1
|
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: 0.5] [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.
Collapse
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
| |
Collapse
|
2
|
Natural Course of Residual Hearing with Reference to GJB2 and SLC26A4 Genotypes: Clinical Implications for Hearing Rehabilitation. Ear Hear 2021; 42:644-653. [PMID: 33928925 DOI: 10.1097/aud.0000000000000965] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND Understanding the characteristics of residual hearing at low frequencies and its natural course in relation to molecular genetic etiology may be important in developing rehabilitation strategies. Thus, we aimed to explore the characteristics and natural course of residual hearing at low frequencies associated with the two most frequent deafness genes: GJB2 and SLC26A4. METHODS Initially, 53 GJB2 and 65 SLC26A4 subjects were enrolled, respectively. Only those whose audiograms exhibited hearing thresholds ≤70 dB at 250 and 500 Hz, and who had at least 1-year follow-up period between the first and last audiograms, were included. Collectively, the clinical characteristics of 14 ears from eight subjects with GJB2 variants, and 31 ears from 22 subjects with SLC26A4 variants fulfilled the strict criteria. In this study, a dropout rate refers to an incidence of dropping out of the cohort by cochlear implant surgery due to severe hearing deterioration. RESULTS Among the ears with complete serial audiogram data set, significant residual hearing at low frequencies at the time of inclusion was observed in 18.8% of those with GJB2 variants (15 out of 80 ears) and 42.6% of those with SLC26A4 variants (46 out of 108 ears), revealing a difference between two deafness genes. Subsequently, ears with SLC26A4 variants (11 of 46 ears, 23.9%) turned out to have a higher dropout rate for cochlear implantation due to hearing deterioration within the first year than those with GJB2 variants (1 of 15, 6.7%), albeit with no statistical significance. Throughout the follow-up period (mean: 37.2 ± 6.8, range: 12 to 80 months), deterioration of residual hearing at low frequencies at 250 Hz (dB HL/y) and 500 Hz (dB HL/y) of those with GJB2 variants exhibited 3.1 ± 1.3 (range: 0 to 15) and 5.2 ± 1.6 (range: 0 to 20), respectively, suggesting the deterioration of residual hearing in GJB2 variants was rather slow and gradual. Specifically, GJB2 p.Leu79Cysfs*3 show less remarkable residual hearing at low frequencies, but then a relatively stable nature. In contrast, SLC26A4 variants demonstrated a significantly higher dropout rate due to severe hearing deterioration requiring cochlear implantation compared with the GJB2 variants. This trend was observed not only in the first-year follow-up period but also in the follow-up periods thereafter. The p.His723Arg;c.919-2A>G genotype of SLC26A4, in particular, was associated with a high propensity for sudden hearing deterioration, as indicated by the dropout rate, which was as high as 46.2% for cochlear implantation due to hearing deterioration during the first year follow-up period. Furthermore, the dropout rate for cochlear implantation was observed in 7.1% of those with GJB2 variants (one out of 14 ears) and 30.3% of those with SLC26A4 variants (10 out of 33 ears) throughout the entire follow-up period. CONCLUSIONS Our results suggest that there is a difference with respect to the progressive nature of residual hearing at low frequencies between the two most common genes responsible for hearing loss, which may provide clinical implications of having individualized rehabilitation and timely intervention.
Collapse
|
3
|
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: 2.3] [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.
Collapse
|
4
|
|
5
|
Figueroa-Ildefonso E, Bademci G, Rajabli F, Cornejo-Olivas M, Villanueva RDC, Badillo-Carrillo R, Inca-Martinez M, Neyra KM, Sineni C, Tekin M. Identification of Main Genetic Causes Responsible for Non-Syndromic Hearing Loss in a Peruvian Population. Genes (Basel) 2019; 10:E581. [PMID: 31370293 PMCID: PMC6723399 DOI: 10.3390/genes10080581] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 07/23/2019] [Accepted: 07/30/2019] [Indexed: 12/30/2022] Open
Abstract
: Hearing loss (HL) is a common sensory disorder affecting over 5% of the global population. The etiology underlying HL includes congenital and acquired causes; genetic factors are the main cause in over 50% of congenital cases. Pathogenic variants in the GJB2 gene are a major cause of congenital non-syndromic hearing loss (NSHL), while their distribution is highly heterogeneous in different populations. To the best of our knowledge, there is no data regarding the genetic etiologies of HL in Peru. In this study, we screened 133 Peruvian families with NSHL living in Lima. We sequenced both exons of the GJB2 gene for all probands. Seven probands with familial NSHL that remained negative for GJB2 variants underwent whole genome sequencing (WGS). We identified biallelic pathogenic variants in GJB2 in 43 probands; seven were heterozygous for only one allele. The c.427C>T variant was the most common pathogenic variant followed by the c.35delG variant. WGS revealed three novel variants in MYO15A in two probands, one of them was predicted to affect splicing and the others produce a premature stop codon. The Peruvian population showed a complex profile for genetic variants in the GJB2 gene, this particular profile might be a consequence of the admixture history in Peru.
Collapse
Affiliation(s)
- Erick Figueroa-Ildefonso
- Neurogenetics Research Center, Instituto Nacional de Ciencias Neurológicas, Lima 15003, Peru
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Guney Bademci
- John P. Hussman Institute for Human Genomics, 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
| | - Farid Rajabli
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Mario Cornejo-Olivas
- Neurogenetics Research Center, Instituto Nacional de Ciencias Neurológicas, Lima 15003, Peru
- Center for Global Health, Universidad Peruana Cayetano Heredia, Lima 15102, Peru
| | - Ruy Diego Chacón Villanueva
- Neurogenetics Research Center, Instituto Nacional de Ciencias Neurológicas, Lima 15003, Peru
- Inter-units Program in Biotechnology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-270, Brazil
| | - Rodolfo Badillo-Carrillo
- Centro de Investigaciones Básicas en el Área Otoneurológica, Instituto Nacional de Ciencias Neurológicas, Lima 15003, Peru
| | - Miguel Inca-Martinez
- Neurogenetics Research Center, Instituto Nacional de Ciencias Neurológicas, Lima 15003, Peru
- Lerner Research Institute, Genomic Medicine, Cleveland Clinic Foundation, Cleveland, OH 44195, USA
| | - Karina Milla Neyra
- Neurogenetics Research Center, Instituto Nacional de Ciencias Neurológicas, Lima 15003, Peru
| | - Claire Sineni
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Mustafa Tekin
- John P. Hussman Institute for Human Genomics, 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.
| |
Collapse
|
6
|
Han JJ, Nguyen PD, Oh DY, Han JH, Kim AR, Kim MY, Park HR, Tran LH, Dung NH, Koo JW, Lee JH, Oh SH, Anh Vu H, Choi BY. Elucidation of the unique mutation spectrum of severe hearing loss in a Vietnamese pediatric population. Sci Rep 2019; 9:1604. [PMID: 30733538 PMCID: PMC6367484 DOI: 10.1038/s41598-018-38245-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 12/17/2018] [Indexed: 11/09/2022] Open
Abstract
The mutational spectrum of deafness in Indochina Peninsula, including Vietnam, remains mostly undetermined. This significantly hampers the progress toward establishing an effective genetic screening method and early customized rehabilitation modalities for hearing loss. In this study, we evaluated the genetic profile of severe-to-profound hearing loss in a Vietnamese pediatric population using a hierarchical genetic analysis protocol that screened 11 known deafness-causing variants, followed by massively parallel sequencing targeting 129 deafness-associated genes. Eighty-seven children with isolated severe-to-profound non-syndromic hearing loss without family history were included. The overall molecular diagnostic yield was estimated to be 31.7%. The mutational spectrum for severe-to-profound non-syndromic hearing loss in our Vietnamese population was unique: The most prevalent variants resided in the MYO15A gene (7.2%), followed by GJB2 (6.9%), MYO7A (5.5%), SLC26A4 (4.6%), TMC1 (1.8%), ESPN (1.8%), POU3F4 (1.8%), MYH14 (1.8%), EYA1 (1.8%), and MR-RNR1 (1.1%). The unique spectrum of causative genes in the Vietnamese deaf population was similar to that in the southern Chinese deaf population. It is our hope that the mutation spectrum provided here could aid in establishing an efficient protocol for genetic analysis of severe-to-profound hearing loss and a customized screening kit for the Vietnamese population.
Collapse
Affiliation(s)
- Jae Joon Han
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Pham Dinh Nguyen
- Department of Otorhinolaryngology, Children's Hospital 1, Ho Chi Minh City, Vietnam
| | - Doo-Yi Oh
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Jin Hee Han
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Ah-Reum Kim
- Biomedical Research Institute, Seoul National University Hospital, Seoul, Korea
| | - Min Young Kim
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Hye-Rim Park
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Lam Huyen Tran
- Department of Otorhinolaryngology, University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Nguyen Huu Dung
- Department of Otorhinolaryngology, University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Ja-Won Koo
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Jun Ho Lee
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Hospital, Seoul, Korea
| | - Seung Ha Oh
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Hospital, Seoul, Korea
| | - Hoang Anh Vu
- Center for Molecular Biomedicine, University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam.
| | - Byung Yoon Choi
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Bundang Hospital, Seongnam, Korea.
| |
Collapse
|
7
|
Large scale newborn deafness genetic screening of 142,417 neonates in Wuhan, China. PLoS One 2018; 13:e0195740. [PMID: 29634755 PMCID: PMC5892933 DOI: 10.1371/journal.pone.0195740] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 03/28/2018] [Indexed: 11/19/2022] Open
Abstract
Almost one third of the three million people in China suffering severe deafness are children, and 50% of these cases are believed to have genetic components to their etiology. Newborn hearing genetic screening can complement Universal Neonatal Hearing Screening for the diagnosis of congenital hearing loss as well as identifying children at risk for late-onset and progressive hearing impairment. The aim of this joint academic and Ministry of Health project was to prototype a cost effective newborn genetic screen in a community health setting on a city-wide level, and to ascertain the prevalence of variation at loci that have been associated with non-syndromic hearing loss. With the participation of 143 local hospitals in the city of Wuhan, China we screened 142,417 neonates born between May 2014 and Dec. 2015. The variants GJB2 c.235delC, SLC26A4 c.919-2A>G, and mitochondrial variants m.1555A>G and m.1494C>T were assayed using real time PCR. Newborns found to carry a variant were re-assayed by sequencing in duplicate. Within a subset of 707 newborns we assayed using real-time PCR and ARMS-PCR to compare cost, sensitivity and operating procedure. The most frequent hearing loss associated allele detected in this population was the 235delC variant in GJB2 gene. In total, 4289 (3.01%) newborns were found to carry at least one allele of either GJB2 c.235delC, SLC26A4 c.919-2A>G or two assayed MT-RNR1 variants. There was complete accordance between the real-time PCR and the ARMS PCR, though the real-time PCR had a much lower failure rate. Real-time PCR had a lower cost and operating time than ARMS PCR. Ongoing collaboration with the participating hospitals will determine the specificity and sensitivity of the association of the variants with hearing loss at birth and arising in early childhood, allowing an estimation of the benefits of newborn hearing genetic screening in a large-scale community setting.
Collapse
|
8
|
Han KH, Kim AR, Kim MY, Ahn S, Oh SH, Song JH, Choi BY. Establishment of a Flexible Real-Time Polymerase Chain Reaction-Based Platform for Detecting Prevalent Deafness Mutations Associated with Variable Degree of Sensorineural Hearing Loss in Koreans. PLoS One 2016; 11:e0161756. [PMID: 27583405 PMCID: PMC5008798 DOI: 10.1371/journal.pone.0161756] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 08/11/2016] [Indexed: 11/19/2022] Open
Abstract
Many cutting-edge technologies based on next-generation sequencing (NGS) have been employed to identify candidate variants responsible for sensorineural hearing loss (SNHL). However, these methods have limitations preventing their wide clinical use for primary screening, in that they remain costly and it is not always suitable to analyze massive amounts of data. Several different DNA chips have been developed for screening prevalent mutations at a lower cost. However, most of these platforms do not offer the flexibility to add or remove target mutations, thereby limiting their wider use in a field that requires frequent updates. Therefore, we aimed to establish a simpler and more flexible molecular diagnostic platform based on ethnicity-specific mutation spectrums of SNHL, which would enable bypassing unnecessary filtering steps in a substantial portion of cases. In addition, we expanded the screening platform to cover varying degrees of SNHL. With this aim, we selected 11 variants of 5 genes (GJB2, SLC26A4, MTRNR1, TMPRSS3, and CDH23) showing high prevalence with varying degrees in Koreans and developed the U-TOP™ HL Genotyping Kit, a real-time PCR-based method using the MeltingArray technique and peptide nucleic acid probes. The results of 271 DNA samples with wild type sequences or mutations in homo- or heterozygote form were compared between the U-TOP™ HL Genotyping Kit and Sanger sequencing. The positive and negative predictive values were 100%, and this method showed perfect agreement with Sanger sequencing, with a Kappa value of 1.00. The U-TOP™ HL Genotyping Kit showed excellent performance in detecting varying degrees and phenotypes of SNHL mutations in both homozygote and heterozygote forms, which are highly prevalent in the Korean population. This platform will serve as a useful and cost-effective first-line screening tool for varying degrees of genetic SNHL and facilitate genome-based personalized hearing rehabilitation for the Korean population.
Collapse
Affiliation(s)
- Kyu-Hee Han
- Department of Otorhinolaryngology-Head and Neck Surgery, National Medical Center, Seoul, Korea
| | - Ah Reum Kim
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, Korea
- Biomedical Research Institute, Seoul National University Hospital, 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
| | - Soyeon Ahn
- Medical Research Collaborating Center, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Seung-Ha Oh
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Ju Hun Song
- Department of Otorhinolaryngology-Head and Neck Surgery, National Medical 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
- Wide River Institute of Immunology, Seoul National University College of Medicine, Hongcheon, Korea
- * E-mail:
| |
Collapse
|
9
|
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: 2.5] [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.
Collapse
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
| |
Collapse
|
10
|
Kim SY, Kim AR, Kim NKD, Lee C, Kim MY, Jeon EH, Park WY, Choi BY. Unraveling of Enigmatic Hearing-Impaired GJB2 Single Heterozygotes by Massive Parallel Sequencing: DFNB1 or Not? Medicine (Baltimore) 2016; 95:e3029. [PMID: 27057829 PMCID: PMC4998745 DOI: 10.1097/md.0000000000003029] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The molecular etiology of nonsyndromic sensorineural hearing loss (SNHL) in subjects with only one detectable autosomal recessive GJB2 mutation is unclear. Here, we report GJB2 single heterozygotes with various final genetic diagnoses and suggest appropriate diagnostic strategies. A total of 160 subjects with SNHL without phenotypic markers were screened for GJB2 mutations. Single-nucleotide variants or structural variations within the DFNB1 locus or in other deafness genes were examined by Sanger sequencing, breakpoint PCR, and targeted exome sequencing (TES) of 129 deafness genes. We identified 27 subjects with two mutations and 10 subjects with only one detectable mutation in GJB2. The detection rate of the single GJB2 mutation among the 160 SNHL subjects in the present study (6.25%) was higher than 2.58% in normal hearing controls in Korean. The DFNB1 was clearly excluded as a molecular etiology in four (40%) subjects: other recessive deafness genes (N = 3) accounted for SNHL and the causative gene for the other non-DFNB1 subject (N = 1) was not identified. The etiology of additional two subjects was potentially explained by digenic etiology (N = 2) of GJB2 with MITF and GJB3, respectively. The contribution of the single GJB2 mutation in the four remaining subjects is unclear. Comprehensive diagnostic testing including TES is prerequisite for understanding GJB2 single heterozygotes.
Collapse
Affiliation(s)
- So Young Kim
- From the Department of Otorhinolaryngology-Head and Neck Surgery, CHA medical center, CHA university, Seongnam (SYK), Department of Otorhinolaryngology-Head and Neck Surgery (SYK, ARK), Seoul National University Hospital, Seoul National University College of Medicine; Samsung Genome Institue (NKDK, CL), Samsung Medical Center, Seoul, Korea; Department of Health Sciences and Technology (CL), SAIHST, Sungkyunkwan University, Seobu-ro, Jangan-gu, Suwon, Republic of Korea; Department of Otorhinolaryngology-Head and Neck Surgery (MYK, E-HJ, BYC), Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam; Samsung Genome Institute (W-YP), Samsung Medical Center; Department of Molecular Cell Biology, School of Medicine (W-YP), Sungkyunkwan University; Sensory Organ Research Institute (BYC), Seoul National University Medical Research Center, Seoul, Korea; and Wide River Institute of Immunology (BYC), Seoul National University College of Medicine, Hongcheon, Republic of Korea
| | | | | | | | | | | | | | | |
Collapse
|