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Joo SY, Jang SH, Kim JA, Kim SJ, Kim B, Kim HY, Choi JY, Gee HY, Jung J. Prevalence and Clinical Characteristics of Mitochondrial DNA Mutations in Korean Patients With Sensorineural Hearing Loss. J Korean Med Sci 2023; 38:e355. [PMID: 38084023 PMCID: PMC10713439 DOI: 10.3346/jkms.2023.38.e355] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 09/12/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Mutations in mitochondrial DNA (mtDNA) are associated with several genetic disorders, including sensorineural hearing loss. However, the prevalence of mtDNA mutations in a large cohort of Korean patients with hearing loss has not yet been investigated. Thus, this study aimed to investigate the frequency of mtDNA mutations in a cohort of with pre- or post-lingual hearing loss of varying severity. METHODS A total of 711 Korean families involving 1,099 individuals were evaluated. Six mitochondrial variants associated with deafness (MTRNR1 m.1555A>G, MTTL1 m.3243A>G, MTCO1 m.7444G>A and m.7445A>G, and MTTS1 m.7471dupC and m.7511T>C) were screened using restriction fragment length polymorphism. The prevalence of the six variants was also analyzed in a large control dataset using whole-genome sequencing data from 4,534 Korean individuals with unknown hearing phenotype. RESULTS Overall, 12 of the 711 (1.7%) patients with hearing loss had mtDNA variants, with 10 patients from independent families positive for the MTRNR1 m.1555A>G mutation and 2 patients positive for the MTCO1 m.7444G>A mutation. The clinical characteristics of patients with the mtDNA variants were characterized by post-lingual progressive hearing loss due to the m.1555A>G variant (9 of 472; 1.9%). In addition, 18/4,534 (0.4%) of the Korean population have mitochondrial variants associated with hearing loss, predominantly the m.1555A>G variant. CONCLUSION A significant proportion of Korean patients with hearing loss is affected by the mtDNA variants, with the m.1555A>G variant being the most prevalent. These results clarify the genetic basis of hearing loss in the Korean population and emphasize the need for genetic testing for mtDNA variants.
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Affiliation(s)
- Sun Young Joo
- Department of Pharmacology, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, Korea
- Won-Sang Lee Institute for Hearing Loss, Seoul, Korea
| | - Seung Hyun Jang
- Department of Pharmacology, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, Korea
- Won-Sang Lee Institute for Hearing Loss, Seoul, Korea
| | - Jung Ah Kim
- Department of Pharmacology, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, Korea
- Won-Sang Lee Institute for Hearing Loss, Seoul, Korea
| | - Se Jin Kim
- Department of Pharmacology, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, Korea
- Won-Sang Lee Institute for Hearing Loss, Seoul, Korea
| | - Bonggi Kim
- Department of Otorhinolaryngology, Yonsei University College of Medicine, Seoul, Korea
| | - Hye-Youn Kim
- Department of Pharmacology, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, Korea
- Won-Sang Lee Institute for Hearing Loss, Seoul, Korea
| | - Jae Young Choi
- Won-Sang Lee Institute for Hearing Loss, Seoul, Korea
- Department of Otorhinolaryngology, Yonsei University College of Medicine, Seoul, Korea
| | - Heon Yung Gee
- Department of Pharmacology, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, Korea
- Won-Sang Lee Institute for Hearing Loss, Seoul, Korea.
| | - Jinsei Jung
- Won-Sang Lee Institute for Hearing Loss, Seoul, Korea
- Department of Otorhinolaryngology, Yonsei University College of Medicine, Seoul, Korea.
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Hegde S, Hegde R, Kulkarni SS, Das KK, Gai PB, Bulagouda RS. Analysis of Genetic Variations in Connexin 26 (GJB2) Gene among Nonsyndromic Hearing Impairment: Familial Study. Glob Med Genet 2022; 9:152-158. [PMID: 35707775 PMCID: PMC9192169 DOI: 10.1055/s-0042-1743257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 12/29/2021] [Indexed: 11/24/2022] Open
Abstract
Objective
The goal of this research was to investigate the gap junction beta 2 (
GJB2
) gene mutations associated with nonsyndromic hearing loss individuals in North Karnataka, India.
Materials and Methods
For this study, patients with sensorineural genetic hearing abnormalities and a family history of deafness were included. A total of 35 patients from 20 families have been included in the study. The patient's DNA was isolated from peripheral blood samples. The
GJB2
gene coding region was analyzed through Sanger sequencing.
Results
There is no changes in the first exon of the
GJB2
gene. Nine different variants were recorded in second exon of the targeted gene. W24X and W77X are two nonsense mutations and three polymorphisms viz. R127H, V153I, and I33T were reported along with four 3′-UTR variants. A total (9/20) of 45% of families have been identified with mutations in the targeted gene.
Conclusion
GJB2
mutations were identified in 19 deaf-mute patients (19/35), and 13 patients were homozygous for the mutations identified in our study cohort. In our study, W24X mutation was found to be the pathogenic with a high percentage, prompting further evaluation of the other genes, along with the study of additional genetic or external causes in the families, which is essential.
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Affiliation(s)
- Smita Hegde
- Human Genetics Laboratory, Department of Anatomy, Shri B.M. Patil Medical College, Hospital and Research Centre, BLDE University (Deemed to be University), Vijayapura, Karnataka, India
- Division of Human Genetics, Karnataka Institute for DNA Research, Dharwad, Karnataka, India
| | - Rajat Hegde
- Division of Human Genetics, Karnataka Institute for DNA Research, Dharwad, Karnataka, India
- Laboratory of Vascular Physiology and Medicine, Department of Physiology, Shri B.M. Patil Medical College, Hospital and Research Centre, BLDE University (Deemed to be University), Vijayapura, Karnataka, India
| | - Suyamindra S. Kulkarni
- Division of Human Genetics, Karnataka Institute for DNA Research, Dharwad, Karnataka, India
| | - Kusal K. Das
- Laboratory of Vascular Physiology and Medicine, Department of Physiology, Shri B.M. Patil Medical College, Hospital and Research Centre, BLDE University (Deemed to be University), Vijayapura, Karnataka, India
| | - Pramod B. Gai
- Division of Human Genetics, Karnataka Institute for DNA Research, Dharwad, Karnataka, India
| | - Rudragouda S. Bulagouda
- Human Genetics Laboratory, Department of Anatomy, Shri B.M. Patil Medical College, Hospital and Research Centre, BLDE University (Deemed to be University), Vijayapura, Karnataka, India
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Ray M, Sarkar S, Sable MN. Genetics Landscape of Nonsyndromic Hearing Loss in Indian Populations. J Pediatr Genet 2021; 11:5-14. [PMID: 35186384 PMCID: PMC8847051 DOI: 10.1055/s-0041-1740532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 11/12/2021] [Indexed: 12/16/2022]
Abstract
Congenital nonsyndromic hearing loss (NSHL) has been considered as one of the most prevalent chronic disorder in children. It affects the physical and mental conditions of a large children population worldwide. Because of the genetic heterogeneity, the identification of target gene is very challenging. However, gap junction β-2 ( GJB2 ) is taken as the key gene for hearing loss, as its involvement has been reported frequently in NSHL cases. This study aimed to identify the association of GJB2 mutants in different Indian populations based on published studies in Indian population. This will provide clear genetic fundamental of NSHL in Indian biogeography, which would be helpful in the diagnosis process.
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Affiliation(s)
- Manisha Ray
- Department of Pathology and Lab Medicine, All India Institute of Medical Sciences, Bhubaneswar, Odisha, India
| | - Saurav Sarkar
- Department of Otolaryngology, All India Institute of Medical Sciences, Bhubaneswar, Odisha, India
| | - Mukund Namdev Sable
- Department of Pathology and Lab Medicine, All India Institute of Medical Sciences, Bhubaneswar, Odisha, India,Address for correspondence Mukund Namdev Sable, MD Department of Pathology and Lab Medicine, All India Institute of Medical SciencesBhubaneswar 751019, OdishaIndia
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Duan M, Chen L, Ge Q, Lu N, Li J, Pan X, Qiao Y, Tu J, Lu Z. Evaluating heteroplasmic variations of the mitochondrial genome from whole genome sequencing data. Gene 2019; 699:145-154. [PMID: 30876822 DOI: 10.1016/j.gene.2019.03.016] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Revised: 03/08/2019] [Accepted: 03/11/2019] [Indexed: 12/23/2022]
Abstract
BACKGROUND Detecting heteroplasmic variations in the mitochondrial genome can help identify potential pathogenic possibilities, which is significant for disease prevention. The development of next-generation sequencing changed the quantification of mitochondrial DNA (mtDNA) heteroplasmy from scanning limited recorded points to the entire mitochondrial genome. However, due to the presence of nuclear mtDNA homologous sequences (nuMTs), maximally retaining real variations while excluding falsest heteroplasmic variations from nuMTs and sequencing errors presents a dilemma. RESULTS Herein, we used an improved method for detecting low-frequency mtDNA heteroplasmic variations from whole genome sequencing data, including point variations and short-fragment length alterations, and evaluated the effect of this method. A two-step alignment was designed and performed to accelerate data processing, to obtain and retain the true mtDNA reads and to eliminate most nuMTs reads. After analyzing whole genome sequencing data of K562 and GM12878 cells, ~90% of heteroplasmic point variations were identified in MitoMap. The results were consistent with the results of an amplification refractory mutation system qPCR. Many linkages of the detected heteroplasmy variations were also discovered. CONCLUSIONS Our improved method is a simple, efficient and accurate way to mine mitochondrial low-frequency heteroplasmic variations from whole genome sequencing data. By evaluating the highest misalignment possibility caused by the remaining nuMTs-like reads and sequencing errors, our procedure can detect mtDNA heteroplasmic variations whose heteroplasmy frequencies are as low as 0.2%.
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Affiliation(s)
- Mengqin Duan
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Liang Chen
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Qinyu Ge
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Na Lu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Junji Li
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Xuan Pan
- Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing Medical University Affiliated Cancer Hospital, Nanjing 210009, China
| | - Yi Qiao
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Jing Tu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China.
| | - Zuhong Lu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China.
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Singh PK, Ghosh M, Sharma S, Shastri S, Gupta N, Chowdhury MR, Anand A, Kabra M. Identification of a novel homozygous mutation in transmembrane channel like 1 ( TMC1) gene, one of the second-tier hearing loss genes after GJB2 in India. Indian J Med Res 2018; 145:492-497. [PMID: 28862181 PMCID: PMC5663163 DOI: 10.4103/ijmr.ijmr_397_15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Background & objectives: Hearing impairment is a common and heterogeneous sensory disorder in humans. Among about 90 genes, which are known to be associated with hearing impairment, mutations in the GJB2 (gap junction protein beta 2) gene are the most prevalent in individuals with hereditary hearing loss. Contribution of the other deafness-causing genes is relatively poorly understood. Here, we present our findings on two families with transmembrane channel like 1 (TMC1) gene variants of the 47 families with nonsyndromic hearing loss (NSHL) studied. Methods: Forty seven families including 26 consanguineous families with at least two hearing impaired children and one normal hearing child and 21 non-consanguineous families having at least three hearing impaired children and one normal hearing child were enrolled for this study. Genetic linkage studies were carried out in 41 families that were GJB2 (Connexin 26) negative. Seven polymorphic short tandem repeat markers at the DFNB7/11 locus were studied employing fluorescently labelled markers. Results: A novel homozygous missense mutation c.1283C>A (p.Ala428Asp) was identified co-segregating with hearing loss. This change results in substitution of a highly conserved polar alanine to a charged aspartic acid and is predicted to be deleterious. In addition, a previously reported nonsense mutation, p.R34X in TMC1, was found. Interpretation & conclusions: While mutations in TMC1 are not as common a cause of NSHL as those in GJB2, TMC1 should be considered for diagnostic investigations in cases of NSHL in GJB2-negative families.
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Affiliation(s)
- Pawan Kumar Singh
- Division of Genetics, Department of Pediatrics, All Institute of Medical Sciences, New Delhi, India
| | - Manju Ghosh
- Division of Genetics, Department of Pediatrics, All Institute of Medical Sciences, New Delhi, India
| | - Shipra Sharma
- Division of Genetics, Department of Pediatrics, All Institute of Medical Sciences, New Delhi, India
| | - Shivaram Shastri
- Division of Genetics, Department of Pediatrics, All Institute of Medical Sciences, New Delhi, India
| | - Neerja Gupta
- Division of Genetics, Department of Pediatrics, All Institute of Medical Sciences, New Delhi, India
| | - Madhumita Roy Chowdhury
- Division of Genetics, Department of Pediatrics, All Institute of Medical Sciences, New Delhi, India
| | - Anuranjan Anand
- Molecular Biology & Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, India
| | - Madhulika Kabra
- Division of Genetics, Department of Pediatrics, All Institute of Medical Sciences, New Delhi, India
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Subathra M, Ramesh A, Selvakumari M, Karthikeyen NP, Srisailapathy CRS. Genetic Epidemiology of Mitochondrial Pathogenic Variants Causing Nonsyndromic Hearing Loss in a Large Cohort of South Indian Hearing Impaired Individuals. Ann Hum Genet 2017; 80:257-73. [PMID: 27530448 DOI: 10.1111/ahg.12161] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 05/16/2016] [Indexed: 01/28/2023]
Abstract
Mitochondria play a critical role in the generation of metabolic energy in the form of ATP. Tissues and organs that are highly dependent on aerobic metabolism are involved in mitochondrial disorders including nonsyndromic hearing loss (NSHL). Seven pathogenic variants leading to NSHL have so far been reported on two mitochondrial genes: MT-RNR1 encoding 12SrRNA and MT-TS1 encoding tRNA for Ser((UCN)) . We screened 729 prelingual NSHL subjects to determine the prevalence of MT-RNR1 variants at position m.961, m.1555A>G and m.1494C>T, and MT-TS1 m.7445A>G, m.7472insC m.7510T>C and m.7511T>C variants. Mitochondrial pathogenic variants were found in eight probands (1.1%). Five of them were found to have the m.1555A>G variant, two others had m.7472insC and one proband had m.7444G>A. The extended relatives of these probands showed variable degrees of hearing loss and age at onset. This study shows that mitochondrial pathogenic alleles contribute to about 1% prelingual hearing loss. This study will henceforth provide the reference for the prevalence of mitochondrial pathogenic alleles in the South Indian population, which to date has not been estimated. The m.1555A>G variant is a primary predisposing genetic factor for the development of hearing loss. Our study strongly suggests that mitochondrial genotyping should be considered for all hearing impaired individuals and particularly in families where transmission is compatible with maternal inheritance, after ruling out the most common variants.
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Affiliation(s)
- Mahalingam Subathra
- Department of Genetics, Dr. ALM Post Graduate Institute of Basic Medical Sciences, University of Madras, Taramani Campus, Chennai, India
| | - Arabandi Ramesh
- Department of Genetics, Dr. ALM Post Graduate Institute of Basic Medical Sciences, University of Madras, Taramani Campus, Chennai, India
| | - Mathiyalagan Selvakumari
- Department of Genetics, Dr. ALM Post Graduate Institute of Basic Medical Sciences, University of Madras, Taramani Campus, Chennai, India
| | - N P Karthikeyen
- DOAST (Doctrine Oriented Art of Symbiotic Treatment) Hearing Care Center and Integrated Therapy Center for Autism, Anna Nagar West, Chennai, India
| | - C R Srikumari Srisailapathy
- Department of Genetics, Dr. ALM Post Graduate Institute of Basic Medical Sciences, University of Madras, Taramani Campus, Chennai, India
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