO, Hong SP. Performance evaluation of the TheraTyper-GJB2 assay for detection of GJB2 gene mutations. J Mol Diagn 2014; 16:573-583. [PMID: 24998936 DOI: 10.1016/j.jmoldx.2014.04.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2014] [Revised: 04/14/2014] [Accepted: 04/23/2014] [Indexed: 01/01/2023] Open
Abstract
Mutations in the GJB2 gene are the most common cause of congenital hearing loss in many populations. This study describes the development of a matrix-assisted laser desorption/ionization time-of-flight mass spectrometry-based minisequencing assay, TheraTyper-GJB2, for the detection of c.35delG, c.167delT, and c.235delC mutations in the GJB2 gene. This assay was evaluated for analytic performance, including detection limit, interference, cross-reactivity, and precision, using GJB2 reference standards prepared by site-directed mutagenesis of a molecular clone. The detection limit was as low as 0.040 ng of human genomic DNA per PCR. No cross-reactivity with bacteria and viruses and no negative effects of increased levels of various potential interfering substances was observed. A precision test involving repetitive analysis of 2400 replicates showed 99.9% agreement (2397 of 2,400) with 99.8% (95% CI, 99.7%-99.8%) sensitivity and 100.0% (95% CI, 99.3%-100.0%) specificity. TheraTyper-GJB2 and direct sequencing assays showed 100% concordance for detecting mutations in 1,113 clinical specimens. Overall, TheraTyper-GJB2 showed comparable performance for detecting GJB2 mutations in reference and clinical samples with that of direct sequencing, and easier interpretation of results for analysis of a large quantity of samples. Therefore, the TheraTyper-GJB2 assay will be practically useful for the diagnosis of GJB2 mutations associated with congenital hearing loss with faster, cheaper, more reliable, and high-throughput capability.
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Affiliation(s)
- Ji-Yong Chun
- Research and Development Center, GeneMatrix, Inc., Seongnam, South Korea
| | - Soo-Kyung Shin
- Research and Development Center, GeneMatrix, Inc., Seongnam, South Korea
| | - Kyung Tae Min
- Research and Development Center, GeneMatrix, Inc., Seongnam, South Korea
| | - Woojae Cho
- Research and Development Center, GeneMatrix, Inc., Seongnam, South Korea
| | - Jaeil Kim
- Research and Development Center, GeneMatrix, Inc., Seongnam, South Korea
| | - Soo-Ok Kim
- Research and Development Center, GeneMatrix, Inc., Seongnam, South Korea
| | - Sun Pyo Hong
- Research and Development Center, GeneMatrix, Inc., Seongnam, South Korea.
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Associations between GJB2, mitochondrial 12S rRNA, SLC26A4 mutations, and hearing loss among three ethnicities. BIOMED RESEARCH INTERNATIONAL 2014; 2014:746838. [PMID: 24804242 PMCID: PMC3996913 DOI: 10.1155/2014/746838] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Accepted: 03/11/2014] [Indexed: 11/24/2022]
Abstract
The epidemiological researches show that the mutations of GJB2, mitochondrial 12S rRNA, and SLC26A4 genes have played an important role in the hearing loss. This study aims to investigate the mutation spectrum of GJB2, mitochondrial 12S rRNA, and SLC26A4 genes of Han Chinese, Hui people, and Uyghur ethnicities in sensorineural hearing loss (SNHL) patients in northwest of China. Mutational analyses in the three genes were brought by direct sequencing and each fragment was analyzed using an ABI 3730 DNA Sequencer. The mutation frequencies for the three HL causative genes were 34.05% in Han Chinese participants, 27.47% in Hui people, and 14.44% in Uyghur participants, respectively. The prevalence of GJB2 mutations was 13.7%, 11.4%, and 11.4% in Han Chinese, Hui people, and Uyghur participants (χ2 = 10.2, P < 0.05), respectively. The prevalence of mtDNA 12S rRNA A1555G homozygous mutations was 6.05%, 3.27%, and 1.44% in Han Chinese, Hui people, and Uyghur participants (χ2 = 13.9, P < 0.05), respectively. The prevalence of SLC26A4 mutations was 14.3%, 12.8%, and 1.6% in Han Chinese, Hui people, and Uyghur participants, respectively. In summary, we find that Uyghur and Hui SNHL individuals vary significantly from Han Chinese patients in three causative HL genes' mutational spectrum, especially for Uyghur.
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Chung J, Park SM, Chang SO, Chung T, Lee KY, Kim AR, Park JH, Kim V, Park WY, Oh SH, Kim D, Park WJ, Choi BY. A novel mutation of TMPRSS3 related to milder auditory phenotype in Korean postlingual deafness: a possible future implication for a personalized auditory rehabilitation. J Mol Med (Berl) 2014; 92:651-63. [PMID: 24526180 DOI: 10.1007/s00109-014-1128-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Revised: 01/14/2014] [Accepted: 01/24/2014] [Indexed: 11/25/2022]
Abstract
UNLABELLED Appropriate customized auditory rehabilitation for hearing impaired subjects requires prediction of residual hearing and progression of hearing loss. Mutations in TMPRSS3 encoding a transmembrane serine protease were reported to be associated with two different autosomal recessive nonsyndromic hearing loss (arNSHL) phenotypes, DFNB8 and DFNB10, in terms of residual hearing that may mandate different rehabilitation. We aimed to reveal the genetic contribution of TMPRSS3 mutations among Korean populations and to correlate the clinical phenotype with TMPRSS3 genotypes. Fifty families that segregated arNSHL and have visited our clinic recently for 2 years were recruited for TMPRSS3 screening. Novel TMPRSS3 variants detected in our cohort were modeled using a predicted three-dimensional (3D) structure of the serine protease domain. The prevalence reached up to 11.2 % (3/27) among subjects with either prelingual hearing loss but retaining some degree of language development or with postlingual ski-slope hearing loss. We also found that a p.A306T allele is a founder allele in this population. Based upon the 3D modeling, we were able to correlate significant retention of residual low-frequency hearing and slower progression of its loss to this novel variant p.T248M that was predicted to have milder pathogenicity. A yeast-based protease assay confirmed a mild pathogenic potential of the p.T248M variant and a tight correlation between the protease activity and the residual hearing. Preservation of this low-frequency hearing should be of utmost importance when considering auditory rehabilitation. Our results significantly narrow down the candidate population for TMPRSS3 sequencing for more efficient genetic diagnosis. More importantly, genotype-phenotype correlation of this gene observed in our cohort suggests that TMPRSS3 can be an appropriate candidate for personalized and customized auditory rehabilitation. KEY MESSAGE The prevalence of TMPRSS3 mutations among Korean postlingual hearing loss is 8.3 %. The p.A306T variant of TMPRSS3 is the common founder allele in Koreans. A novel variant, p.T248M of TMPRSS3, was predicted to have milder pathogenicity. There was a genotype-phenotype correlation of this gene in Koreans. Our data support implication of this gene for personalized rehabilitation.
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Affiliation(s)
- Juyong Chung
- Department of Otolaryngology, Ajou University School of Medicine, Suwon, South Korea
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Schrijver I, Gardner P. Hereditary sensorineural hearing loss: advances in molecular genetics and mutation analysis. Expert Rev Mol Diagn 2014; 6:375-86. [PMID: 16706740 DOI: 10.1586/14737159.6.3.375] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Hearing loss has a genetic etiology in the majority of cases and is very common. The universal newborn hearing screening program, together with remarkable recent progress in the characterization of genes associated with the function of hearing, have resulted in increased demand and exciting possibilities of detecting the molecular basis of hereditary hearing loss through DNA testing. Future molecular diagnostic assays are expected to offer a greater variety of gene-specific tests, as well as combined mutation panels, which will aid in the management of the impressive genetic heterogeneity observed in hereditary hearing loss, especially in individuals with nonsyndromic forms. This review addresses the genetics of hearing loss, discusses the most commonly offered genetic assays for nonsyndromic hearing loss, with advantages and limitations, proposes a practical testing algorithm, and highlights current developments.
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Affiliation(s)
- Iris Schrijver
- Stanford University School of Medicine, Department of Pathology & Pediatrics, L235, 300 Pasteur Drive, Stanford, CA 94305, USA.
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Xin F, Yuan Y, Deng X, Han M, Wang G, Zhao J, Gao X, Liu J, Yu F, Han D, Dai P. Genetic mutations in nonsyndromic deafness patients of Chinese minority and Han ethnicities in Yunnan, China. J Transl Med 2013; 11:312. [PMID: 24341454 PMCID: PMC3878508 DOI: 10.1186/1479-5876-11-312] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Accepted: 12/11/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Each year in China, 30,000 babies are born with congenital hearing impairment. However, the molecular etiology of hearing impairment in the Yunnan Province population where more than 52 minorities live has not been thoroughly investigated. To provide appropriate genetic testing and counseling to these families, we investigated the molecular etiology of nonsyndromic deafness in this population. METHODS Unrelated students with hearing loss (n = 235) who attended Kunming Huaxia secondary specialized school in Yunnan enrolled in this study. Three prominent deafness-related genes, GJB2, SLC26A4 and mtDNA 12S rRNA, were analyzed. High-resolution temporal bone computed tomography (CT) scan examinations were performed in 100 cases, including 16 cases with SLC26A4 gene variants, and 37 minorities and 47 Han cases without any SLC26A4 gene mutation. RESULTS The GJB2 mutation was detected in 16.67% (7/42) of minority patients and 17.62% (34/193) of Chinese Han patients (P > 0.05). 235delC was the hotspot mutation in nonsyndromic hearing loss (NSHL) patients, whereas 35delG was not found. The 431_450del19 mutation was detected for the first time in Han NSHL patients, which resulted in a premature stop codon and changed the protein. The SLC26A4 mutation was found in 9.52% (4/42) of minority patients and 9.84% (19/193) of Han Chinese patients (P > 0.05). The frequencies of mtDNA 12S rRNA mutation in minority and Han Chinese patients were 11.90% (5/42) and 7.77% (15/193; P > 0.05), respectively. Sixteen (16/23, 69.57%) patients with SLC26A4 mutations received temporal bone CT scan, and 14 patients were diagnosed with enlarged vestibular aqueducts (EVAs); the other 2 patients had normal inner ear development. The ratio of EVA in the minorities was 14.63% (6/41). CONCLUSIONS In this study, a total of 35.74% deaf patients showed evidence of genetic involvement, based on either genetic screening or family history; 17.45%, 9.79%, and 8.51% of the patients were determined to have inherited hearing impairment caused by GJB2, SLC26A4, and mtDNA 1555A > G mutations. There was no significant difference in deafness associated gene mutational spectrum and frequency between the Yunnan minority and Han patients.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Pu Dai
- Department of Otolaryngology and Genetic Testing Center for Deafness, Chinese PLA General Hospital, Beijing 100853, P,R, China.
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A novel splice-site mutation in the GJB2 gene causing mild postlingual hearing impairment. PLoS One 2013; 8:e73566. [PMID: 24039984 PMCID: PMC3765306 DOI: 10.1371/journal.pone.0073566] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Accepted: 07/19/2013] [Indexed: 11/26/2022] Open
Abstract
The DFNB1 subtype of autosomal recessive, nonsyndromic hearing impairment, caused by mutations affecting the GJB2 (connection-26) gene, is highly prevalent in most populations worldwide. DFNB1 hearing impairment is mostly severe or profound and usually appears before the acquisition of speech (prelingual onset), though a small number of hypomorphic missense mutations result in mild or moderate deafness of postlingual onset. We identified a novel GJB2 splice-site mutation, c. -22-2A>C, in three siblings with mild postlingual hearing impairment that were compound heterozygous for c. -22-2A>C and c.35delG. Reverse transcriptase-PCR experiments performed on total RNA extracted from saliva samples from one of these siblings confirmed that c. -22-2A>C abolished the acceptor splice site of the single GJB2 intron, resulting in the absence of normally processed transcripts from this allele. However, we did isolate transcripts from the c. -22-2A>C allele that keep an intact GJB2 coding region and that were generated by use of an alternative acceptor splice site previously unknown. The residual expression of wild-type connection-26 encoded by these transcripts probably underlies the mild severity and late onset of the hearing impairment of these subjects.
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Riahi Z, Hammami H, Ouragini H, Messai H, Zainine R, Bouyacoub Y, Romdhane L, Essaid D, Kefi R, Rhimi M, Bedoui M, Dhaouadi A, Feldmann D, Jonard L, Besbes G, Abdelhak S. Update of the spectrum of GJB2 gene mutations in Tunisian families with autosomal recessive nonsyndromic hearing loss. Gene 2013; 525:1-4. [DOI: 10.1016/j.gene.2013.04.078] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2012] [Revised: 02/20/2013] [Accepted: 04/24/2013] [Indexed: 11/25/2022]
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Naito T, Nishio SY, Iwasa YI, Yano T, Kumakawa K, Abe S, Ishikawa K, Kojima H, Namba A, Oshikawa C, Usami SI. Comprehensive genetic screening of KCNQ4 in a large autosomal dominant nonsyndromic hearing loss cohort: genotype-phenotype correlations and a founder mutation. PLoS One 2013; 8:e63231. [PMID: 23717403 PMCID: PMC3662675 DOI: 10.1371/journal.pone.0063231] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2012] [Accepted: 04/02/2013] [Indexed: 11/28/2022] Open
Abstract
The present study of KCNQ4 mutations was carried out to 1) determine the prevalence by unbiased population-based genetic screening, 2) clarify the mutation spectrum and genotype/phenotype correlations, and 3) summarize clinical characteristics. In addition, a review of the reported mutations was performed for better understanding of this deafness gene. The screening using 287 probands from unbiased Japanese autosomal dominant nonsyndromic hearing loss (ADNSHL) families identified 19 families with 7 different disease causing mutations, indicating that the frequency is 6.62% (19/287). While the majority were private mutations, one particular recurrent mutation, c.211delC, was observed in 13 unrelated families. Haplotype analysis in the vicinity of c.211delC suggests existence of a common ancestor. The majority of the patients showed all frequency, but high-frequency predominant, sensorineural hearing loss. The present study adds a new typical audiogram configuration characterized by mid-frequency predominant hearing loss caused by the p.V230E mutation. A variant at the N-terminal site (c. 211delC) showed typical ski-slope type audiogram configuration. Concerning clinical features, onset age was from 3 to 40 years old, and mostly in the teens, and hearing loss was gradually progressive. Progressive nature is a common feature of patients with KCNQ4 mutations regardless of the mutation type. In conclusion, KCNQ4 mutations are frequent among ADNSHL patients, and therefore screening of the gene and molecular confirmation of these mutations have become important in the diagnosis of these conditions.
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Affiliation(s)
- Takehiko Naito
- Department of Otorhinolaryngology, Shinshu University School of Medicine, Matsumoto, Japan
| | - Shin-ya Nishio
- Department of Otorhinolaryngology, Shinshu University School of Medicine, Matsumoto, Japan
| | - Yoh-ichiro Iwasa
- Department of Otorhinolaryngology, Shinshu University School of Medicine, Matsumoto, Japan
| | - Takuya Yano
- Department of Otorhinolaryngology, Shinshu University School of Medicine, Matsumoto, Japan
| | - Kozo Kumakawa
- Department of Otolaryngology, Toranomon Hospital, Tokyo, Japan
| | - Satoko Abe
- Department of Otolaryngology, Toranomon Hospital, Tokyo, Japan
| | - Kotaro Ishikawa
- Department of Otorhinolaryngology, Jichi Medical University, Tochigi, Japan
| | - Hiromi Kojima
- Department of Otorhinolaryngology, Jikei University School of Medicine, Tokyo, Japan
| | - Atsushi Namba
- Department of Otorhinolaryngology, Hirosaki University School of Medicine, Hirosaki, Japan
| | - Chie Oshikawa
- Department of Otorhinolaryngology, Kyushu University School of Medicine, Fukuoka, Japan
| | - Shin-ichi Usami
- Department of Otorhinolaryngology, Shinshu University School of Medicine, Matsumoto, Japan
- * E-mail:
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EMQN Best Practice guidelines for diagnostic testing of mutations causing non-syndromic hearing impairment at the DFNB1 locus. Eur J Hum Genet 2013; 21:1325-9. [PMID: 23695287 PMCID: PMC3798855 DOI: 10.1038/ejhg.2013.83] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
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Sagong B, Baek JI, Oh SK, Na KJ, Bae JW, Choi SY, Jeong JY, Choi JY, Lee SH, Lee KY, Kim UK. A rapid method for simultaneous screening of multi-gene mutations associated with hearing loss in the Korean population. PLoS One 2013; 8:e57237. [PMID: 23469187 PMCID: PMC3585873 DOI: 10.1371/journal.pone.0057237] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Accepted: 01/18/2013] [Indexed: 12/20/2022] Open
Abstract
Hearing loss (HL) is a congenital disease with a high prevalence, and patients with hearing loss need early diagnosis for treatment and prevention. The GJB2, MT-RNR1, and SLC26A4 genes have been reported as common causative genes of hearing loss in the Korean population and some mutations of these genes are the most common mutations associated with hearing loss. Accordingly, we developed a method for the simultaneous detection of seven mutations (c.235delC of GJB2, c.439A>G, c.919-2A>G, c.1149+3A>G, c.1229C>T, c.2168A>G of SLC26A4, and m.1555A>G of the MT-RNR1 gene) using multiplex SNaPshot minisequencing to enable rapid diagnosis of hereditary hearing loss. This method was confirmed in patients with hearing loss and used for genetic diagnosis of controls with normal hearing and neonates. We found that 4.06% of individuals with normal hearing and 4.32% of neonates were heterozygous carriers. In addition, we detected that an individual is heterozygous for two different mutations of GJB2 and SLC26A4 gene, respectively and one normal hearing showing the heteroplasmy of m.1555A>G. These genotypes corresponded to those determined by direct sequencing. Overall, we successfully developed a robust and cost-effective diagnosis method that detects common causative mutations of hearing loss in the Korean population. This method will be possible to detect up to 40% causative mutations associated with prelingual HL in the Korean population and serve as a useful genetic technique for diagnosis of hearing loss for patients, carriers, neonates, and fetuses.
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Affiliation(s)
- Borum Sagong
- Department of Biology, College of Natural Sciences, Kyungpook National University, Daegu, South Korea
| | - Jeong-In Baek
- Department of Biology, College of Natural Sciences, Kyungpook National University, Daegu, South Korea
| | - Se-Kyung Oh
- Department of Biology, College of Natural Sciences, Kyungpook National University, Daegu, South Korea
| | - Kyung Jin Na
- Department of Otorhinolaryngology-Head and Neck Surgery, College of Medicine, Kyungpook National University, Daegu, South Korea
| | - Jae Woong Bae
- Department of Biology, College of Natural Sciences, Kyungpook National University, Daegu, South Korea
| | - Soo Young Choi
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Ji Yun Jeong
- Department of Endocrinology and Metabolism, Kyungpook National University Hospital, Kyungpook National University School of Medicine, Daegu, South Korea
| | - Jae Young Choi
- Department of Otorhinolaryngology, Yonsei University College of Medicine, Seoul, South Korea
| | - Sang-Heun Lee
- Department of Otorhinolaryngology-Head and Neck Surgery, College of Medicine, Kyungpook National University, Daegu, South Korea
| | - Kyu-Yup Lee
- Department of Otorhinolaryngology-Head and Neck Surgery, College of Medicine, Kyungpook National University, Daegu, South Korea
- * E-mail: (KYL); (UKK)
| | - Un-Kyung Kim
- Department of Biology, College of Natural Sciences, Kyungpook National University, Daegu, South Korea
- * E-mail: (KYL); (UKK)
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Zhou L, Du F, Zhao Y, Yameen A, Chen H, Tang Z. DNAzyme based gap-LCR detection of single-nucleotide polymorphism. Biosens Bioelectron 2013; 45:141-7. [PMID: 23455054 DOI: 10.1016/j.bios.2013.01.061] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Revised: 01/24/2013] [Accepted: 01/30/2013] [Indexed: 11/18/2022]
Abstract
Fast and accurate detection of single-nucleotide polymorphism (SNP) is thought more and more important for understanding of human physiology and elucidating the molecular based diseases. A great deal of effort has been devoted to developing accurate, rapid, and cost-effective technologies for SNP analysis. However most of those methods developed to date incorporate complicated probe labeling and depend on advanced equipment. The DNAzyme based Gap-LCR detection method averts any chemical modification on probes and circumvents those problems by incorporating a short functional DNA sequence into one of LCR primers. Two kinds of exonuclease are utilized in our strategy to digest all the unreacted probes and release the DNAzymes embedded in the LCR product. The DNAzyme applied in our method is a versatile tool to report the result of SNP detection in colorimetric or fluorometric ways for different detection purposes.
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Affiliation(s)
- Li Zhou
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, PR China
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Carlsson PI, Karltorp E, Carlsson-Hansén E, Åhlman H, Möller C, Vondöbeln U. GJB2 (Connexin 26) gene mutations among hearing-impaired persons in a Swedish cohort. Acta Otolaryngol 2012; 132:1301-5. [PMID: 23039283 DOI: 10.3109/00016489.2012.701018] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
CONCLUSION The most common mutation in the Swedish population was Connexin 26 (C×26) 35delG, which indicates that the percentage of Swedish persons with C×26 mutations and polymorphisms in the GJB2 gene among non-syndromic hearing-impaired (HI) persons is comparable to the rest of Europe. The results strongly support a Swedish policy to offer all children with diagnosed hearing impairment genetic tests for the C×26 35delG mutation. OBJECTIVES The aim of the present study was to search for mutations in the GBJ2 gene among Swedish persons with non-syndromic hearing impairment to further clarify how common these mutations are in Sweden, one of the northernmost countries in Europe. METHODS Seventy-nine patients with non-syndromic hearing impairment participated in the study. For 87% of the participants, a pure tone audiogram showed a severe or profound hearing impairment. Dried blood spots on filter paper, taken at 3-5 days of age in the Swedish nationwide neonatal screening programme for congenital disorders and saved in a biobank, were used for the molecular genetic analyses. RESULTS The total number of subjects with one or two pathologic mutations or a mutation of unknown consequence found in the GJB2 gene was 28 of 79 (35%). Nineteen (19) persons (24%) were homozygotes for the 35delG mutation.
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Affiliation(s)
- Per-Inge Carlsson
- Department of Otorhinolaryngology, Central Hospital, Karlstad, Sweden.
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ANGELI SIMON, LIN XI, LIU XUEZHONG. Genetics of hearing and deafness. Anat Rec (Hoboken) 2012; 295:1812-29. [PMID: 23044516 PMCID: PMC4523052 DOI: 10.1002/ar.22579] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Accepted: 07/24/2012] [Indexed: 01/20/2023]
Abstract
This article is a review of the genes and genetic disorders that affect hearing in humans and a few selected mouse models of deafness. Genetics is playing an increasingly critical role in the practice of medicine. This is not only in part to the importance that genetic knowledge has on traditional genetic diseases but also in part to the fact that genetic knowledge provides an understanding of the fundamental biological process of most diseases. The proteins coded by the genes related to hearing loss (HL) are involved in many functions in the ear, such as cochlear fluid homeostasis, ionic channels, stereocilia morphology and function, synaptic transmission, gene regulation, and others. Mouse models play a crucial role in understanding of the pathogenesis associated with these genes. Different types of familial HL have been recognized for years; however, in the last two decades, there has been tremendous progress in the discovery of gene mutations that cause deafness. Most of the cases of genetic deafness recognized today are monogenic disorders that can be broadly classified by the mode of inheritance (i.e., autosomal dominant, autosomal recessive, X-linked, and mitochondrial inheritance) and by the presence of associated phenotypic features (i.e., syndromic; and nonsyndromic). In terms of nonsyndromic HL, the chromosomal locations are currently known for ∼ 125 loci (54 for dominant and 71 for recessive deafness), 64 genes have been identified (24 for dominant and 40 for recessive deafness), and there are many more loci for syndromic deafness and X-linked and mitochondrial DNA disorders (http://hereditaryhearingloss.org). Thus, today's clinician must understand the science of medical genetics as this knowledge can lead to more effective disease diagnosis, counseling, treatment, and prevention.
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Affiliation(s)
- SIMON ANGELI
- Department of Otolaryngology, University of Miami, Miami, Florida
| | - XI LIN
- Department of Otolaryngology, Emory University School of Medicine, Atlanta, Georgia
| | - XUE ZHONG LIU
- Department of Otolaryngology, University of Miami, Miami, Florida
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Yao J, Lu Y, Wei Q, Cao X, Xing G. A systematic review and meta-analysis of 235delC mutation of GJB2 gene. J Transl Med 2012; 10:136. [PMID: 22747691 PMCID: PMC3443034 DOI: 10.1186/1479-5876-10-136] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2011] [Accepted: 06/15/2012] [Indexed: 12/17/2022] Open
Abstract
Background The 235delC mutation of GJB2 gene is considered as a risk factor for the non-syndromic hearing loss (NSHL), and a significant difference in the frequency and distribution of the 235delC mutation has been described world widely. Methods A systematic review was performed by means of a meta-analysis to evaluate the influence of the 235delC mutation on the risk of NSHL. A literature search in electronic databases using keywords “235delC”, “GJB2” associated with “carrier frequency” was conducted to include all papers from January 1999 to June 2011. A total of 36 papers were included and there contained 13217 cases and 6521 controls derived from Oceania, American, Europe and Asian. Results A remarkable heterogeneity between these studies was observed. The combined results of meta-analysis showed that the 235delC mutant increased the risk of NSHL (OR = 7.9, 95%CI 4.77 ~ 13.11, P <0.00001). Meanwhile, heterogeneity of genetic effect was also observed due to the ethnic specificity and regional disparity. Therefore, the stratified meta-analysis was subsequently conducted and the results indicated that the 235delC mutation was significantly correlated with the risk of NHSL in the East Asian and South-east Asian populations (OR = 12.05, 95%CI 8.33~17.44, P <0.00001), but not significantly in the Oceania and European populations (OR = 10.36, 95%CI: 4.68~22.96, Z = 1.68, P >0.05). Conclusions The 235delC mutation of GJB2 gene increased the risk of NHSL in the East Asian and South-east Asian populations, but non-significantly associated with the NSHL susceptibility in Oceania and European populations, suggesting a significant ethnic specificity of this NSHL-associated mutation.
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Affiliation(s)
- Jun Yao
- Department of Biotechnology, School of Basic Medical Science, Nanjing Medical University, Nanjing 210029, People’s Republic of China
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Tang W, Qian D, Ahmad S, Mattox D, Todd NW, Han H, Huang S, Li Y, Wang Y, Li H, Lin X. A low-cost exon capture method suitable for large-scale screening of genetic deafness by the massively-parallel sequencing approach. Genet Test Mol Biomarkers 2012; 16:536-42. [PMID: 22480152 DOI: 10.1089/gtmb.2011.0187] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Current major barriers for using next-generation sequencing (NGS) technologies in genetic mutation screening on an epidemiological scale appear to be the high accuracy demanded by clinical applications and high per-sample cost. How to achieve high efficiency in enriching targeted disease genes while keeping a low cost/sample is a key technical hurdle to overcome. We validated a cDNA-probe-based approach for capturing exons of a group of genes known to cause deafness. Polymerase chain reaction amplicons were made from cDNA clones of the targeted genes and used as bait probes in hybridization for capturing human genomic DNA (gDNA) fragments. The cDNA library containing the clones of targeted genes provided a readily available, low-cost, and regenerable source for producing capture probes with standard molecular biology equipment. Captured gDNA fragments by our method were sequenced by the Illumina NGS platform. Results demonstrated that targeted exons captured by our approach achieved specificity, multiplexicity, uniformity, and depth of coverage suitable for accurate sequencing applications by the NGS systems. Reliable genotype calls for various homozygous and heterozygous mutations were achieved. The results were confirmed independently by conventional Sanger sequencing. The method validated here could be readily expanded to include all-known deafness genes for applications such as genetic hearing screening in newborns. The high coverage depth and cost benefits of the cDNA-probe-based exon capture approach may also facilitate widespread applications in clinical practices beyond screening mutations in deafness genes.
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Affiliation(s)
- Wenxue Tang
- Department of Otolaryngology, Emory University School of Medicine, Atlanta, Georgia 30322, USA
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