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Liu J, Wang X, Jiang W, Azoitei A, Eiseler T, Eckstein M, Hartmann A, Stilgenbauer S, Elati M, Hohwieler M, Kleger A, John A, Wezel F, Zengerling F, Bolenz C, Günes C. Impairment of α-tubulin and F-actin interactions of GJB3 induces aneuploidy in urothelial cells and promotes bladder cancer cell invasion. Cell Mol Biol Lett 2024; 29:94. [PMID: 38956497 PMCID: PMC11218312 DOI: 10.1186/s11658-024-00609-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 06/14/2024] [Indexed: 07/04/2024] Open
Abstract
BACKGROUND We have previously identified an unsuspected role for GJB3 showing that the deficiency of this connexin protein induces aneuploidy in human and murine cells and accelerates cell transformation as well as tumor formation in xenograft models. The molecular mechanisms by which loss of GJB3 leads to aneuploidy and cancer initiation and progression remain unsolved. METHODS GJB3 expression levels were determined by RT-qPCR and Western blot. The consequences of GJB3 knockdown on genome instability were assessed by metaphase chromosome counting, multinucleation of cells, by micronuclei formation and by the determination of spindle orientation. Interactions of GJB3 with α-tubulin and F-actin was analyzed by immunoprecipitation and immunocytochemistry. Consequences of GJB3 deficiency on microtubule and actin dynamics were measured by live cell imaging and fluorescence recovery after photobleaching experiments, respectively. Immunohistochemistry was used to determine GJB3 levels on human and murine bladder cancer tissue sections. Bladder cancer in mice was chemically induced by BBN-treatment. RESULTS We find that GJB3 is highly expressed in the ureter and bladder epithelium, but it is downregulated in invasive bladder cancer cell lines and during tumor progression in both human and mouse bladder cancer. Downregulation of GJB3 expression leads to aneuploidy and genomic instability in karyotypically stable urothelial cells and experimental modulation of GJB3 levels alters the migration and invasive capacity of bladder cancer cell lines. Importantly, GJB3 interacts both with α-tubulin and F-actin. The impairment of these interactions alters the dynamics of these cytoskeletal components and leads to defective spindle orientation. CONCLUSION We conclude that deregulated microtubule and actin dynamics have an impact on proper chromosome separation and tumor cell invasion and migration. Consequently, these observations indicate a possible role for GJB3 in the onset and spreading of bladder cancer and demonstrate a molecular link between enhanced aneuploidy and invasive capacity cancer cells during tumor cell dissemination.
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Affiliation(s)
- Junnan Liu
- Department of Urology, Ulm University Hospital, Helmholtzstr. 10, 89081, Ulm, Germany
- Department of Urology, Mayo Clinic College of Medicine and Science, Rochester, MN, USA
| | - Xue Wang
- Department of Urology, Ulm University Hospital, Helmholtzstr. 10, 89081, Ulm, Germany
- Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic College of Medicine and Science, Rochester, MN, USA
| | - Wencheng Jiang
- Department of Urology, Ulm University Hospital, Helmholtzstr. 10, 89081, Ulm, Germany
| | - Anca Azoitei
- Department of Urology, Ulm University Hospital, Helmholtzstr. 10, 89081, Ulm, Germany
| | - Tim Eiseler
- Department of Internal Medicine I, Ulm University Hospital, Ulm, Germany
| | - Markus Eckstein
- Institute of Pathology, Friedrich-Alexander University, Erlangen, Germany
| | - Arndt Hartmann
- Institute of Pathology, Friedrich-Alexander University, Erlangen, Germany
| | | | - Mohamed Elati
- CANTHER, ONCOLille Institute, University of Lille, CNRS, UMR 1277, Inserm U9020, 59045, Lille Cedex, France
| | - Meike Hohwieler
- Institute of Molecular Oncology and Stem Cell Biology, Ulm University Hospital, Ulm, Germany
| | - Alexander Kleger
- Institute of Molecular Oncology and Stem Cell Biology, Ulm University Hospital, Ulm, Germany
| | - Axel John
- Department of Urology, Ulm University Hospital, Helmholtzstr. 10, 89081, Ulm, Germany
| | - Felix Wezel
- Department of Urology, Ulm University Hospital, Helmholtzstr. 10, 89081, Ulm, Germany
| | - Friedemann Zengerling
- Department of Urology, Ulm University Hospital, Helmholtzstr. 10, 89081, Ulm, Germany
| | - Christian Bolenz
- Department of Urology, Ulm University Hospital, Helmholtzstr. 10, 89081, Ulm, Germany
| | - Cagatay Günes
- Department of Urology, Ulm University Hospital, Helmholtzstr. 10, 89081, Ulm, Germany.
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Yu Y, Zhang J, Zhan Y, Luo G. A novel method for detecting nine hotspot mutations of deafness genes in one tube. Sci Rep 2024; 14:454. [PMID: 38172427 PMCID: PMC10764868 DOI: 10.1038/s41598-023-50928-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 12/28/2023] [Indexed: 01/05/2024] Open
Abstract
Deafness is a common sensory disorder. In China, approximately 70% of hereditary deafness originates from four common deafness-causing genes: GJB2, SLC26A4, GJB3, and MT-RNR1. A single-tube rapid detection method based on 2D-PCR technology was established for nine mutation sites in the aforementioned genes, and Sanger sequencing was used to verify its reliability and accuracy. The frequency of hotspot mutations in deafness genes was analysed in 116 deaf students. 2D-PCR identified 27 genotypes of nine loci according to the melting curve of the FAM, HEX, and Alexa568 fluorescence channels. Of the 116 deaf patients, 12.9% (15/116) carried SLC26A4 mutations, including c.919-2A > G and c.2168A > G (allele frequencies, 7.3% and 2.2%, respectively). The positivity rate (29.3%; 34/116) was highest for GJB2 (allele frequency, 15.9% for c.235delC, 6.0% for c.299_300delAT, and 2.6% for c.176-191del16). Sanger sequencing confirmed the consistency of results between the detection methods based on 2D-PCR and DNA sequencing. Common pathogenic mutations in patients with non-syndromic deafness in Changzhou were concentrated in GJB2 (c.235delC, c.299_300delAT, and c.176-191del16) and SLC26A4 (c.919-2A > G and c.2168 A > G). 2D-PCR is an effective method for accurately and rapidly identifying deafness-related genotypes using a single-tube reaction, and is superior to DNA sequencing, which has a high cost and long cycle.
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Affiliation(s)
- Yang Yu
- Comprehensive Laboratory, The Third Affiliated Hospital of Soochow University, Changzhou, 213003, People's Republic of China
| | - Jun Zhang
- Comprehensive Laboratory, The Third Affiliated Hospital of Soochow University, Changzhou, 213003, People's Republic of China
| | - Yuxia Zhan
- Comprehensive Laboratory, The Third Affiliated Hospital of Soochow University, Changzhou, 213003, People's Republic of China
| | - Guanghua Luo
- Comprehensive Laboratory, The Third Affiliated Hospital of Soochow University, Changzhou, 213003, People's Republic of China.
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Zheng K, Lin S, Gao J, Chen S, Su J, Liu Z, Duan S. Novel compound heterozygous MYO15A splicing variants in autosomal recessive non-syndromic hearing loss. BMC Med Genomics 2024; 17:4. [PMID: 38167320 PMCID: PMC10763153 DOI: 10.1186/s12920-023-01777-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 12/13/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND Hereditary hearing loss is a highly heterogeneous disorder. This study aimed to identify the genetic cause of a Chinese family with autosomal recessive non-syndromic sensorineural hearing loss (ARNSHL). METHODS Clinical information and peripheral blood samples were collected from the proband and its parents. Two-step high-throughput next-generation sequencing on the Ion Torrent platform was applied to detect variants as follows. First, long-range PCR was performed to amplify all the regions of the GJB2, GJB3, SLC26A4, and MT-RNR1 genes, followed by next-generation sequencing. If no candidate pathogenetic variants were found, the targeted exon sequencing with AmpliSeq technology was employed to examine another 64 deafness-associated genes. Sanger sequencing was used to identify variants and the lineage co-segregation. The splicing of the MYO15A gene was assessed by in silico bioinformatics prediction and minigene assays. RESULTS Two candidate MYO15A gene (OMIM, #602,666) heterozygous splicing variants, NG_011634.2 (NM_016239.3): c.6177 + 1G > T and c.9690 + 1G > A, were identified in the proband, and these two variants were both annotated as pathogenic according to the American College of Medical Genetics and Genomics (ACMG) guidelines. Further bioinformatic analysis predicted that the c.6177 + 1G > T variant might cause exon skipping and that the c.9690 + 1G > A variant might activate a cryptic splicing donor site in the downstream intronic region. An in vitro minigene assay confirmed the above predictions. CONCLUSIONS We identified a compound heterozygous splicing variant in the MYO15A gene in a Han Chinese family with ARNSHL. Our results broaden the spectrum of MYO15A variants, potentially benefiting the early diagnosis, prevention, and treatment of the disease.
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Affiliation(s)
- Kaifeng Zheng
- Laboratory of Molecular Medicine, Institute of Maternal and Child Medicine, Affiliated Shenzhen Maternity & Child Healthcare Hospital, Southern Medical University, Shenzhen, China
| | - Sheng Lin
- Shenzhen Health Development Research and Data Management Center, Shenzhen, China
| | - Jian Gao
- Laboratory of Molecular Medicine, Institute of Maternal and Child Medicine, Affiliated Shenzhen Maternity & Child Healthcare Hospital, Southern Medical University, Shenzhen, China
| | - Shiguo Chen
- Laboratory of Molecular Medicine, Institute of Maternal and Child Medicine, Affiliated Shenzhen Maternity & Child Healthcare Hospital, Southern Medical University, Shenzhen, China
| | - Jindi Su
- Laboratory of Molecular Medicine, Institute of Maternal and Child Medicine, Affiliated Shenzhen Maternity & Child Healthcare Hospital, Southern Medical University, Shenzhen, China
| | - Zhiqiang Liu
- Shenzhen Health Development Research and Data Management Center, Shenzhen, China
| | - Shan Duan
- Laboratory of Molecular Medicine, Institute of Maternal and Child Medicine, Affiliated Shenzhen Maternity & Child Healthcare Hospital, Southern Medical University, Shenzhen, China.
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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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Jung J, Noh SH, Jo S, Song D, Kang MJ, Shin MH, Lee HJ, Pyun JC, Namkung W, Han G, Lee MG, Choi JY. Novel small molecule-mediated restoration of the surface expression and anion exchange activity of mutated pendrin causing Pendred syndrome and DFNB4. Biomed Pharmacother 2023; 167:115445. [PMID: 37690388 DOI: 10.1016/j.biopha.2023.115445] [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: 07/07/2023] [Revised: 08/28/2023] [Accepted: 09/04/2023] [Indexed: 09/12/2023] Open
Abstract
Variants in SLC26A4 (pendrin) are the most common reasons for genetic hearing loss and vestibular dysfunction in East Asians. In patients with Pendred syndrome and DFNB4 (autosomal recessive type of genetic hearing loss 4), caused by variants in SLC26A4, the hearing function is residual at birth and deteriorates over several years, with no curative treatment for these disorders. In the present study, we revealed that a novel small molecule restores the expression and function of mutant pendrin. High-throughput screening of 54,000 small molecules was performed. We observed that pendrin corrector (PC2-1) increased the surface expression and anion exchange activity of p.H723R pendrin (H723R-PDS), the most prevalent genetic variant that causes Pendred syndrome and DFNB4. Furthermore, in endogenous H723R-PDS-expressing human nasal epithelial cells, PC2-1 significantly increased the surface expression of pendrin. PC2-1 exhibited high membrane permeability in vitro and high micromolar concentrations in the cochlear perilymph in vivo. In addition, neither inhibition of Kv11.1 activity in the human ether-a-go-go-related gene assay nor cell toxicity in the cell proliferation assay was observed at a high PC2-1 concentration (30 μM). These preclinical data support the hypothesis of the druggability of mutant pendrin using the novel corrector molecule PC2-1. In conclusion, PC2-1 may be a new therapeutic molecule for ameliorating hearing loss and treating vestibular disorders in patients with Pendred syndrome or DFNB4.
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Affiliation(s)
- Jinsei Jung
- Department of Otorhinolaryngology, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul 03722, Republic of Korea; Won-Sang Lee Institute for Hearing Loss, Seoul 03722, Republic of Korea
| | - Shin Hye Noh
- Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Sungwoo Jo
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon, Republic of Korea
| | - Doona Song
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon, Republic of Korea; Department of Integrated OMICS for Biomedical Science, Yonsei University, Seoul 03722, Republic of Korea; Translational Research Center for Protein Function Control, Department of Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
| | - Min Jin Kang
- Department of Otorhinolaryngology, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul 03722, Republic of Korea; Won-Sang Lee Institute for Hearing Loss, Seoul 03722, Republic of Korea
| | - Mi Hwa Shin
- Department of Otorhinolaryngology, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul 03722, Republic of Korea; Won-Sang Lee Institute for Hearing Loss, Seoul 03722, Republic of Korea
| | - Hyun Jae Lee
- Otolaryngology Branch, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, USA
| | - Jae-Chul Pyun
- Department of Materials Science and Engineering, Yonsei University, Seoul 03722, Republic of Korea
| | - Wan Namkung
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon, Republic of Korea.
| | - Gyoonhee Han
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon, Republic of Korea; Department of Integrated OMICS for Biomedical Science, Yonsei University, Seoul 03722, Republic of Korea; Translational Research Center for Protein Function Control, Department of Biotechnology, Yonsei University, Seoul 03722, Republic of Korea.
| | - Min Goo Lee
- Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul 03722, Republic of Korea; Department of Pharmacology, Graduate School of Medical Science, Brain Korea 21 Project, Republic of Korea, Seoul 03722, Republic of Korea.
| | - Jae Young Choi
- Department of Otorhinolaryngology, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul 03722, Republic of Korea; Won-Sang Lee Institute for Hearing Loss, Seoul 03722, Republic of Korea.
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Huang Y, Li L, Pan L, Ling X, Wang C, Huang C, Huang Y. Non-syndromic enlarged vestibular aqueduct caused by novel compound mutations of the SLC26A4 gene: a case report and literature review. Front Genet 2023; 14:1240701. [PMID: 37745850 PMCID: PMC10512862 DOI: 10.3389/fgene.2023.1240701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 08/18/2023] [Indexed: 09/26/2023] Open
Abstract
Enlarged vestibular aqueduct is an autosomal genetic disease mainly caused by mutations in the SLC26A4 gene and includes non-syndromic and syndromic types. This study aimed to identify genetic defects in a Chinese patient with non-syndromic enlarged vestibular aqueduct (NSEVA) and to investigate the impact of variants on the severity of non-syndromic enlarged vestibular aqueduct. A male patient with NSEVA, aged approximately 6 years, was recruited for this study. The clinical characteristics and results of auxiliary examinations, including laboratory and imaging examinations, were collected, and 127 common hereditary deafness genes were detected by chip capture high-throughput sequencing. Protein structure predictions, the potential impact of mutations, and multiple sequence alignments were analyzed in silico. Compound heterozygote mutations c.1523_1528delinsAC (p.Thr508Asnfs*3) and c.422T>C (p.Phe141Ser) in the SLC26A4 gene were identified. The novel frameshift mutation c.1523_1528delinsAC produces a severely truncated pendrin protein, and c.422T>C has been suggested to be a disease-causing mutation. Therefore, this study demonstrates that the novel mutation c.1523_1528delinsAC in compound heterozygosity with c.422T>C in the SLC26A4 gene is likely to be the cause of NSEVA. Cochlear implants are the preferred treatment modality for patients with NSEVA and severe-to-profound sensorineural hearing loss Genetic counseling and prenatal diagnosis are essential for early diagnosis. These findings expand the mutational spectrum of SLC26A4 and improve our understanding of the molecular mechanisms underlying NSEVA.
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Affiliation(s)
- Yunhua Huang
- Department of Clinical Laboratory, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
- Key Laboratory of Clinical Laboratory Medicine of Guangxi Department of Education, Guangxi Medical University, Nanning, Guangxi, China
| | - Linlin Li
- Department of Clinical Laboratory, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
- Key Laboratory of Clinical Laboratory Medicine of Guangxi Department of Education, Guangxi Medical University, Nanning, Guangxi, China
| | - Liqiu Pan
- Department of Clinical Laboratory, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
- Key Laboratory of Clinical Laboratory Medicine of Guangxi Department of Education, Guangxi Medical University, Nanning, Guangxi, China
| | - Xiaoting Ling
- Department of Clinical Laboratory, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
- Key Laboratory of Clinical Laboratory Medicine of Guangxi Department of Education, Guangxi Medical University, Nanning, Guangxi, China
| | - Chenghan Wang
- Department of Clinical Laboratory, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
- Key Laboratory of Clinical Laboratory Medicine of Guangxi Department of Education, Guangxi Medical University, Nanning, Guangxi, China
| | - Chaoyu Huang
- Department of Clinical Laboratory, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
- Key Laboratory of Clinical Laboratory Medicine of Guangxi Department of Education, Guangxi Medical University, Nanning, Guangxi, China
| | - Yifang Huang
- Department of Clinical Laboratory, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
- Key Laboratory of Clinical Laboratory Medicine of Guangxi Department of Education, Guangxi Medical University, Nanning, Guangxi, China
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Zeng B, Xu H, Yu Y, Li S, Tian Y, Li T, Yang Z, Wang H, Wang G, Chang M, Tang W. Increased diagnostic yield in a cohort of hearing loss families using a comprehensive stepwise strategy of molecular testing. Front Genet 2022; 13:1057293. [PMID: 36568381 PMCID: PMC9768221 DOI: 10.3389/fgene.2022.1057293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 11/14/2022] [Indexed: 12/12/2022] Open
Abstract
Hearing loss is one of the most common sensory disorders in humans. This study proposes a stepwise strategy of deafness gene detection using multiplex PCR combined with high-throughput sequencing, Sanger sequencing, multiplex ligation-dependent probe amplification (MLPA), and whole-exome sequencing (WES) to explore its application in molecular diagnosis of hearing loss families. A total of 152 families with hearing loss were included in this study, the highest overall diagnosis rate was 73% (111/152). The diagnosis rate of multiplex PCR combined with high-throughput sequencing was 52.6% (80/152). One families was diagnosed by Sanger sequencing of GJB2 exon 1. Two families were diagnosed by MLPA analysis of the STRC gene. The diagnosis rate with additional contribution from WES was 18.4% (28/152). We identified 21 novel variants from 15 deafness genes by WES. Combining WES and deep clinical phenotyping, we diagnosed 11 patients with syndromic hearing loss (SHL). This study demonstrated improved diagnostic yield in a cohort of hearing loss families and confirmed the advantages of a stepwise strategy in the molecular diagnosis of hearing loss.
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Affiliation(s)
- Beiping Zeng
- BGI College and Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China,National Health Commission Key Laboratory of Birth Defects Prevention, Henan Key Laboratory of Population Defects Prevention, Henan Institute of Reproduction Health Science and Technology, Zhengzhou, China
| | - Hongen Xu
- Precision Medicine Center, Academy of Medical Science, Zhengzhou University, Zhengzhou, China,The Research and Application Center of Precision Medicine, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yanan Yu
- Precision Medicine Center, Academy of Medical Science, Zhengzhou University, Zhengzhou, China
| | - Siqi Li
- Department of Physiology and Neurobiology, Academy of Medical Science, Zhengzhou University, Zhengzhou, China
| | - Yongan Tian
- Precision Medicine Center, Academy of Medical Science, Zhengzhou University, Zhengzhou, China
| | - Tiandong Li
- College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Zengguang Yang
- Precision Medicine Center, Academy of Medical Science, Zhengzhou University, Zhengzhou, China
| | - Haili Wang
- National Health Commission Key Laboratory of Birth Defects Prevention, Henan Key Laboratory of Population Defects Prevention, Henan Institute of Reproduction Health Science and Technology, Zhengzhou, China
| | - Guangke Wang
- Department of Otorhinolaryngology Head and Neck Surgery, Henan Provincial People’s Hospital, Zhengzhou, China
| | - Mingxiu Chang
- National Health Commission Key Laboratory of Birth Defects Prevention, Henan Key Laboratory of Population Defects Prevention, Henan Institute of Reproduction Health Science and Technology, Zhengzhou, China,*Correspondence: Mingxiu Chang, ; Wenxue Tang,
| | - Wenxue Tang
- The Research and Application Center of Precision Medicine, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, China,*Correspondence: Mingxiu Chang, ; Wenxue Tang,
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Danilchenko VY, Zytsar MV, Maslova EA, Posukh OL. Selection of Diagnostically Significant Regions of the SLC26A4 Gene Involved in Hearing Loss. Int J Mol Sci 2022; 23:ijms232113453. [PMID: 36362242 PMCID: PMC9655724 DOI: 10.3390/ijms232113453] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 10/23/2022] [Accepted: 11/01/2022] [Indexed: 11/06/2022] Open
Abstract
Screening pathogenic variants in the SLC26A4 gene is an important part of molecular genetic testing for hearing loss (HL) since they are one of the common causes of hereditary HL in many populations. However, a large size of the SLC26A4 gene (20 coding exons) predetermines the difficulties of its complete mutational analysis, especially in large samples of patients. In addition, the regional or ethno-specific prevalence of SLC26A4 pathogenic variants has not yet been fully elucidated, except variants c.919-2A>G and c.2168A>G (p.His723Arg), which have been proven to be most common in Asian populations. We explored the distribution of currently known pathogenic and likely pathogenic (PLP) variants across the SLC26A4 gene sequence presented in the Deafness Variation Database for the selection of potential diagnostically important parts of this gene. As a result of this bioinformatic analysis, we found that molecular testing ten SLC26A4 exons (4, 6, 10, 11, 13−17 and 19) with flanking intronic regions can provide a diagnostic rate of 61.9% for all PLP variants in the SLC26A4 gene. The primary sequencing of these SLC26A4 regions may be applied as an initial effective diagnostic testing in samples of patients of unknown ethnicity or as a subsequent step after the targeted testing of already-known ethno- or region-specific pathogenic SLC26A4 variants.
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Affiliation(s)
- Valeriia Yu. Danilchenko
- Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Marina V. Zytsar
- Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Ekaterina A. Maslova
- Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Olga L. Posukh
- Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Novosibirsk State University, 630090 Novosibirsk, Russia
- Correspondence:
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Wu T, Cui L, Mou Y, Guo W, Liu D, Qiu J, Xu C, Zhou J, Han F, Sun Y. A newly identified mutation (c.2029 C > T) in SLC26A4 gene is associated with enlarged vestibular aqueducts in a Chinese family. BMC Med Genomics 2022; 15:49. [PMID: 35249537 PMCID: PMC8898487 DOI: 10.1186/s12920-022-01200-4] [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: 06/19/2021] [Accepted: 02/28/2022] [Indexed: 11/29/2022] Open
Abstract
Background The enlarged vestibular aqueduct (EVA), associated with mutations in the SLC26A4 gene, characterized by non-syndromic hearing loss, is an autosomal recessive disorder. Here, we intended to investigate genetic causes of hearing loss in a Han Chinese man. Method First, whole-exome sequencing was performed to identify the gene mutations responsible for hearing loss in the proband. Sanger sequencing was used to verify the candidate mutations detected in the family. Next, we collected blood samples and clinical data from the three-generation pedigree. Finally, SLC26A4 mRNA and protein expression levels were detected by qPCR and western blotting. Result The proband suffered from bilateral progressive sensorineural hearing loss with EVA. The sequence analysis of SLC26A4 revealed that the proband and his sister both harbored a compound heterozygous mutation of c.2168A > G/c.2029C > T, inherited from their father and mother respectively. c.2029C > T mutation has not been recorded in the relevant literature previously. Relative mRNA levels of the SLC26A4 gene in individuals carrying a compound heterozygous mutation were significantly lower compared to a heterozygous mutation. SLC26A4 protein levels of 293t cells which transfected with recombinant plasmids [GV219-SLC26A4-mut (c.2029C > T) and GV219-SLC26A4-mut (c.2168A > G/c.2029C > T)] were significantly lower than normal control recombinant plasmids (GV219-SLC26A4-wt). Conclusion This study found a novel heterozygous mutation c.2029 (exon17) C > T compound with c.2168 (exon19) A > G in the SLC26A4 gene in a patient with EVA. The c.2029 (exon17) C > T mutation is proved to be pathogenic. This finding broadens the spectrum of variants in SLC26A4 gene. Supplementary Information The online version contains supplementary material available at 10.1186/s12920-022-01200-4.
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10
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Ray M, Rath SN, Sarkar S, Sable MN. Presentation of potential genes and deleterious variants associated with non-syndromic hearing loss: a computational approach. Genomics Inform 2022; 20:e5. [PMID: 35399004 PMCID: PMC9001992 DOI: 10.5808/gi.21070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 02/17/2022] [Indexed: 11/20/2022] Open
Abstract
Non-syndromic hearing loss (NSHL) is a common hereditary disorder. Both clinical and genetic heterogeneity has created many obstacles to understanding the causes of NSHL. The present study has attempted to ravel the genetic aetiology in NSHL progression and to screen out potential target genes using computational approaches. The reported NSHL target genes (2009-2020) have been studied by analyzing different biochemical and signaling pathways, interpretation of their functional association network, and discovery of important regulatory interactions with three previously established miRNAs in the human inner ear as well as in NSHL such as miR-183, miR-182, and miR-96. This study has identified SMAD4 and SNAI2 as the most putative target genes of NSHL. But pathogenic and deleterious non-synonymous single nucleotide polymorphisms discovered within SMAD4 is anticipated to have an impact on NSHL progression. Additionally, the identified deleterious variants in the functional domains of SMAD4 added a supportive clue for further study. Thus, the identified deleterious variant i.e., rs377767367 (G491V) in SMAD4 needs further clinical validation. The present outcomes would provide insights into the genetics of NSHL progression.
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Affiliation(s)
- Manisha Ray
- Department of Pathology and Lab Medicine, All India Institute of Medical Sciences, Bhubaneswar, Odisha 751019, India
| | - Surya Narayan Rath
- Department of Bioinformatics, Odisha University of Agriculture and Technology, Bhubaneswar, Odisha 751003, India
| | - Saurav Sarkar
- Department of Ear Nose Throat, All India Institute of Medical Sciences, Bhubaneswar, Odisha 751019, India
| | - Mukund Namdev Sable
- Department of Pathology and Lab Medicine, All India Institute of Medical Sciences, Bhubaneswar, Odisha 751019, India
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11
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Li N, Zhang Y, Shen M, Xu Y. A fully integrated SNP genotyping system for hereditary hearing-loss detection. LAB ON A CHIP 2022; 22:697-708. [PMID: 34923580 DOI: 10.1039/d1lc00805f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Hereditary hearing loss is one of the most common human neurosensory disorders, and there is a great need for early intervention methods such as genetically screening newborns. Single nucleotide polymorphisms (SNPs) are the major genetic targets for hearing-loss screening. In this study, a fully integrated SNP genotyping system was constructed to identify hereditary hearing loss-related genetic markers from human whole blood. The entire detection process, including blood cell lysis, nucleic acid extraction, the reaction mixture distribution, the chambers sealing and the two-colour multiplex competitive allele-specific polymerase chain reaction (KASP), can be automatically conducted in a self-contained cassette within 3 hours. To critically evaluate the performance of the system, its specificity, sensitivity and stability were assessed. Then, 13 clinical samples were genotyped with this fluidic cassette system to detect seven hotspot deafness-associated mutations in three genes (MT-RNR1, GJB2 and SLC26A4). The detection results of the cassette system were 100% concordant with those obtained by Sanger sequencing, proving its accuracy in the genetic screening of inherited hearing loss.
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Affiliation(s)
- Nan Li
- State Key Laboratory of Membrane Biology, Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China.
| | - Yuanyue Zhang
- State Key Laboratory of Membrane Biology, Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China.
| | - Minjie Shen
- State Key Laboratory of Membrane Biology, Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China.
| | - Youchun Xu
- State Key Laboratory of Membrane Biology, Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China.
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12
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Niu L, Liu L, Tian J, Chen W, Zhang C, Lan X. Genetic screening of common genetic deafness in 60,391 women of childbearing age and intervention of birth defects. Arch Med Sci 2022; 20:113-123. [PMID: 38414474 PMCID: PMC10895943 DOI: 10.5114/aoms/146024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 01/22/2022] [Indexed: 02/29/2024] Open
Abstract
Introduction At least 60% of cases of severe hearing loss result from genetic factors. In this study genetic screening was carried out for common genetic deafness in women of childbearing age to prevent deafness and birth defects via providing genetic counseling and follow-up services for high-risk families. Material and methods In total 60,391 pre-pregnancy/early-gestation women who received treatment in second-level or above hospitals in Weihai from February 2017 to December 2019 were selected. Venous or peripheral blood was collected to make dried blood slices on filter paper to extract genomic DNA, and high-throughput sequencing was applied to detect 20 variant sites in 4 common deafness genes (GJB2, GJB3, SLC26A4 and mitochondrial 12S rRNA) in the Chinese population. The spouses of women with deafness gene variants were sequenced. Results In total 3,761 carriers with deafness gene variants were detected in 60,391 women of childbearing age, with a carrier rate of 6.2%. Among them, 1,739 women (2.88%) only carried GJB2 pathogenic variants. The carrying rate of c.235delC in GJB2 pathogenic variants was the highest at 2.08%. 1,553 women (2.58%) only carried SLC26A4 pathogenic variants. The carrying rate of c.919-2A>G in SLC26A4 pathogenic variants was the highest at 1.63%. 300 women (0.5%) only carried GJB3 variants, and 125 women (0.2%) carried the mitochondrial drug-sensitive gene variant. Conclusions This screening model will greatly reduce the birth rate of children with hearing disabilities and is an effective way to prevent newborn deafness. In addition, genetic screening provided the related knowledge of hereditary deafness, especially strengthening genetic counseling and the clinical decision making from the genetic screening.
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Affiliation(s)
- Linyuan Niu
- Weihai Second Municipal Hospital Affiliated to Qingdao University, Weihai Maternal and Child Health Hospital, Weihai, China
| | - Liqin Liu
- Weihai Second Municipal Hospital Affiliated to Qingdao University, Weihai Maternal and Child Health Hospital, Weihai, China
| | - Jinjun Tian
- Weihai Second Municipal Hospital Affiliated to Qingdao University, Weihai Maternal and Child Health Hospital, Weihai, China
| | - Wei Chen
- Weihai Second Municipal Hospital Affiliated to Qingdao University, Weihai Maternal and Child Health Hospital, Weihai, China
| | - Chunxiao Zhang
- Weihai Second Municipal Hospital Affiliated to Qingdao University, Weihai Maternal and Child Health Hospital, Weihai, China
| | - Xinqiang Lan
- Weihai Second Municipal Hospital Affiliated to Qingdao University, Weihai Maternal and Child Health Hospital, Weihai, China
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13
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Jin X, Huang S, An L, Zhang C, Dai P, Gao H, Ma X. Variant analysis of 92 Chinese Han families with hearing loss. BMC Med Genomics 2022; 15:12. [PMID: 35062939 PMCID: PMC8781451 DOI: 10.1186/s12920-022-01158-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 01/07/2022] [Indexed: 01/31/2024] Open
Abstract
Abstract
Background
Hearing loss (HL) is the most frequent sensory deficit in humans, HL has strong genetic heterogeneity. The genetic diagnosis of HL is very important to aid treatment decisions and to provide prognostic information and genetic counseling for the patient’s family.
Methods
We undertook pedigree analysis in 92 Chinese non-syndromic HL patients by targeted next-generation sequencing and Sanger sequencing.
Results
Among the 92 HL patients, 18 were assigned a molecular diagnosis with 33 different variants in 14 deafness genes. Eighteen of the variants in 12 deafness genes were novel. Variants in TMC1, CDH23, LOXHD1 and USH2A were each detected in two probands, and variants in POU3F4, OTOA, GPR98, GJB6, TRIOBP, SLC26A4, MYO15A, TNC, STRC and TMPRSS3 were each detected in one proband.
Conclusion
Our findings expand the spectrum of deafness gene variation, which will inform genetic diagnosis of deafness and add to the theoretical basis for the prevention of deafness.
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14
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Dai Q, Dai W, Wang D, Liu X, Zou L, Chen J, Zheng H, Duan M. Molecular screening of patients with profound hearing loss from Chengdu, China. Acta Otolaryngol 2022; 142:57-60. [PMID: 34936523 DOI: 10.1080/00016489.2021.2014564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
BACKGROUND The rate of genetic deafness in Chengdu is still underestimated. OBJECTIVE To investigate patients' molecular etiology with profound hearing loss and facilitate genetic counseling for their families, we screened deafness-related genes of profound hearing loss in the population. METHODS A total of 1427 unrelated patients with profound hearing loss containing all age groups in the administrative area of City Chengdu (Sichuan, China) were enrolled in this study, and the average examination rate is 81.13%. Nine loci of four deaf-associated genes (GJB2, GJB3, SLC26A4, and mitochondrial 12SrRNA gene) were analyzed. Then we examined all the deaf-associated mutations and compared them between groups. RESULTS The average age of all subjects is 48.537 ± 19.077 years, peak range in 41-70 years (985/1427, 69.03%). The positive mutation rates of patients in GJB2, SLC26A4, and 12S rRNA are respectively 8.90%, 4.84%, and 5.96%, and GJB3 none. In group A the GJB2 and SLC26A4 mutation rate is 14.17% (36/254), which is remarkably higher than group B (6.14%, 72/1173). The frequency of 12SrRNA mutations is 3.15% (8/254) in group A, which is significantly different (χ2 = 4.34, p < .05) from that of group B (6.56%, 77/1173). CONCLUSIONS AND SIGNIFICANCE The mutation rate of mtDNA 12SrRNA is higher than SLC26A4 gene in our study, which is different from other parts of China. And the deaf-related gene mutation spectrums have a distinct age difference.
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Affiliation(s)
- Qingqing Dai
- Department of Otolaryngology, West China Hospital, Sichuan University, Chengdu, China
- Department of Otolaryngology Head and Neck & Audiology and Neurotology, Department of Clinical Science, Intervention and Technology, Karolinska University Hospital, Karolinska Institute, Stockholm, Sweden
| | - Wei Dai
- Department of Otolaryngology, West China Hospital, Sichuan University, Chengdu, China
| | - Dan Wang
- Department of Otolaryngology, West China Hospital, Sichuan University, Chengdu, China
| | - Xia Liu
- Sichuan Hearing and Language Rehabilitation Center, Chengdu, China
| | - Ling Zou
- Chengdu Women’s and Children’s Central Hospital, Chengdu, China
| | - Jiani Chen
- Department of Otolaryngology, West China Hospital, Sichuan University, Chengdu, China
| | - Hong Zheng
- Department of Otolaryngology, West China Hospital, Sichuan University, Chengdu, China
| | - Maoli Duan
- Department of Otolaryngology Head and Neck & Audiology and Neurotology, Department of Clinical Science, Intervention and Technology, Karolinska University Hospital, Karolinska Institute, Stockholm, Sweden
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15
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Luo H, Yang Y, Wang X, Xu F, Huang C, Liu D, Zhang L, Huang T, Ma P, Lu Q, Huang S, Yang B, Zou Y, Liu Y. Concurrent newborn hearing and genetic screening of common hearing loss variants with bloodspot-based targeted next generation sequencing in Jiangxi province. Front Pediatr 2022; 10:1020519. [PMID: 36389375 PMCID: PMC9659731 DOI: 10.3389/fped.2022.1020519] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 10/06/2022] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND AND AIMS Concurrent hearing and genetic screening of newborns have been widely adopted as an effective strategy in early diagnosis and intervention for hearing loss in many cities in China. Here, we aimed to firstly explore the efficacy of combining conventional hearing screening with genetic screening among the large-scale newborns in Jiangxi Province. METHODS A total of 24,349 newborns from Jiangxi Maternal and Child Health Hospital were enrolled in our study from April 2021 to June 2022. Newborn hearing screening was conducted using otoacoustic emission (OAE) and automated auditory brainstem response (AABR). Meanwhile, newborn dried blood spots were collected and twenty common variants in four genes, including GJB2, SLC26A4, MT-RNR1(12SrRNA), and GJB3, were screened using a BGISEQ-500 next generation sequencing platform. Whole coding regions sequencing of GJB2 and SLC26A4 were performed by Sanger sequencing and NGS, respectively. Following up of hearing for the newborns was undertaken by phone interviews. RESULTS Among the 24,349 newborns, 7.00% (1,704/24,349) were bilaterally or unilaterally referred in their initial hearing screening, whereas 1.30% (316/24,349) exhibited bilateral or unilateral hearing loss in the repeated screening. Genetic screening revealed that 4.813% (1,172/24,349) of the screened newborns were positive for at least one mutant allele (heterozygote, homozygote, or compound heterozygote in one gene, mtDNA homoplasmy or heteroplasmy and combined variants in different genes). A total of 1,146 individuals were identified with mutant allele in one gene, including 525 of GJB2, 371 of SLC26A4, 189 as homoplasmic or heteroplasmic of MT-RNR1, and 61 of GJB3, indicating that GJB2 and SLC26A4 are the most common endemic deafness-associated genes among newborns in Jiangxi Province. Nineteen newborns were detected with combined heterozygous variants in different genes, with "c.235delC heterozygous and c.919-2A > G heterozygous" as the most prevalent genotype. Additionally, seven newborns were screened as homozygotes or compound heterozygotes responsible for congenital or late-onset prelingual hearing loss, including three cases with GJB2 c.235delC homozygous and one with SLC26A4 c.919-2A > G homozygous variant, one case with compound heterozygous variants for GJB2 and two with compound heterozygous variants for SLC26A4. Coding regions sequencing of GJB2 or SLC26A4 for overall 265 infants revealed that 14 individuals were identified as compound heterozygote with a second pathogenic variant not screened by our genetic panel. CONCLUSIONS Herein our study firstly investigated the efficacy of concurrent hearing screening and genetic screening of common hearing impairment variants among large-scale newborns in Jiangxi Province. Concurrent screening provides a more comprehensive approach for management of congenital or delayed onset prelingual hearing loss and prevention of drug-induced hearing impairment for newborns at risk as well as their maternal relatives. An insight into the molecular epidemiology for hearing loss genes among Jiangxi population will also be beneficial to the genetic counseling and birth defect prevention.
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Affiliation(s)
- Haiyan Luo
- Department of Medical Genetics, Jiangxi Key Laboratory of Birth Defect Prevention and Control, Jiangxi Maternal and Child Health Hospital, Nanchang, China
| | - Yan Yang
- Department of Medical Genetics, Jiangxi Key Laboratory of Birth Defect Prevention and Control, Jiangxi Maternal and Child Health Hospital, Nanchang, China
| | - Xinrong Wang
- Department of Medical Genetics, Jiangxi Key Laboratory of Birth Defect Prevention and Control, Jiangxi Maternal and Child Health Hospital, Nanchang, China
| | - Fangping Xu
- Department of Obstetrics, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, China
| | - Cheng Huang
- Department of Medical Genetics, Jiangxi Key Laboratory of Birth Defect Prevention and Control, Jiangxi Maternal and Child Health Hospital, Nanchang, China
| | - Danping Liu
- Department of Medical Genetics, Jiangxi Key Laboratory of Birth Defect Prevention and Control, Jiangxi Maternal and Child Health Hospital, Nanchang, China
| | - Liuyang Zhang
- Department of Medical Genetics, Jiangxi Key Laboratory of Birth Defect Prevention and Control, Jiangxi Maternal and Child Health Hospital, Nanchang, China
| | - Ting Huang
- Department of Medical Genetics, Jiangxi Key Laboratory of Birth Defect Prevention and Control, Jiangxi Maternal and Child Health Hospital, Nanchang, China
| | - Pengpeng Ma
- Department of Medical Genetics, Jiangxi Key Laboratory of Birth Defect Prevention and Control, Jiangxi Maternal and Child Health Hospital, Nanchang, China
| | - Qing Lu
- Department of Medical Genetics, Jiangxi Key Laboratory of Birth Defect Prevention and Control, Jiangxi Maternal and Child Health Hospital, Nanchang, China
| | - Shuhui Huang
- Department of Medical Genetics, Jiangxi Key Laboratory of Birth Defect Prevention and Control, Jiangxi Maternal and Child Health Hospital, Nanchang, China
| | - Bicheng Yang
- Department of Medical Genetics, Jiangxi Key Laboratory of Birth Defect Prevention and Control, Jiangxi Maternal and Child Health Hospital, Nanchang, China
| | - Yongyi Zou
- Department of Medical Genetics, Jiangxi Key Laboratory of Birth Defect Prevention and Control, Jiangxi Maternal and Child Health Hospital, Nanchang, China
| | - Yanqiu Liu
- Department of Medical Genetics, Jiangxi Key Laboratory of Birth Defect Prevention and Control, Jiangxi Maternal and Child Health Hospital, Nanchang, China
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16
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Tian Y, Xu H, Liu D, Zhang J, Yang Z, Zhang S, Liu H, Li R, Tian Y, Zeng B, Li T, Lin Q, Wang H, Li X, Lu W, Shi Y, Zhang Y, Zhang H, Jiang C, Xu Y, Chen B, Liu J, Tang W. Increased diagnosis of enlarged vestibular aqueduct by multiplex PCR enrichment and next-generation sequencing of the SLC26A4 gene. Mol Genet Genomic Med 2021; 9:e1734. [PMID: 34170635 PMCID: PMC8404235 DOI: 10.1002/mgg3.1734] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 04/30/2021] [Accepted: 05/24/2021] [Indexed: 12/11/2022] Open
Abstract
Background The enlarged vestibular aqueduct (EVA) is the commonest malformation of inner ear accompanied by sensorineural hearing loss in children. Three genes SLC26A4, FOXI1, and KCNJ10 have been associated with EVA, among them SLC26A4 being the most common. Yet, hotspot mutation screening can only diagnose a small number of patients. Methods Thus, in this study, we designed a new molecular diagnosis panel for EVA based on multiplex PCR enrichment and next‐generation sequencing of the exon and flanking regions of SLC26A4. A total of 112 hearing loss families with EVA were enrolled and the pathogenicity of the rare variants detected was interpreted according to the American College of Medical Genetics and Genomics (ACMG) guidelines. Results Our results showed that 107/112 (95.54%) families carried SLC26A4 biallelic mutations, 4/112 (3.57%) carried monoallelic variants, and 1/112 (0.89%) had none variant, resulting in a diagnostic rate of 95.54%. A total of 49 different variants were detected in those patients and we classified 30 rare variants as pathogenic/likely pathogenic, of which 13 were not included in the Clinvar database. Conclusion Our diagnostic panel has an increased diagnostic yield with less cost, and the curated list of pathogenic variants in the SLC26A4 gene can be directly used to aid the genetic counseling to patients.
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Affiliation(s)
- Yongan Tian
- BGI College, Zhengzhou University, Zhengzhou, China.,Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China.,Precision Medicine Center, Academy of Medical Science, Zhengzhou University, Zhengzhou, China
| | - Hongen Xu
- The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Danhua Liu
- The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Juanli Zhang
- Henan Province Medical Instrument Testing Institute, Zhengzhou, China
| | | | - Sen Zhang
- School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Huanfei Liu
- Precision Medicine Center, Academy of Medical Science, Zhengzhou University, Zhengzhou, China
| | - Ruijun Li
- Precision Medicine Center, Academy of Medical Science, Zhengzhou University, Zhengzhou, China
| | | | - Beiping Zeng
- BGI College, Zhengzhou University, Zhengzhou, China.,Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Tong Li
- BGI College, Zhengzhou University, Zhengzhou, China.,Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Qianyu Lin
- School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Haili Wang
- National Health Commission Key Laboratory of Birth Defects Prevention, Henan Key Laboratory of Population Defects Prevention, Zhengzhou, China
| | - Xiaohua Li
- Department of Otology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Wei Lu
- Department of Otology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Ying Shi
- The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yan Zhang
- The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Hui Zhang
- The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Chang Jiang
- Department of Otology, Henan Provincial People's Hospital, Zhengzhou, China
| | - Ying Xu
- Zhengzhou Children's Hospital, Zhengzhou, China
| | - Bei Chen
- Department of Otology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jun Liu
- Department of Otology, Henan Provincial People's Hospital, Zhengzhou, China
| | - Wenxue Tang
- The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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17
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Machine learning-based genetic diagnosis models for hereditary hearing loss by the GJB2, SLC26A4 and MT-RNR1 variants. EBioMedicine 2021; 69:103322. [PMID: 34161886 PMCID: PMC8237285 DOI: 10.1016/j.ebiom.2021.103322] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 03/18/2021] [Accepted: 03/18/2021] [Indexed: 12/16/2022] Open
Abstract
Background Hereditary hearing loss (HHL) is the most common sensory deficit, which highly afflicts humans. With gene sequencing technology development, more variants will be identified and support genetic diagnoses, which is difficult for human experts to diagnose. This study aims to develop a machine learning-based genetic diagnosis model of HHL-related variants of GJB2, SLC26A4 and MT-RNR1. Methods This case-control study included 1898 subjects, among which 1354 were HHL patients and 544 were carriers. Risk assessment models were established based on variants at 144 sites in three genes related to HHL by building six machine learning (ML) models. We compared the ML models with the genetic risk score (GRS) and expert interpretation (EI) to verify the clinical performance. Findings Among the six ML models, the support vector machine (SVM) showed the best performance. For the prediction of HHL-related gene sites in subjects with variants, the area under the receiver operating characteristic (AUC) of the SVM model was 0.803 (0.680–0.814) in the 10-fold stratified cross-validation and 0.751 (0.635–0.779) in external validation. The predicted results were better than both EI and GRS. Furthermore, 11 sites were identified as the smallest feature set that can be accurately predicted. Interpretation The developed SVM model has great potential to be an efficient and effective tool for HHL prediction when high throughput sequencing data are available.
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18
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Duan S, Guo Y, Chen X, Li Y. Genetic mutations in patients with nonsyndromic hearing impairment of minority and Han Chinese ethnicities in Qinghai, China. J Int Med Res 2021; 49:3000605211000892. [PMID: 33827324 PMCID: PMC8040579 DOI: 10.1177/03000605211000892] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Objective Mutations in GJB2, SLC26A4, and mitochondrial (mt)DNA 12S rRNA genes are the main cause of nonsyndromic hearing impairment. The present study analyzed these mutations in ethnic minority and Han Chinese patients with nonsyndromic hearing impairment from Qinghai, China. Methods The SNPscan assay was used to analyze mutation spectra and frequencies in the two patient groups. Results GJB2 mutations were detected in 9.5% (20/210) of minority patients and 20.88% (48/230) of Han Chinese patients. The most common Han Chinese GJB2 variants were c.235delC and c.299_300delAT, whereas c.235delC and c.109G > A were the most prevalent in minority patients. SLC26A4 mutations were detected in 5.71% (12/210) of minority patients and 14.35% (33/230) of Han Chinese patients, and mtDNA 12S rRNA mutations were detected in 4.28% (9/210) of minority patients and 9.13% (21/230) of Han Chinese patients. Conclusions These data indicate that the mutation frequencies of three deafness-associated genes were significantly higher in Han Chinese patients than in minority patients. Moreover, the GJB2 mutation spectrum was shown to differ between these two patient groups.
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Affiliation(s)
- Shihong Duan
- Department of Otolaryngology-Head and Neck Surgery, Second Hospital of Lanzhou University, Lanzhou, China
| | - Yufen Guo
- Department of Otolaryngology-Head and Neck Surgery, Second Hospital of Lanzhou University, Lanzhou, China
| | - Xingjian Chen
- Department of Otolaryngology-Head and Neck Surgery, Second Hospital of Lanzhou University, Lanzhou, China
| | - Yong Li
- Department of Otolaryngology-Head and Neck Surgery, Second Hospital of Lanzhou University, Lanzhou, China
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19
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Hu H, Zhou P, Wu J, Lei W, Wang Y, Yang Y, Liu H. Genetic testing involving 100 common mutations for antenatal diagnosis of hereditary hearing loss in Chongqing, China. Medicine (Baltimore) 2021; 100:e25647. [PMID: 33907123 PMCID: PMC8084083 DOI: 10.1097/md.0000000000025647] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 03/15/2021] [Accepted: 03/18/2021] [Indexed: 11/25/2022] Open
Abstract
ABSTRACT To understand the possible carrier status of genes associated with hereditary hearing loss (HHL) in the general population among local residents and to give genetic counseling for pregnant women.A total of 3541 subjects were recruited. We used multiplex PCR technology combined with next-generation sequencing technology to detect 100 hotspot mutations in 18 common deafness-related genes. The homozygous mutation screening results were verified using Sanger sequencing.Of the 3541 participants, 37 alleles of 8 deafness genes were detected. A total of 145 (4.09%) were found to be GJB2 gene mutation carriers, and the hotspot mutation was c.235delC (1.54%). Twenty three (0.65%) were found to be GJB3 gene mutation carriers. A total of 132 (3.37%) were found to be SLC26A4 gene mutation carriers, and the hotspot mutation was c.919-2A > G (0.49%). Forty four (1.24%) were found to be mitochondrial DNA mutation carriers. Sanger sequencing results verified that 2 cases were homozygous for the c.235delC mutation and that 1 case was homozygous for the c.754T > C mutation.Genetic testing for pregnant women and their partners allows early identification of the molecular etiology of hearing loss (HL). On the one hand, it could give genetic counseling for pregnant women, such as early diagnosis of delayed deafness and drug-susceptible deafness. On the other hand, it could be used to assess hearing conditions during pregnancy, leading to prevention and timely intervention for newborns.
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Affiliation(s)
- Hua Hu
- Second Affiliated Hospital, Army Military Medical University, Chongqing
| | - Peng Zhou
- Second Affiliated Hospital, Army Military Medical University, Chongqing
| | - Jiayan Wu
- Second Affiliated Hospital, Army Military Medical University, Chongqing
| | - Wei Lei
- CapitalBio Genomics Co., Ltd., Dongguan, China
| | - Yang Wang
- CapitalBio Genomics Co., Ltd., Dongguan, China
| | - Ying Yang
- Second Affiliated Hospital, Army Military Medical University, Chongqing
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Xiao C, Liu S, Wang H, Ding Y, Chen Y, Liu H. Genetic etiology study of four Chinese families with two nonsyndromic deaf children in succession by targeted next-generation sequencing. Mol Genet Genomic Med 2021; 9:e1634. [PMID: 33638616 PMCID: PMC8123758 DOI: 10.1002/mgg3.1634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 12/09/2020] [Accepted: 02/10/2021] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Genetic components contribute significantly to the cause of hearing loss. Nonsyndromic hearing loss has been shown to have high genetic heterogeneity. For families who had given birth to two nonsyndromic deaf children in succession, it seems that their deafness was highly related to genetics. OBJECTIVES This study aimed to disclose the genetic causes of the subjects from the four Chinese families with two nonsyndromic deaf children in succession who failed to find the genetic etiology of the hearing loss by common deafness genetic screening (GJB2, GJB3, SLC26A4, and MT-RNR1, including 20 hot variants in 4 genes). METHODS Targeted next-generation sequencing (NGS) of 127 known deafness genes was performed in probands of four families, followed by a series of comprehensive analyses of all family members combined with a literature review of related genes. RESULTS We identified pathogenic variants in three families including c.919-2A>G/c.1985G>A in SLC26A4; c.109G>A (p.V37I) in GJB2; and m.7505T>C in MT-TS1. Sanger sequencing confirmed that these variants segregated with the hearing impairment of each family. We also identified c.331C>T/c.625-5C>T/c.5717G>A in CDH23; c.138T>C in POU3F4 in two families, in which the pathogenicity in clinical was likely pathogenic or unknown. CONCLUSIONS Using the NGS detection technology, we found the genetic etiology of the HL in part of deaf families. Our study provided a useful piece of information for the variant spectrum of hearing loss in Chinese families with two deaf children in succession.
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Affiliation(s)
- Caixia Xiao
- Tianjin Women and Children Healthcare CenterTianjinChina
| | - Shuang Liu
- Tianjin Women and Children Healthcare CenterTianjinChina
| | - Hongyue Wang
- Tianjin Women and Children Healthcare CenterTianjinChina
| | - Yibing Ding
- Tianjin Women and Children Healthcare CenterTianjinChina
| | - Yaqiu Chen
- Tianjin Women and Children Healthcare CenterTianjinChina
| | - Haiyan Liu
- Tianjin Women and Children Healthcare CenterTianjinChina
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21
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Missense Variant of Endoplasmic Reticulum Region of WFS1 Gene Causes Autosomal Dominant Hearing Loss without Syndromic Phenotype. BIOMED RESEARCH INTERNATIONAL 2021; 2021:6624744. [PMID: 34258273 PMCID: PMC8260318 DOI: 10.1155/2021/6624744] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 02/01/2021] [Accepted: 02/14/2021] [Indexed: 12/13/2022]
Abstract
Objective Genetic variants in the WFS1 gene can cause Wolfram syndrome (WS) or autosomal dominant nonsyndromic low-frequency hearing loss (HL). This study is aimed at investigating the molecular basis of HL in an affected Chinese family and the genotype-phenotype correlation of WFS1 variants. Methods The clinical phenotype of the five-generation Chinese family was characterized using audiological examinations and pedigree analysis. Target exome sequencing of 129 known deafness genes and bioinformatics analysis were performed among six patients and four normal subjects to screen suspected pathogenic variants. We built a complete WFS1 protein model to assess the potential effects of the variant on protein structure. Results A novel heterozygous pathogenic variant NM_006005.3 c.2020G>T (p.Gly674Trp) was identified in the WFS1 gene, located in the C-terminal domain of the wolframin protein. We further showed that HL-related WFS1 missense variants were mainly concentrated in the endoplasmic reticulum (ER) domain. In contrast, WS-related missense variants are randomly distributed throughout the protein. Conclusions In this family, we identified a novel variant p.Gly674Trp of WFS1 as the primary pathogenic variant causing the low-frequency sensorineural HL, enriching the mutational spectrum of the WFS1 gene.
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Xie F, Zhou X, Lin T, Wang L, Liu C, Luo X, Luo L, Chen H, Guo K, Wei H, Wang Y. Production of gene-edited pigs harboring orthologous human mutations via double cutting by CRISPR/Cas9 with long single-stranded DNAs as homology-directed repair templates by zygote injection. Transgenic Res 2020; 29:587-598. [PMID: 33170439 DOI: 10.1007/s11248-020-00218-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 10/21/2020] [Indexed: 12/14/2022]
Abstract
Precise gene editing of model organisms is required for accurately modeling human diseases and deciphering gene functions. In this study, we used a pair of guide RNAs (sgRNAs), which in vitro transcribed along with other CRISPR RNA components, to generate two cleavage sites flanking pig GJB2 (pGJB2) CDS. By using long single-stranded DNAs (lssDNA) as homology-directed repair (HDR) templates, we efficiently obtained two gene-edited pigs, of which GJB2 CDS replaced with CDSs containing human GJB2 c.235delC mutation and orthologous human p.V37I mutation, respectively. These mutations were commonly observed in patients with hearing loss. Genetic analysis of the two gene-edited pigs showed that the HDR-derived gene-editing efficiency were as high as 80% (4/5) and 50% (2/4), respectively. While no mutation was observed in the group of single cutting with one sgRNA covering the 235th nucleotide C in pGJB2 CDS, using a short single-stranded oligo DNA containing c.235delC mutation as HDR template. Extra experiments proved that the intended mutations were successfully transmitted to offspring or extensively integrated into various tissues including gonad of founder pigs. Our work indicated that the new "double cutting with lssDNA template" gene editing method can expand sgRNA selection scope and avoids direct cutting of gene CDS. Additionally, can introduce precise mutations into mammalian genomic sites, especially those with unavailable proper protospacer sequence or being resistant to gene editing. Moreover, this method can be performed with CRISPR RNA reagents instead of CRISPR ribonucleoproteins applied in previous reports.
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Affiliation(s)
- Fei Xie
- Department of Laboratory Animal Science, College of Basic Medical Sciences, Army Medical University, Third Military Medical University, Chongqing, 400038, China
| | - Xiaoyang Zhou
- Department of Laboratory Animal Science, College of Basic Medical Sciences, Army Medical University, Third Military Medical University, Chongqing, 400038, China
| | - Tingting Lin
- Department of Laboratory Animal Science, College of Basic Medical Sciences, Army Medical University, Third Military Medical University, Chongqing, 400038, China
| | - Lulu Wang
- Department of Laboratory Animal Science, College of Basic Medical Sciences, Army Medical University, Third Military Medical University, Chongqing, 400038, China
| | - Chuanhong Liu
- Department of Laboratory Animal Science, College of Basic Medical Sciences, Army Medical University, Third Military Medical University, Chongqing, 400038, China
| | - Xi Luo
- Department of Foreign Languages Studies, College of Basic Medical Sciences, Army Medical University, Third Military Medical University, Chongqing, 400038, China
| | - Lihua Luo
- Department of Laboratory Animal Science, College of Basic Medical Sciences, Army Medical University, Third Military Medical University, Chongqing, 400038, China
| | - Huayu Chen
- Department of Laboratory Animal Science, College of Basic Medical Sciences, Army Medical University, Third Military Medical University, Chongqing, 400038, China
| | - Kenan Guo
- Department of Laboratory Animal Science, College of Basic Medical Sciences, Army Medical University, Third Military Medical University, Chongqing, 400038, China
| | - Hong Wei
- Department of Laboratory Animal Science, College of Basic Medical Sciences, Army Medical University, Third Military Medical University, Chongqing, 400038, China.
| | - Yong Wang
- Department of Laboratory Animal Science, College of Basic Medical Sciences, Army Medical University, Third Military Medical University, Chongqing, 400038, China.
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Four Novel Variants in POU4F3 Cause Autosomal Dominant Nonsyndromic Hearing Loss. Neural Plast 2020; 2020:6137083. [PMID: 32684921 PMCID: PMC7349627 DOI: 10.1155/2020/6137083] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 05/16/2020] [Accepted: 06/09/2020] [Indexed: 12/30/2022] Open
Abstract
Hereditary hearing loss is one of the most common sensory disabilities worldwide. Mutation of POU domain class 4 transcription factor 3 (POU4F3) is considered the pathogenic cause of autosomal dominant nonsyndromic hearing loss (ADNSHL), designated as autosomal dominant nonsyndromic deafness 15. In this study, four novel variants in POU4F3, c.696G>T (p.Glu232Asp), c.325C>T (p.His109Tyr), c.635T>C (p.Leu212Pro), and c.183delG (p.Ala62Argfs∗22), were identified in four different Chinese families with ADNSHL by targeted next-generation sequencing and Sanger sequencing. Based on the American College of Medical Genetics and Genomics guidelines, c.183delG (p.Ala62Argfs∗22) is classified as a pathogenic variant, c.696G>T (p.Glu232Asp) and c.635T>C (p.Leu212Pro) are classified as likely pathogenic variants, and c.325C>T (p.His109Tyr) is classified as a variant of uncertain significance. Based on previous reports and the results of this study, we speculated that POU4F3 pathogenic variants are significant contributors to ADNSHL in the East Asian population. Therefore, screening of POU4F3 should be a routine examination for the diagnosis of hereditary hearing loss.
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Xi Y, Chen G, Lei C, Wu J, Zhang S, Xiao M, Zhang W, Zhang Y, Sun X. Expanded carrier screening in Chinese patients seeking the help of assisted reproductive technology. Mol Genet Genomic Med 2020; 8:e1340. [PMID: 32573981 PMCID: PMC7507411 DOI: 10.1002/mgg3.1340] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 04/27/2020] [Accepted: 05/12/2020] [Indexed: 01/05/2023] Open
Abstract
Background Expanded carrier screening (ECS) has emerged as an effective approach to identify at‐risk couples (ARCs)—before they initiate attempts at reproduction—who possess a high probability of having a child affected by severe recessive diseases. The objective of this study was to evaluate the clinical utility of ECS in Chinese patients seeking the help of assisted reproductive technology (ART). Methods An ECS test, which covers 201 genes implicated in 135 recessive (autosomal or X‐linked) diseases, was routinely offered to all ART patients in a single genetics and in vitro fertilization clinic. Additional options for preimplantation or prenatal genetic diagnosis were discussed and offered to all ARCs. All ECS results were aggregated and the clinical decisions of the ARCs were surveyed. Results A total of 2,923 ART patients, representing 1,462 couples, were screened. Overall, 46.73% of the individuals were found to be the carriers for at least 1 of the 135 diseases. Of the tested couples, 2.26% (n = 33) were identified as ARCs. As of the completion of this study, 21 (63.6%) ARCs have decided to avert an affected pregnancy with the help of preimplantation genetic testing for monogenetic conditions. The cumulative carrier rate of the 187 autosomal recessive genes in the ECS panel for the 2,836 Han Chinese individuals without a family history was estimated to be 45.91%. The estimated at‐risk couple rate indicates that the screening for only the top 31 genes with gene carrier rates >0.5% would identify more than 94% of the ARCs identified by screening all 187 genes. Conclusion Our study demonstrates that ESC yields a significant clinical value for ART patients in China. In addition, by estimating the yields of the ECS panel, we identify genes that are appropriate for screening the Han population.
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Affiliation(s)
- Yanping Xi
- Shanghai Ji Ai Genetics & IVF Institute, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Guangquan Chen
- WuXi NextCODE Genomics (Shanghai) Co., Ltd., Shanghai, China
| | - Caixia Lei
- Shanghai Ji Ai Genetics & IVF Institute, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Junping Wu
- Shanghai Ji Ai Genetics & IVF Institute, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Shuo Zhang
- Shanghai Ji Ai Genetics & IVF Institute, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Min Xiao
- Shanghai Ji Ai Genetics & IVF Institute, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Wenbi Zhang
- Shanghai Ji Ai Genetics & IVF Institute, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Yueping Zhang
- Shanghai Ji Ai Genetics & IVF Institute, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Xiaoxi Sun
- Shanghai Ji Ai Genetics & IVF Institute, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China.,Key Laboratory of Female Reproductive Endocrine Related Diseases, Obstetrics, and Gynecology Hospital of Fudan University, Shanghai, China
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Jiang F, Kuper H, Bright T, Qin WZ. Etiology of Childhood Bilateral Sensorineural Hearing Loss in Shandong Province, China. Am J Audiol 2020; 29:236-243. [PMID: 32437266 DOI: 10.1044/2020_aja-19-00029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Objectives The purpose of this study is to ascertain the etiology of bilateral sensorineural hearing loss (SNHL) in children aged ≤ 18 years living in Shandong province. Method Data were taken from a cross-sectional study, which was conducted between 2015 and 2017. The study included children aged ≤ 18 years, recruited from special schools for children with hearing loss and from hearing rehabilitation centers in Shandong province of China. Children were screened for bilateral SNHL through audiological testing. Clinical examination, genetic testing, and structured interviews were conducted for those children who were identified as having hearing loss to identify the potential cause. Results The etiology of bilateral SNHL in our sample was genetic in 874 (39.3%), acquired in 650 (29.3%), and unknown in 697 (31.4%) children. Among children with acquired SNHL, the cause was maternal viral infection in 75 (11.5%); perinatal factors in 238 (36.6%); meningitis, measles, and mumps in 146 (22.5%); and ototoxic exposure in 117 (18%) children. Among the children with genetic SNHL, only 44 (4.9%) were identified as having syndromic hearing loss, and the remainder (95.1%) were classified as nonsyndromic hearing loss. Conclusion The findings indicated that nearly 30% of bilateral SNHL in Shandong province could be preventable through immunization, early prenatal diagnosis, proper treatment of infections, and avoidance of prescription of ototoxic drugs. This finding emphasizes the need for programs aimed at improving the health services at primary and secondary levels of health care, which will in turn prevent childhood hearing loss.
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Affiliation(s)
- Fan Jiang
- School of Public Health, Shandong University, Jinan, China
| | - Hannah Kuper
- International Centre for Evidence in Disability, London School of Hygiene & Tropical Medicine, United Kingdom
| | - Tess Bright
- International Centre for Evidence in Disability, London School of Hygiene & Tropical Medicine, United Kingdom
| | - Wen-Zhe Qin
- School of Public Health, Shandong University, Jinan, China
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Wen C, Wang S, Zhao X, Wang X, Wang X, Cheng X, Huang L. Mutation analysis of the SLC26A4 gene in three Chinese families. Biosci Trends 2019; 13:441-447. [PMID: 31656273 DOI: 10.5582/bst.2019.01282] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
In order to investigate the genetic causes of hearing loss in a Chinese proband (in Family A) with enlarged vestibular aqueduct (EVA) and to investigate the genotype of two Chinese probands with SLC26A4 singe-allelic mutation and normal hearing (in Families B and C, respectively), the three probands and their parents were clinically and genetically evaluated. Twenty exons and flanking splice sites of the SLC26A4 gene were screened for pathogenic mutations via amplification with PCR and bidirectional sequencing. As controls, a group of 400 healthy newborns from the same ethnic background underwent SLC26A4 gene screening using the same method. The three probands all harbored two mutations in the SLC26A4 gene in the form of compound heterozygosity. The genotypes of mutations in Families A, B, and C are c.1211C>A/c.919-2A>G, c.1729G>A/c.919-2A>G, and c.1286C>A/c.919-2A>G, respectively. The missense mutations c.1211C>A (p.T430Q) in exon 10 and c.1729G>A (p.V577I) in exon 16 are both reported for the first time and were absent in 400 healthy newborns. c.1211C>A has Glutamine (Gln) at amino acid 430 instead of Threonine (Thr), and c.1729G>A has Isoleucine (Ile) at amino acid 577 instead of Valine (Val). c.1286C>A, a mutation previously reported in DVD and HGMD, was associated with Mondini deformity, but a proband with the c.1286C>A mutation in this study was normal. This study has demonstrated that the novel missense mutation c.1211C>A in compound heterozygosity with c.919-2A>G in the SLC26A4 gene is likely to be the cause of deafness in Family A. A novel variant, c.1729G>A, was identified and is likely benign. The pathogenicity of the c.1286C>A mutation warrants more in-depth study. These findings will broaden the spectrum of known SLC26A4 mutations in the Chinese population, providing more information for genetic counseling and diagnosis of hearing loss with EVA.
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Affiliation(s)
- Cheng Wen
- Beijing Tongren Hospital, Capital Medical University; Beijing Institute of Otolaryngology; Key Laboratory of Otolaryngology, Head and Neck Surgery, Ministry of Education, Beijing, China
| | - Shijie Wang
- No. 731 Hospital of China Aerospace Science and Industry Corp, Beijing, China
| | - Xuelei Zhao
- Beijing Tongren Hospital, Capital Medical University; Beijing Institute of Otolaryngology; Key Laboratory of Otolaryngology, Head and Neck Surgery, Ministry of Education, Beijing, China
| | - Xianlei Wang
- Beijing Tongren Hospital, Capital Medical University; Beijing Institute of Otolaryngology; Key Laboratory of Otolaryngology, Head and Neck Surgery, Ministry of Education, Beijing, China
| | - Xueyao Wang
- Beijing Tongren Hospital, Capital Medical University; Beijing Institute of Otolaryngology; Key Laboratory of Otolaryngology, Head and Neck Surgery, Ministry of Education, Beijing, China
| | - Xiaohua Cheng
- Beijing Tongren Hospital, Capital Medical University; Beijing Institute of Otolaryngology; Key Laboratory of Otolaryngology, Head and Neck Surgery, Ministry of Education, Beijing, China
| | - Lihui Huang
- Beijing Tongren Hospital, Capital Medical University; Beijing Institute of Otolaryngology; Key Laboratory of Otolaryngology, Head and Neck Surgery, Ministry of Education, Beijing, China
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Dai P, Huang LH, Wang GJ, Gao X, Qu CY, Chen XW, Ma FR, Zhang J, Xing WL, Xi SY, Ma BR, Pan Y, Cheng XH, Duan H, Yuan YY, Zhao LP, Chang L, Gao RZ, Liu HH, Zhang W, Huang SS, Kang DY, Liang W, Zhang K, Jiang H, Guo YL, Zhou Y, Zhang WX, Lyu F, Jin YN, Zhou Z, Lu HL, Zhang X, Liu P, Ke J, Hao JS, Huang HM, Jiang D, Ni X, Long M, Zhang L, Qiao J, Morton CC, Liu XZ, Cheng J, Han DM. Concurrent Hearing and Genetic Screening of 180,469 Neonates with Follow-up in Beijing, China. Am J Hum Genet 2019; 105:803-812. [PMID: 31564438 PMCID: PMC6817518 DOI: 10.1016/j.ajhg.2019.09.003] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 09/04/2019] [Indexed: 02/05/2023] Open
Abstract
Concurrent hearing and genetic screening of newborns is expected to play important roles not only in early detection and diagnosis of congenital deafness, which triggers intervention, but also in predicting late-onset and progressive hearing loss and identifying individuals who are at risk of drug-induced HL. Concurrent hearing and genetic screening in the whole newborn population in Beijing was launched in January 2012. This study included 180,469 infants born in Beijing between April 2013 and March 2014, with last follow-up on February 24, 2018. Hearing screening was performed using transiently evoked otoacoustic emission (TEOAE) and automated auditory brainstem response (AABR). For genetic testing, dried blood spots were collected and nine variants in four genes, GJB2, SLC26A4, mtDNA 12S rRNA, and GJB3, were screened using a DNA microarray platform. Of the 180,469 infants, 1,915 (1.061%) were referred bilaterally or unilaterally for hearing screening; 8,136 (4.508%) were positive for genetic screening (heterozygote, homozygote, or compound heterozygote and mtDNA homoplasmy or heteroplasmy), among whom 7,896 (4.375%) passed hearing screening. Forty (0.022%) infants carried two variants in GJB2 or SLC26A4 (homozygote or compound heterozygote) and 10 of those infants passed newborn hearing screening. In total, 409 (0.227%) infants carried the mtDNA 12S rRNA variant (m.1555A>G or m.1494C>T), and 405 of them passed newborn hearing screening. In this cohort study, 25% of infants with pathogenic combinations of GJB2 or SLC26A4 variants and 99% of infants with an m.1555A>G or m.1494C>T variant passed routine newborn hearing screening, indicating that concurrent screening provides a more comprehensive approach for management of congenital deafness and prevention of ototoxicity.
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Affiliation(s)
- Pu Dai
- Department of Otolaryngology Head and Neck Surgery, Chinese People's Liberation Army (PLA) General Hospital, Beijing, 100853, P. R. China
| | - Li-Hui Huang
- Department of Otolaryngology Head and Neck Surgery, Beijing TongRen Hospital, Capital Medical University, Beijing, 100730, P. R. China; Beijing Institute of Otolaryngology, Beijing, 100005, P. R. China; Key Laboratory of Otolaryngology Head and Neck Surgery, Ministry of Education, Beijing, 100005, P. R. China
| | - Guo-Jian Wang
- Department of Otolaryngology Head and Neck Surgery, Chinese People's Liberation Army (PLA) General Hospital, Beijing, 100853, P. R. China
| | - Xue Gao
- Department of Otolaryngology Head and Neck Surgery, Chinese People's Liberation Army (PLA) General Hospital, Beijing, 100853, P. R. China
| | - Chun-Yan Qu
- China Rehabilitation Research Center for Hearing and Speech Impairment, A8, Huixinli, Anwai, Chaoyang District, Beijing, 100029, P. R. China
| | - Xiao-Wei Chen
- Department of Otorhinolaryngology Head and Neck Surgery, Peking Union Medical College Hospital, Beijing, 100730, P. R. China
| | - Fu-Rong Ma
- Department of Otorhinolaryngology Head and Neck Surgery, Peking University Third Hospital, Beijing, 100191, P. R. China
| | - Jie Zhang
- Beijing Children's Hospital, Capital Medical University, National Center of Children's Health, Beijing, 100045, P. R. China
| | - Wan-Li Xing
- Department of Biomedical Engineering, Tsinghua University School of Medicine, Beijing, 100084, P. R. China
| | - Shu-Yan Xi
- Beijing Municipal Health Commission, Beijing, 100053, P. R. China
| | - Bin-Rong Ma
- School of Biomedical Engineering, Capital Medical University, Beijing, 100069, P. R. China
| | - Ying Pan
- Department of MCH, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing Maternal and Child Health Care Hospital, Beijing, 100026, P. R. China
| | - Xiao-Hua Cheng
- Department of Otolaryngology Head and Neck Surgery, Beijing TongRen Hospital, Capital Medical University, Beijing, 100730, P. R. China; Beijing Institute of Otolaryngology, Beijing, 100005, P. R. China; Key Laboratory of Otolaryngology Head and Neck Surgery, Ministry of Education, Beijing, 100005, P. R. China
| | - Hong Duan
- Department of Otolaryngology Head and Neck Surgery, Chinese People's Liberation Army (PLA) General Hospital, Beijing, 100853, P. R. China
| | - Yong-Yi Yuan
- Department of Otolaryngology Head and Neck Surgery, Chinese People's Liberation Army (PLA) General Hospital, Beijing, 100853, P. R. China
| | - Li-Ping Zhao
- Department of Otolaryngology Head and Neck Surgery, Beijing TongRen Hospital, Capital Medical University, Beijing, 100730, P. R. China; Beijing Institute of Otolaryngology, Beijing, 100005, P. R. China; Key Laboratory of Otolaryngology Head and Neck Surgery, Ministry of Education, Beijing, 100005, P. R. China
| | - Liang Chang
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, 100191, P.R. China; National Clinical Research Center for Obstetrics and Gynecology, Beijing, 100191, P. R. China
| | - Ru-Zhen Gao
- Department of Otorhinolaryngology Head and Neck Surgery, Peking Union Medical College Hospital, Beijing, 100730, P. R. China
| | - Hai-Hong Liu
- Beijing Children's Hospital, Capital Medical University, National Center of Children's Health, Beijing, 100045, P. R. China
| | - Wei Zhang
- Department of Otolaryngology Head and Neck Surgery, Beijing TongRen Hospital, Capital Medical University, Beijing, 100730, P. R. China; Beijing Institute of Otolaryngology, Beijing, 100005, P. R. China; Key Laboratory of Otolaryngology Head and Neck Surgery, Ministry of Education, Beijing, 100005, P. R. China
| | - Sha-Sha Huang
- Department of Otolaryngology Head and Neck Surgery, Chinese People's Liberation Army (PLA) General Hospital, Beijing, 100853, P. R. China
| | - Dong-Yang Kang
- Department of Otolaryngology Head and Neck Surgery, Chinese People's Liberation Army (PLA) General Hospital, Beijing, 100853, P. R. China
| | - Wei Liang
- China Rehabilitation Research Center for Hearing and Speech Impairment, A8, Huixinli, Anwai, Chaoyang District, Beijing, 100029, P. R. China
| | - Ke Zhang
- Department of Otorhinolaryngology Head and Neck Surgery, Peking University Third Hospital, Beijing, 100191, P. R. China
| | - Hong Jiang
- Department of Otorhinolaryngology Head and Neck Surgery, Peking Union Medical College Hospital, Beijing, 100730, P. R. China
| | - Yong-Li Guo
- Beijing Children's Hospital, Capital Medical University, National Center of Children's Health, Beijing, 100045, P. R. China
| | - Yi Zhou
- Beijing Children's Hospital, Capital Medical University, National Center of Children's Health, Beijing, 100045, P. R. China
| | - Wan-Xia Zhang
- Department of MCH, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing Maternal and Child Health Care Hospital, Beijing, 100026, P. R. China
| | - Fan Lyu
- Beijing Municipal Health Commission, Beijing, 100053, P. R. China
| | - Ying-Nan Jin
- Beijing Municipal Health Commission, Beijing, 100053, P. R. China
| | - Zhen Zhou
- School of Biomedical Engineering, Capital Medical University, Beijing, 100069, P. R. China
| | - Hong-Li Lu
- CapitalBio Corporation & National Engineering Research Center for Beijing Biochip Technology, Beijing, 102206, P. R. China
| | - Xin Zhang
- Department of Otolaryngology Head and Neck Surgery, Chinese People's Liberation Army (PLA) General Hospital, Beijing, 100853, P. R. China
| | - Ping Liu
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, 100191, P.R. China; National Clinical Research Center for Obstetrics and Gynecology, Beijing, 100191, P. R. China
| | - Jia Ke
- Department of Otorhinolaryngology Head and Neck Surgery, Peking University Third Hospital, Beijing, 100191, P. R. China
| | - Jin-Sheng Hao
- Beijing Children's Hospital, Capital Medical University, National Center of Children's Health, Beijing, 100045, P. R. China
| | - Hai-Meng Huang
- CapitalBio Corporation & National Engineering Research Center for Beijing Biochip Technology, Beijing, 102206, P. R. China
| | - Di Jiang
- CapitalBio Corporation & National Engineering Research Center for Beijing Biochip Technology, Beijing, 102206, P. R. China
| | - Xin Ni
- Beijing Children's Hospital, Capital Medical University, National Center of Children's Health, Beijing, 100045, P. R. China
| | - Mo Long
- China Rehabilitation Research Center for Hearing and Speech Impairment, A8, Huixinli, Anwai, Chaoyang District, Beijing, 100029, P. R. China
| | - Luo Zhang
- Department of Otolaryngology Head and Neck Surgery, Beijing TongRen Hospital, Capital Medical University, Beijing, 100730, P. R. China; Beijing Institute of Otolaryngology, Beijing, 100005, P. R. China; Key Laboratory of Otolaryngology Head and Neck Surgery, Ministry of Education, Beijing, 100005, P. R. China
| | - Jie Qiao
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, 100191, P.R. China; National Clinical Research Center for Obstetrics and Gynecology, Beijing, 100191, P. R. China
| | - Cynthia Casson Morton
- Department of Obstetrics and Gynecology and of Pathology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Manchester Center for Audiology and Deafness, School of Health Sciences, University of Manchester, Manchester, M13 9PL, UK
| | - Xue-Zhong Liu
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Jing Cheng
- Department of Biomedical Engineering, Tsinghua University School of Medicine, Beijing, 100084, P. R. China; Center for Precision Medicine, West China Hospital, Sichuan University, Chengdu, 610041, P. R. China.
| | - De-Min Han
- Department of Otolaryngology Head and Neck Surgery, Beijing TongRen Hospital, Capital Medical University, Beijing, 100730, P. R. China; Key Laboratory of Otolaryngology Head and Neck Surgery, Ministry of Education, Beijing, 100005, P. R. China.
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Kim MA, Kim SH, Ryu N, Ma JH, Kim YR, Jung J, Hsu CJ, Choi JY, Lee KY, Wangemann P, Bok J, Kim UK. Gene therapy for hereditary hearing loss by SLC26A4 mutations in mice reveals distinct functional roles of pendrin in normal hearing. Theranostics 2019; 9:7184-7199. [PMID: 31695761 PMCID: PMC6831294 DOI: 10.7150/thno.38032] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Accepted: 08/06/2019] [Indexed: 12/13/2022] Open
Abstract
Rationale: Mutations of SLC26A4 that abrogate pendrin, expressed in endolymphatic sac, cochlea and vestibule, are known to cause autosomal recessive sensorineural hearing loss with enlargement of the membranous labyrinth. This is the first study to demonstrate the feasibility of gene therapy for pendrin-related hearing loss. Methods: We used a recombinant viral vector to transfect Slc26a4 cDNA into embryonic day 12.5 otocysts of pendrin-deficient knock-out (Slc26a4∆/∆ ) and pendrin-deficient knock-in (Slc26a4tm1Dontuh/tm1Dontuh ) mice. Results: Local gene-delivery resulted in spatially and temporally limited pendrin expression, prevented enlargement, failed to restore vestibular function, but succeeded in the restoration of hearing. Restored hearing phenotypes included normal hearing as well as sudden, fluctuating, and progressive hearing loss. Conclusion: Our study illustrates the feasibility of gene therapy for pendrin-related hearing loss, suggests differences in the requirement of pendrin between the cochlea and the vestibular labyrinth, and documents that insufficient pendrin expression during late embryonal and early postnatal development of the inner ear can cause sudden, fluctuating and progressive hearing loss without obligatory enlargement of the membranous labyrinth.
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Affiliation(s)
- Min-A Kim
- Department of Biology, College of Natural Sciences, Kyungpook National University, Daegu 41566, Republic of Korea
- School of Life Sciences, BK21 Plus KNU Creative BioResearch Group, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Sung Huhn Kim
- Department of Otorhinolaryngology, Head and Neck Surgery, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Nari Ryu
- Department of Biology, College of Natural Sciences, Kyungpook National University, Daegu 41566, Republic of Korea
- School of Life Sciences, BK21 Plus KNU Creative BioResearch Group, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Ji-Hyun Ma
- Department of Anatomy, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Ye-Ri Kim
- Department of Biology, College of Natural Sciences, Kyungpook National University, Daegu 41566, Republic of Korea
- School of Life Sciences, BK21 Plus KNU Creative BioResearch Group, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Jinsei Jung
- Department of Otorhinolaryngology, Head and Neck Surgery, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Chuan-Jen Hsu
- Department of Otolaryngology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Jae Young Choi
- Department of Otorhinolaryngology, Head and Neck Surgery, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Kyu-Yup Lee
- Department of Otorhinolaryngology-Head and Neck Surgery, School of Medicine, Kyungpook National University, Daegu 41944, Republic of Korea
| | - Philine Wangemann
- Department of Anatomy and Physiology, Kansas State University, Manhattan, United States of America
| | - Jinwoong Bok
- Department of Otorhinolaryngology, Head and Neck Surgery, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
- Department of Anatomy, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
- BK21PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Un-Kyung Kim
- Department of Biology, College of Natural Sciences, Kyungpook National University, Daegu 41566, Republic of Korea
- School of Life Sciences, BK21 Plus KNU Creative BioResearch Group, Kyungpook National University, Daegu 41566, Republic of Korea
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Comprehensive genetic testing of Chinese SNHL patients and variants interpretation using ACMG guidelines and ethnically matched normal controls. Eur J Hum Genet 2019; 28:231-243. [PMID: 31541171 PMCID: PMC6974605 DOI: 10.1038/s41431-019-0510-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Revised: 05/10/2019] [Accepted: 08/29/2019] [Indexed: 11/10/2022] Open
Abstract
Hereditary hearing loss is a monogenic disease with high genetic heterogeneity. Variants in more than 100 deafness genes underlie the basis of its pathogenesis. The aim of this study was to assess the ratio of SNVs in known deafness genes contributing to the etiology of both sporadic and familial sensorineural hearing loss patients from China. DNA samples from 1127 individuals, including normal hearing controls (n = 616), sporadic SNHL patients (n = 433), and deaf individuals (n = 78) from 30 hearing loss pedigrees were collected. The NGS tests included analysis of sequence alterations in 129 genes. The variants were interpreted according to the ACMG/AMP guidelines for genetic hearing loss combined with NGS data from 616 ethnically matched normal hearing adult controls. We identified a positive molecular diagnosis in 226 patients with sporadic SNHL (52.19%) and in patients from 17 deafness pedigrees (56.67%). Ethnically matched MAF filtering reduced the variants of unknown significance by 8.7%, from 6216 to 5675. Some complexities that may restrict causative variant identification are discussed. This report highlight the clinical utility of NGS panels identifying disease-causing variants for the diagnosis of hearing loss and underlines the importance of a broad data of control and ACMG/AMP standards for accurate clinical delineation of VUS variants.
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Zou S, Mei X, Yang W, Zhu R, Yang T, Hu H. Whole-exome sequencing identifies rare pathogenic and candidate variants in sporadic Chinese Han deaf patients. Clin Genet 2019; 97:352-356. [PMID: 31486067 DOI: 10.1111/cge.13638] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 08/29/2019] [Accepted: 09/01/2019] [Indexed: 12/21/2022]
Abstract
Genetic causes of hearing loss are highly heterogeneous and often ethnically specific. In recent years, a variety of next-generation sequencing (NGS) panels have been developed to target deafness-causative genes. Whole-exome sequencing (WES), on the other hand, was rarely used for genetic testing for deafness. In this study, we performed WES in 38 sporadic Chinese Han deaf patients who have been pre-excluded for mutations in common deafness genes GJB2, SLC26A4 and MT-RNR1. Non-synonymous variants have been filtered based on their minor allele frequencies in public databases and ethnically matched controls. Bi-allelic pathogenic mutations in eight deafness genes, OTOF, TRIOBP, ESPN, HARS2, CDH23, MYO7A, USH1C and TJP2, were identified in 10 patients, with 17 mutations identified in this study not being associated with deafness previously. For the rest 28 patients, possibly bi-allelic rare non-synonymous variants in an averaged 4.7 genes per patient were identified as candidate pathogenic causes for future analysis. Our study showed that WES may provide a unified platform for genetic testing of deafness and enables retro-analyzing when new causative genes are revealed.
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Affiliation(s)
- Songfeng Zou
- Department of Otorhinolaryngology, Peking University Shenzhen Hospital, Shenzhen, China
| | - Xueshuang Mei
- Department of Otorhinolaryngology, Peking University Shenzhen Hospital, Shenzhen, China
| | - Weiqiang Yang
- Department of Otorhinolaryngology, Peking University Shenzhen Hospital, Shenzhen, China
| | - Rvfei Zhu
- Department of Otorhinolaryngology, Peking University Shenzhen Hospital, Shenzhen, China
| | - Tao Yang
- Department of Otorhinolaryngology-Head and Neck Surgery, Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China.,Ear Institute, Shanghai Jiaotong University School of Medicine, Shanghai, China.,Shanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases, Shanghai, China
| | - Hongyi Hu
- Department of Otorhinolaryngology, Peking University Shenzhen Hospital, Shenzhen, China
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31
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Xiang YB, Tang SH, Li HZ, Xu CY, Chen C, Xu YZ, Ding LR, Xu XQ. Mutation analysis of common deafness-causing genes among 506 patients with nonsyndromic hearing loss from Wenzhou city, China. Int J Pediatr Otorhinolaryngol 2019; 122:185-190. [PMID: 31035178 DOI: 10.1016/j.ijporl.2019.04.024] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 04/16/2019] [Accepted: 04/16/2019] [Indexed: 12/17/2022]
Abstract
OBJECTIVES The frequency and spectrum of mutations in deafness-causing genes differs significantly according to the ethnic population and region under investigation. The molecular etiology of nonsyndromic hearing loss (NSHL) in Wenzhou, China, has not yet been systematically elucidated. To provide accurate genetic testing and counseling in this area, we investigated the molecular etiology of NSHL in a deaf population from Wenzhou. METHODS A total 506 unrelated patients with NSHL were enrolled in this study. Nine hotspot mutations in four major deafness genes were investigated by sequencing (Group I: 187 patients enrolled between 2011 and 2015) or allele-specific PCR-based universal array (Group II: 319 patients enrolled between 2016 and 2017). The investigated genes included GJB2 (c.35delG, c.176_191del16, c.235delC, c.299-300delAT), SLC26A4 (c.2168A > G, c.919-2A > G), mtDNA 12SrRNA (m.1555A > G, m.1494C > T), and GJB3 (c.538C > T). Furthermore, whole coding region sequencing or improved multiplex ligation detection reaction (IMLDR) were performed for patients who carried mono-allelic variants of GJB2 and SLC26A4, in order to detect other mutations among these patients. RESULTS GJB2 mutations were detected in 22.92% (116/506) of the entire cohort and SLC26A4 mutations were found in 6.52% (33/506) of the cohort. GJB3 mutations were detected in 0.79% (4/506) of the cohort. The mutation rate of mitochondrial DNA 12SrRNA in our patients was 17.40% (88/506), including 17.00% (86/506) with the m.1555A > G mutation and 0.40% (2/506) with the m.1494C > T mutation. The allelic frequency of the c.235delC mutation was 14.62% (148/1012), which is significantly higher than that of c.109G > A (33/1012, 3.26%), c.299_300delAT (13/1012, 1.28%), and c.176_191del16 (6/1012, 0.59%). The most common pathogenic mutation of SLC26A4 was the c.919-2A > G mutation (37/1012, 3.66%), followed by c.2168A > G (6/1012, 0.59%), and c.1229C > T (4/1012, 0.40%). Moreover, five rare pathogenic variants of GJB2 and eight rare pathogenic variants of SLC26A4 were identified. CONCLUSION GJB2 is the primary deafness-causing gene in deaf patients from Wenzhou, China; this is consistent with what is observed in most Chinese populations. However, the surprisingly high rate of the m.1555A > G mutation (17.00%) in patients from Wenzhou was significantly higher than in other populations in China. These findings highlight the specificity of the common deafness-causing gene mutation spectrum in the Wenzhou area. This information may be of benefit for genetic counseling and risk assessment for deaf patients from this area.
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Affiliation(s)
- Yan-Bao Xiang
- Key Laboratory of Birth Defects, Department of Genetics, Wenzhou Central Hospital, Wenzhou, China.
| | - Shao-Hua Tang
- Key Laboratory of Birth Defects, Department of Genetics, Wenzhou Central Hospital, Wenzhou, China; Key Laboratory of Medical Genetic, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, China.
| | - Huan-Zheng Li
- Key Laboratory of Birth Defects, Department of Genetics, Wenzhou Central Hospital, Wenzhou, China.
| | - Chen-Yang Xu
- Key Laboratory of Birth Defects, Department of Genetics, Wenzhou Central Hospital, Wenzhou, China.
| | - Chong Chen
- Key Laboratory of Birth Defects, Department of Genetics, Wenzhou Central Hospital, Wenzhou, China.
| | - Yun-Zhi Xu
- Key Laboratory of Birth Defects, Department of Genetics, Wenzhou Central Hospital, Wenzhou, China.
| | - Li-Rong Ding
- Key Laboratory of Birth Defects, Department of Genetics, Wenzhou Central Hospital, Wenzhou, China; Key Laboratory of Medical Genetic, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, China.
| | - Xue-Qin Xu
- Key Laboratory of Birth Defects, Department of Genetics, Wenzhou Central Hospital, Wenzhou, China.
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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: 1.0] [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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Jiang H, Niu Y, Qu L, Huang X, Zhu X, Tang G. A novel compound heterozygous mutation in the GJB2 gene is associated with non-syndromic hearing loss in a Chinese family. Biosci Trends 2019; 12:470-475. [PMID: 30473554 DOI: 10.5582/bst.2018.01156] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Autosomal recessive (AR) non-syndromic hearing loss (NSHL) is the most common form of hereditary deafness. Mutations in the gap junction protein beta 2 (GJB2) gene encoding connexin 26 (Cx26) account for about 50% of cases of ARNSHL. In the current study, a combination of exome sequencing and Sanger sequencing in a Chinese Dong family with ARNSHL allowed identification of a novel compound heterozygous mutation c.240G>C(p. Q80H)/C.109G>A(p.V37I) in exon 2 of the GJB2 gene, which co-segregated with the disease phenotype in this family and was not evident in 100 healthy controls. Bioinformatic analysis revealed that the two mutations in the GJB2 gene were probably pathogenic. Results indicated that the compound heterozygous variants, p.Q80H and p.V37I, in the GJB2 gene are associated with ARNSHL. The Q80H variant was initially identified in patients of Dong Chinese origin with NSHL. The current results broaden the spectrum of GJB2 mutations responsible for NSHL and have important implications for molecular diagnosis, treatment, and genetic counseling for this family.
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Affiliation(s)
- Haiou Jiang
- Department of Cellular Biology and Genetics, Hunan Provincial Key Laboratory of Dong Medicine, Hunan University of Medicine
| | - Youya Niu
- Department of Cellular Biology and Genetics, Hunan Provincial Key Laboratory of Dong Medicine, Hunan University of Medicine
| | - Lingfeng Qu
- Department of Cellular Biology and Genetics, Hunan Provincial Key Laboratory of Dong Medicine, Hunan University of Medicine
| | - Xueshuang Huang
- Department of Cellular Biology and Genetics, Hunan Provincial Key Laboratory of Dong Medicine, Hunan University of Medicine
| | - Xinlong Zhu
- Department of Cellular Biology and Genetics, Hunan Provincial Key Laboratory of Dong Medicine, Hunan University of Medicine
| | - Genyun Tang
- Department of Cellular Biology and Genetics, Hunan Provincial Key Laboratory of Dong Medicine, Hunan University of Medicine
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Alimardani M, Hosseini SM, Khaniani MS, Haghi MR, Eslahi A, Farjami M, Chezgi J, Derakhshan SM, Mojarrad M. Targeted Mutation Analysis of the SLC26A4, MYO6, PJVK and CDH23 Genes in Iranian Patients with AR Nonsyndromic Hearing Loss. Fetal Pediatr Pathol 2019; 38:93-102. [PMID: 30582396 DOI: 10.1080/15513815.2018.1547336] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
BACKGROUND Hearing loss (HL) is the most prevalent sensory disorder. The over 100 genes implicated in autosomal recessive nonsyndromic hearing loss (ARNSHL) makes it difficult to analyze and determine the accurate genetic causes of hearing loss. We sought to de?ne the frequency of seven hearing loss-Causing causing genetic Variants in four genes in an Iranian population with hearing loss. MATERIALS AND METHODS One hundred ARNSHL patients with normal GJB2/GJB6 genes were included, and targeted mutations in SLC26A4, MYO6, PJVK and CDH23 genes were analyzed by ARMS-PCR. The negative and positive results were confirmed by the Sanger sequencing. RESULTS We found only two mutations, one in MYO6 (c.554-1 G > A) gene and another in PJVK (c.547C > T). CONCLUSION c.554-1G > A and c.547C > T mutations are responsible for 1% each of the Iranian ARNSHL patients. These genes are not a frequent cause of ARNSHL in an Iranian population.
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Affiliation(s)
- Maliheh Alimardani
- a Neurosciences Research Center , Tabriz University of Medical Science , Tabriz , Iran.,b Department of Medical Genetics , Tabriz University of Medical Sciences , Tabriz , Iran.,c Student Research Committee, Faculty of Medicine , Mashhad University of Medical Sciences , Mashhad , Iran
| | - Seyed Mojtaba Hosseini
- c Student Research Committee, Faculty of Medicine , Mashhad University of Medical Sciences , Mashhad , Iran.,d Department of Medical Genetics , Mashhad University of Medical Sciences , Mashhad , Iran
| | - Mahmoud Shekari Khaniani
- b Department of Medical Genetics , Tabriz University of Medical Sciences , Tabriz , Iran.,e Ebne Sina Medical Genetic Diagnostic Laboratory , Tabriz University of Medical Sciences , Tabriz , Iran
| | - Mohsen Rajati Haghi
- f Department of Head and Neck Surgery, ENT Research Center , Mashhad University of Medical Sciences , Mashhad , Iran
| | - Atieh Eslahi
- c Student Research Committee, Faculty of Medicine , Mashhad University of Medical Sciences , Mashhad , Iran.,d Department of Medical Genetics , Mashhad University of Medical Sciences , Mashhad , Iran
| | - Mashsa Farjami
- c Student Research Committee, Faculty of Medicine , Mashhad University of Medical Sciences , Mashhad , Iran.,d Department of Medical Genetics , Mashhad University of Medical Sciences , Mashhad , Iran
| | - Javad Chezgi
- c Student Research Committee, Faculty of Medicine , Mashhad University of Medical Sciences , Mashhad , Iran.,d Department of Medical Genetics , Mashhad University of Medical Sciences , Mashhad , Iran
| | - Sima Mansoori Derakhshan
- a Neurosciences Research Center , Tabriz University of Medical Science , Tabriz , Iran.,b Department of Medical Genetics , Tabriz University of Medical Sciences , Tabriz , Iran.,e Ebne Sina Medical Genetic Diagnostic Laboratory , Tabriz University of Medical Sciences , Tabriz , Iran
| | - Majid Mojarrad
- d Department of Medical Genetics , Mashhad University of Medical Sciences , Mashhad , Iran.,g Medical Genetics Research Center, School of Medicine , Mashhad University of Medical Sciences , Mashhad , Iran
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Study on the relationship between the pathogenic mutations of SLC26A4 and CT phenotypes of inner ear in patient with sensorineural hearing loss. Biosci Rep 2019; 39:BSR20182241. [PMID: 30842343 PMCID: PMC6430729 DOI: 10.1042/bsr20182241] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Revised: 02/11/2019] [Accepted: 02/28/2019] [Indexed: 11/23/2022] Open
Abstract
To investigate the possible association of pathogenic mutations of SLC26A4 and computerized tomography (CT) phenotypes of inner ear, and explore the feasibility of using the method of gene sequence analysis. A total of 155 patients with bilateral hearing loss carrying SLC26A4 gene mutations were further subjected to high-resolution temporal bone CT and thyroid B ultrasound tests. The potential relationship between the pathogenic mutations of gene and the CT phenotypes were analyzed. As a result, 65 patients (41.9%, 65/155) carried SLC26A4 gene mutations, and 27 cases were detected with pathogenic mutations of SLC26A4 where IVS7-2A>G (55.6%, 15/27) was the most common pathogenic mutation. Amongst them, 19 patients carrying bi-allelic SLC26A4 mutations were all confirmed to have inner ear malformation by CT scan including four cases of enlarged vestibular aqueduct (EVA) and 15 cases of Mondini dysplasia (MD). However, there was only one in eight cases of single allele pathogenic mutation who was confirmed to have EVA by CT scan. Further, only one patient with EVA was confirmed to be slightly higher of total T3 than normal by thyroid ultrasound scan and thyroid hormone assays. These findings suggested that CT detection and SLC26A4 gene detection are efficient methods to diagnose EVA, which can complement each other. Also, the bi-allelic pathogenic mutations of SLC26A4 are more likely to induce inner ear malformation than single allele pathogenic mutation.
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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.
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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.
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37
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Ming L, Wang Y, Lu W, Sun T. A Mutational Analysis of GJB2, SLC26A4, MT-RNA1, and GJB3 in Children with Nonsyndromic Hearing Loss in the Henan Province of China. Genet Test Mol Biomarkers 2018; 23:51-56. [PMID: 30589569 DOI: 10.1089/gtmb.2018.0146] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Hearing impairment is one of the most common neurosensory disorders afflicting humans. Approximately half of all cases have a genetic etiology. The distribution and frequency of genetic mutations that cause deafness differ significantly by ethnic group and geographic region. METHODS 130 sporadic nonsyndromic hearing loss (NSHL) children from the Henan province were subjected to microarray-based mutation detection. Nine pathogenic mutations were detected in four of the most common deafness-related genes (GJB2, GJB3, SLC26A4, and MT-RNA1). RESULTS Fifty percent of the analyzed patients (65/130) were shown to have genetic defects known to be related to deafness. Slightly >30% (41/130) had biallelic pathogenic mutations. One patient had pathogenic mutations in their mitochondrial genes (MT-RNA1); no mutations were detected in the GJB3 gene. Twenty-three (17.69%) patients were carriers of a single mutation in a recessive gene; these findings alone, however, cannot be interpreted as a cause of hearing loss. Utilizing this molecular strategy, we were able to arrive at a conclusive diagnosis for 42 of the NSHL children. CONCLUSION Genetic factors play a major role in sporadic NSHL patients from the Henan province, but it is clear that our screen needs to be expanded to include additional genes and alleles. Screening of potential pathogenic genes is important for patient risk assessment.
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Affiliation(s)
- Liang Ming
- 1 Key Clinical Laboratory of Henan Province, Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University , Zhengzhou, China
| | - Yangxia Wang
- 1 Key Clinical Laboratory of Henan Province, Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University , Zhengzhou, China
| | - Wei Lu
- 2 Department of Otology, The First Affiliated Hospital of Zhengzhou University , Zhengzhou, China
| | - Ting Sun
- 1 Key Clinical Laboratory of Henan Province, Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University , Zhengzhou, China
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38
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Yu H, Liu D, Yang J, Wu Z. Prevalence of mutations in the GJB2, SLC26A4, GJB3, and MT-RNR1 genes in 103 children with sensorineural hearing loss in Shaoxing, China. EAR, NOSE & THROAT JOURNAL 2018; 97:E33-E38. [PMID: 30036422 DOI: 10.1177/014556131809700603] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Mutations in the GJB2, SLC26A4, GJB3, and MT-RNR1 genes are known to be a common cause of hearing loss. However, the frequency of hot-spot mutations and genotype-phenotype correlations in patients with sensorineural hearing loss (SNHL) has been less frequently reported. We conducted a study of 103 children-56 boys and 47 girls, aged 5 months to 9 years (mean: 4.1 yr)-with SNHL who underwent genetic screening for 20 hot-spot mutations of the GJB2, SLC26A4, GJB3, and MT-RNR1 genes. Mutations were detected by multiple-PCR-based MALDI-TOF MS assay. At least one mutated allele was detected in 48 patients (46.6%), and 30 patients (29.1%) carried pathogenic mutations. Among all the detected mutations, the most common were GJB2 c.235delC and SLC26A4 c.919-2A>G, with allele frequencies of 23.8 and 6.8%, respectively. At least one mutant allele of SLC26A4 was detected in the 13 patients who had an enlarged vestibular aqueduct (EVA). Almost half of the children with SNHL carried a common deafness-related mutation, and nearly one-third carried a pathogenic mutation. The mutations in SLC26A4 were prevalent and correlated strongly with EVA.
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Affiliation(s)
- Hong Yu
- Department of Child Care, Shaoxing Maternal and Child Health Care Hospital, 305 East St., Shaoxing, Zhejiang 312000, China.
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39
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Zhao S, Xiang J, Fan C, Asan, Shang X, Zhang X, Chen Y, Zhu B, Cai W, Chen S, Cai R, Guo X, Zhang C, Zhou Y, Huang S, Liu Y, Chen B, Yan S, Chen Y, Ding H, Guo F, Wang Y, Zhong W, Zhu Y, Wang Y, Chen C, Li Y, Huang H, Mao M, Yin Y, Wang J, Yang H, Xu X, Sun J, Peng Z. Pilot study of expanded carrier screening for 11 recessive diseases in China: results from 10,476 ethnically diverse couples. Eur J Hum Genet 2018; 27:254-262. [PMID: 30275481 PMCID: PMC6336873 DOI: 10.1038/s41431-018-0253-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 07/20/2018] [Accepted: 08/09/2018] [Indexed: 01/23/2023] Open
Abstract
Expanded carrier screening (ECS) has been demonstrated to increase the detection rate of carriers compared with traditional tests. The aim of this study was to assess the potential value of ECS for clinical application in Southern China, a region with high prevalence of thalassemia and with diverse ethnic groups, and to provide a reference for future implementations in areas with similar population characteristics. A total of 10,476 prenatal/preconception couples from 34 self-reported ethnic groups were simultaneously tested and analyzed anonymously for 11 Mendelian disorders using targeted next-generation sequencing. Overall, 27.49% of individuals without self-reported family history of disorders were found to be carriers of at least 1 of the 11 conditions, and the carrier frequency varied greatly between ethnic groups, ranging from 4.15% to 81.35%. Furthermore, 255 couples (2.43%) were identified as carrier couples at an elevated risk having an affected baby, sixty-five of which would not have been identified through the existing screening strategy, which only detects thalassemia. The modeled risk of fetuses being affected by any of the selected disorders was 531 per 100,000 (95% CI, 497-567 per 100,000). Our data demonstrate the feasibility of ECS, and provide evidence that ECS is a promising alternative to traditional one-condition screening strategies. The lessons learned from this experience should be applicable for other countries or regions with diverse ethnic groups.
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Affiliation(s)
- Sumin Zhao
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, 300308, Tianjin, China.,Binhai Genomics Institute, BGI-Tianjin, BGI-Shenzhen, 300308, Tianjin, China
| | - Jiale Xiang
- BGI Genomics, BGI-Shenzhen, 518083, Shenzhen, China
| | - Chunna Fan
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, 300308, Tianjin, China.,Binhai Genomics Institute, BGI-Tianjin, BGI-Shenzhen, 300308, Tianjin, China
| | - Asan
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, 300308, Tianjin, China.,Binhai Genomics Institute, BGI-Tianjin, BGI-Shenzhen, 300308, Tianjin, China
| | - Xuan Shang
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, 510515, Guangzhou, Guangdong, China
| | - Xinhua Zhang
- Department of Hematology, 303rd Hospital of the People's Liberation Army, Nanning, Guangxi, China
| | - Yan Chen
- The Second Department of Pediatrics, Affiliated Hospital of Zunyi Medical College, Zunyi, Guizhou, China
| | - Baosheng Zhu
- Nation Health and Family Planning Commission Key Laboratory For Preconception and Health Birth in Western China, The First People's Hospital of Yunnan Province, Kunming University of Science and Technology, Kunming, China
| | - Wangwei Cai
- Department of Biochemistry and Molecular Biology, Hainan Medical College, Haikou, Hainan, China
| | - Shaoke Chen
- Department of Genetic and Metabolic Laboratory, Guangxi Zhuang Autonomous Region Women and Children Health Care Hospital, Nanning, Guangxi, China
| | - Ren Cai
- Department of Medical Genetics, Liuzhou Municipal Maternity and Child Healthcare Hospital, Liuzhou, Guangxi, China
| | - Xiaoling Guo
- Maternity and Child Health Care Hospital of Foshan City, Foshan, Guangdong, China
| | - Chonglin Zhang
- Guilin Women and Children Health Care Hospital, Guilin, Guangxi, China
| | - Yuqiu Zhou
- Department of Clinical Laboratory, Zhuhai Municipal Maternal and Child Healthcare Hospital, Zhuhai Institute of Medical Genetics, Zhuhai, Guangdong, China
| | - Shuodan Huang
- Maternal and Child Health Hospital in Meizhou, Meizhou, Guangdong, China
| | - Yanhui Liu
- Department of Prenatal Diagnosis Center, Dong Guan Maternal and Child Health Hospital, Dongguan, Guangdong, China
| | - Biyan Chen
- Baise Women and Children Care Hospital, Baise, Guangxi, China
| | - Shanhuo Yan
- Genetic Laboratory, Qinzhou Maternal and Child Health Hospital, Qingzhou, Guangxi, China
| | - Yajun Chen
- Women and Children's Health Hospital of Shaoguan, Shaoguan, Guangdong, China
| | - Hongmei Ding
- Department of Gynecology and Obstetrics, The People's Hospital of Yunfu City, Yunfu, Guangdong, China
| | - Fengyu Guo
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, 300308, Tianjin, China.,Binhai Genomics Institute, BGI-Tianjin, BGI-Shenzhen, 300308, Tianjin, China
| | - Yaoshen Wang
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, 300308, Tianjin, China.,Binhai Genomics Institute, BGI-Tianjin, BGI-Shenzhen, 300308, Tianjin, China
| | - Wenwei Zhong
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, 300308, Tianjin, China.,Binhai Genomics Institute, BGI-Tianjin, BGI-Shenzhen, 300308, Tianjin, China
| | - Yaping Zhu
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, 300308, Tianjin, China.,Binhai Genomics Institute, BGI-Tianjin, BGI-Shenzhen, 300308, Tianjin, China
| | - Yaling Wang
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, 300308, Tianjin, China.,Binhai Genomics Institute, BGI-Tianjin, BGI-Shenzhen, 300308, Tianjin, China
| | - Chao Chen
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, 300308, Tianjin, China.,Binhai Genomics Institute, BGI-Tianjin, BGI-Shenzhen, 300308, Tianjin, China
| | - Yun Li
- BGI Clinical Laboratories-Shenzhen, BGI-Shenzhen, 518083, Shenzhen, China
| | - Hui Huang
- BGI Genomics, BGI-Shenzhen, 518083, Shenzhen, China
| | - Mao Mao
- BGI Genomics, BGI-Shenzhen, 518083, Shenzhen, China
| | - Ye Yin
- BGI Genomics, BGI-Shenzhen, 518083, Shenzhen, China
| | - Jian Wang
- James D. Watson Institute of Genome Sciences, 310058, Hangzhou, China.,BGI-Shenzhen, 518083, Shenzhen, China
| | - Huanming Yang
- James D. Watson Institute of Genome Sciences, 310058, Hangzhou, China.,BGI-Shenzhen, 518083, Shenzhen, China
| | - Xiangmin Xu
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, 510515, Guangzhou, Guangdong, China
| | - Jun Sun
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, 300308, Tianjin, China. .,Binhai Genomics Institute, BGI-Tianjin, BGI-Shenzhen, 300308, Tianjin, China.
| | - Zhiyu Peng
- BGI Genomics, BGI-Shenzhen, 518083, Shenzhen, China. .,BGI-Guangzhou Medical Laboratory, BGI-Shenzhen, 510006, Guangzhou, China.
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40
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Establishment of a Gene Detection System for Hotspot Mutations of Hearing Loss. BIOMED RESEARCH INTERNATIONAL 2018; 2018:6828306. [PMID: 29707576 PMCID: PMC5863321 DOI: 10.1155/2018/6828306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 01/24/2018] [Indexed: 12/02/2022]
Abstract
Hearing loss is an etiologically heterogeneous trait with a high incidence in China. Though conventional newborn hearing screening program has been widely adopted, gene detection can significantly improve the means of early discovering genetic risk factors. Thus, simple and efficient methods with higher sensitivity and lower cost for detecting hotspot mutations of hearing loss are urgently requested. Here we established a mutation detection system based on multiple fluorescent probe technique, which can detect and genotype nine hotspot mutations of four prominent hearing loss-related genes in two reactions on a four-channel real-time PCR instrument, including GJB2 (rs750188782, rs80338943, rs1110333204, and rs80338939), GJB3 (rs74315319), SLC26A4 (rs111033313 and rs121908362), and mtDNA 12S rRNA (rs267606617 and rs267606619). This system is with high sensitivity that enables detecting as low as 10 DNA copies samples per reaction. A comparison study in 268 clinical samples showed that the detection system had 100% concordance to Sanger sequencing. Besides, blood and saliva samples can be directly detected without DNA extraction process, which greatly simplifies the manipulation. The new system with high sensitivity, accuracy, and specimen type compatibility can be expectedly a reliable tool in clinical application.
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41
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Zhao P, Lin L, Lan L. Analysis of mutation spectrum of common deafness-causing genes in Hakka newborns in southern China by semiconductor sequencing. Medicine (Baltimore) 2018; 97:e12285. [PMID: 30235673 PMCID: PMC6160144 DOI: 10.1097/md.0000000000012285] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 08/15/2018] [Indexed: 11/27/2022] Open
Abstract
Hearing loss is a common neurosensory disorder, approximately half of the cases are caused by genetic factors, and approximately 70% of hereditary hearing impairments are nonsyndromic hearing loss (NSHL). The mutations of GJB2 (gap junction beta-2 protein), GJB3 (gap junction beta-3 protein), SLC26A4 (solute carrier family 26 member 4), and MT-RNR1 (mitochondrially encoded 12S RNA) are the most common inherited causes of NSHL. Because of different genetic backgrounds, the mutation spectrum of these common deafness-causing genes varies among different regions in China. Because no data are known on these mutations among the Hakka population of Southern China, we aim to investigate the mutation spectrum to add these to neonatal screening and genetic counseling. A total of 1252 blood samples from newborns have been detected by semiconductor sequencing for 100 mutations loci of 18 deafness-causing genes. Of the participants, 95 subjects carried deafness-causing genes mutations with the carrier rate of 7.59%. The mutation frequencies of GJB2, SLC26A4, GJB3, and mitochondrial genes were 3.04%, 3.51%, 0.16%, and 0.88%, respectively. We followed up subjects with single-gene homozygous or compound heterozygous mutations. Our study firstly analyzed deafness-causing genes mutation spectrum in Hakka population, providing evidence for future neonatal screening and genetic counseling in this area.
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Affiliation(s)
- Pingsen Zhao
- Clinical Core Laboratory
- Center for Precision Medicine, Meizhou People's Hospital (Huangtang Hospital), Meizhou Hospital Affiliated to Sun Yat-sen University
- Guangdong Provincial Engineering and Technology Research Center for Molecular Diagnostics of Cardiovascular Diseases
- Meizhou Municipal Engineering and Technology Research Center for Molecular Diagnostics of Cardiovascular Diseases
- Meizhou Municipal Engineering and Technology Research Center for Molecular Diagnostics of Major Genetic Disorders
- Prenatal Diagnosis Center, Meizhou People's Hospital (Huangtang Hospital), Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, P. R. China
| | - Lifang Lin
- Clinical Core Laboratory
- Center for Precision Medicine, Meizhou People's Hospital (Huangtang Hospital), Meizhou Hospital Affiliated to Sun Yat-sen University
- Guangdong Provincial Engineering and Technology Research Center for Molecular Diagnostics of Cardiovascular Diseases
- Meizhou Municipal Engineering and Technology Research Center for Molecular Diagnostics of Cardiovascular Diseases
- Meizhou Municipal Engineering and Technology Research Center for Molecular Diagnostics of Major Genetic Disorders
- Prenatal Diagnosis Center, Meizhou People's Hospital (Huangtang Hospital), Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, P. R. China
| | - Liubing Lan
- Prenatal Diagnosis Center, Meizhou People's Hospital (Huangtang Hospital), Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, P. R. China
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42
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Li WX, Peng H, Yang L, Hao QQ, Sun W, Ji F, Guo WW, Yang SM. Familial nonsyndromic hearing loss with incomplete partition type II caused by novel DSPP gene mutations. Acta Otolaryngol 2018; 138:685-690. [PMID: 29741433 DOI: 10.1080/00016489.2018.1459832] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Abstract
BACKGROUND Familial nonsyndromic hearing loss (NSHL) with incomplete partition type II (IP-II) is a very rare condition. AIMS/OBJECTIVES To determine the audiological feature, inheritance patterns and genetic etiology of familial NSHL with IP-II in a Chinese family with eight family members. MATERIAL AND METHODS Clinical data were collected from all eight family members, selected deafness genes were sequenced in proband and whole genome sequencing of seven family members was performed. RESULTS The proband were a pair of male nonidentical twins (III:1, III:2). Three patients in this family, including the twins and their father (II:1), were diagnosed with bilateral NSHL with IP-II, and no mutation was found in the genes of SLC26A4, GJB2, GJB3, mitochondrial 12S rRNA, and MITF. Whole genome sequencing data indicated de novo mutations of the gene DSPP, c.3085A > G and c.3087C > T, which resulted in p.N1029D and co-segregated with deafness phenotype, were the underlying genetic etiology. CONCLUSION AND SIGNIFICANCE Familial NSHL with IP-II is extremely rare. In this family, de novo DSPP gene mutations, were considered to be the most probable genetic etiology. And this is the first report to reveal DSPP gene mutations leading to familial NSHL with IP-II.
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Affiliation(s)
- Wan-Xin Li
- Department of Otolaryngology, Head and Neck Surgery, Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, China
- Department of Otolaryngology Head and Neck Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Hong Peng
- Department of Otolaryngology-Head and Neck Surgery, Guangdong No. 2 Provincial People’s Hospital affiliated Southern Medical University, Guangzhou, China
| | - Le Yang
- Department of Otolaryngology-Head and Neck Surgery, Guangdong No. 2 Provincial People’s Hospital affiliated Southern Medical University, Guangzhou, China
| | - Qing-Qing Hao
- Department of Otolaryngology, Head and Neck Surgery, Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, China
| | - Wei Sun
- Department of Communicative Disorders and Sciences, Center for Hearing and Deafness, the State University of New York at Buffalo, Buffalo, NY, USA
| | - Fei Ji
- Department of Otolaryngology, Head and Neck Surgery, Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, China
| | - Wei-Wei Guo
- Department of Otolaryngology, Head and Neck Surgery, Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, China
| | - Shi-Ming Yang
- Department of Otolaryngology, Head and Neck Surgery, Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, China
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Wang F, Zhu L, Liu B, Zhu X, Wang N, Deng T, Kang D, Pan J, Yang W, Gao H, Guo Y. Noninvasive and Accurate Detection of Hereditary Hearing Loss Mutations with Buccal Swab Based on Droplet Digital PCR. Anal Chem 2018; 90:8919-8926. [PMID: 29987923 DOI: 10.1021/acs.analchem.8b01096] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Hereditary hearing loss is a common clinical neurosensory disorder in humans and has a high demand for genetic screening. Current screening techniques using peripheral blood or dried blood spots (DBSs) are invasive. Therefore, this study aims to develop a noninvasive and accurate detection method for eight hotspot deafness-associated mutations based on buccal swab and droplet digital PCR (ddPCR). First, this method was evaluated for analytic performance including specificity, detection limit, dynamic range using plasmid DNA. The specificity was 100% and the detection limit was 5 copies. The dynamic range of this ddPCR-based method was from 10 to 105 copies/μL. Next, the method was found to accurately quantify mitochondrial gene heteroplasmy rate as low as 1% for both m.1494C > T and m.1555A > G sites. Then, we demonstrated that buccal swab was a reliable sample. DNA can be extracted and accurately quantified after a buccal swab had been stored for 90 days at either room temperature or -20 °C. Finally, clinical samples (23 DBSs and 42 buccal swabs) were tested to further evaluate the accuracy and clinical applicability of this method. All clinical samples were accurately quantified and genotyped. This noninvasive and accurate method is highly promising as a genetic screening method for deafness-associated mutations due to its high sensitivity and accuracy.
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Affiliation(s)
- Fang Wang
- Human Genetic Resource Center , National Research Institute for Health and Family Planning , 12 Da Huisi Raod , Beijing 100081 , People's Republic of China.,Chinese Academy of Medical Sciences , Graduate School of Peking Union Medical College , 9 Dongdan Three Road , Beijing 100730 , People's Republic of China
| | - Lingxiang Zhu
- Human Genetic Resource Center , National Research Institute for Health and Family Planning , 12 Da Huisi Raod , Beijing 100081 , People's Republic of China.,Chinese Academy of Medical Sciences , Graduate School of Peking Union Medical College , 9 Dongdan Three Road , Beijing 100730 , People's Republic of China
| | - Baoxia Liu
- Department of Biomedical Engineering, School of Medicine, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases , Tsinghua University , 30 Shuangqing Road , Beijing 100084 , People's Republic of China
| | - Xiurui Zhu
- Department of Biomedical Engineering, School of Medicine, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases , Tsinghua University , 30 Shuangqing Road , Beijing 100084 , People's Republic of China
| | - Nan Wang
- Human Genetic Resource Center , National Research Institute for Health and Family Planning , 12 Da Huisi Raod , Beijing 100081 , People's Republic of China.,Chinese Academy of Medical Sciences , Graduate School of Peking Union Medical College , 9 Dongdan Three Road , Beijing 100730 , People's Republic of China
| | - Tao Deng
- Beijing CapitalBio Medical Laboratory , 88 Kechuang Six Street , Beijing 101111 , People's Republic of China
| | - Dongyang Kang
- Department of Otorhinolaryngology Head Neck Surgery , Chinese PLA General Hospital , 28 Fuxing Road , Beijing 100853 , P. R. China
| | - Junmin Pan
- Human Genetic Resource Center , National Research Institute for Health and Family Planning , 12 Da Huisi Raod , Beijing 100081 , People's Republic of China.,MOE Key Laboratory of Protein Sciences, School of Life Sciences , Tsinghua University , 30 Shuangqing Road , Beijing 100084 , People's Republic of China
| | - Wenjun Yang
- TargetingOne Corporation , 268 Chengfu Road , Beijing 100190 , People's Republic of China
| | - Huafang Gao
- Human Genetic Resource Center , National Research Institute for Health and Family Planning , 12 Da Huisi Raod , Beijing 100081 , People's Republic of China.,Chinese Academy of Medical Sciences , Graduate School of Peking Union Medical College , 9 Dongdan Three Road , Beijing 100730 , People's Republic of China
| | - Yong Guo
- Department of Biomedical Engineering, School of Medicine, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases , Tsinghua University , 30 Shuangqing Road , Beijing 100084 , People's Republic of China
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44
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Zhang W, Kim SM, Wang W, Cai C, Feng Y, Kong W, Lin X. Cochlear Gene Therapy for Sensorineural Hearing Loss: Current Status and Major Remaining Hurdles for Translational Success. Front Mol Neurosci 2018; 11:221. [PMID: 29997477 PMCID: PMC6028713 DOI: 10.3389/fnmol.2018.00221] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 06/06/2018] [Indexed: 12/19/2022] Open
Abstract
Sensorineural hearing loss (SNHL) affects millions of people. Genetic mutations play a large and direct role in both congenital and late-onset cases of SNHL (e.g., age-dependent hearing loss, ADHL). Although hearing aids can help moderate to severe hearing loss the only effective treatment for deaf patients is the cochlear implant (CI). Gene- and cell-based therapies potentially may preserve or restore hearing with more natural sound perception, since their theoretical frequency resolution power is much higher than that of cochlear implants. These biologically-based interventions also carry the potential to re-establish hearing without the need for implanting any prosthetic device; the convenience and lower financial burden afforded by such biologically-based interventions could potentially benefit far more SNHL patients. Recently major progress has been achieved in preclinical studies of cochlear gene therapy. This review critically evaluates recent advances in the preclinical trials of gene therapies for SNHL and the major remaining challenges for the development and eventual clinical translation of this novel therapy. The cochlea bears many similarities to the eye for translational studies of gene therapies. Experience gained in ocular gene therapy trials, many of which have advanced to clinical phase III, may provide valuable guidance in improving the chance of success for cochlear gene therapy in human trials. A discussion on potential implications of translational knowledge gleaned from large numbers of advanced clinical trials of ocular gene therapy is therefore included.
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Affiliation(s)
- Wenjuan Zhang
- Department of Otolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Sun Myoung Kim
- Department of Otolaryngology, Emory University School of Medicine, Atlanta, GA, United States
| | - Wenwen Wang
- Department of Otolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | | | - Yong Feng
- Xiangya School of Medicine, Changsha, China
| | - Weijia Kong
- Department of Otolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xi Lin
- Department of Otolaryngology, Emory University School of Medicine, Atlanta, GA, United States
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Chen K, Wu X, Zong L, Jiang H. GJB3/GJB6 screening in GJB2 carriers with idiopathic hearing loss: Is it necessary? J Clin Lab Anal 2018; 32:e22592. [PMID: 29926981 DOI: 10.1002/jcla.22592] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2018] [Accepted: 05/29/2018] [Indexed: 11/07/2022] Open
Abstract
BACKGROUND Genetic analysis detected excessive mono-allelic recessive GJB2 mutations in individuals with idiopathic deafness; the remaining alleles in trans/cis are underdetermined. The aim of this study was to assess the contributions of variants in GJB3 or GJB6 to non-syndromic sensorineural hearing impairment (NSHI) in Chinese patients with mono-allelic GJB2 mutations. METHODS The entire coding sequences of GJB3/GJB6, as well as deletions in GJB6, in a cohort of NSHI patients (n = 100) carrying likely pathogenic heterozygous GJB2 mutations, were tested. Targeted next generation sequencing was further performed in a multiplex family GDHY with moderate to profound NSHI. RESULTS Putatively causative GJB3 variant underlied 1% (1/100) in this cohort. In family GDHY, we identified a rare GJB3 c.250G>A mutation, as double heterozygotes with GJB2 c.109G>A and/or a novel GJB2 mutation c.638T>C predicted to be damaging in a digenic inheritance after precluding other attributable mutations from 127 deafness genes. No GJB6 mutation was found. CONCLUSIONS GJB3/GJB6 variants account for a low proportion in autosomal recessive GJB2 mutation carriers in our cohort. Environmental causes, or other NSHI relevant genes, revealed by targeted next generation sequencing or whole exome sequencing, may play major roles in triggering deafness in these patients.
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Affiliation(s)
- Kaitian Chen
- Department of Otorhinolaryngology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Institute of Otorhinolaryngology, Sun Yat-sen University, Guangzhou, China
| | - Xuan Wu
- Department of Otorhinolaryngology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Institute of Otorhinolaryngology, Sun Yat-sen University, Guangzhou, China
| | - Ling Zong
- Department of Otorhinolaryngology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Hongyan Jiang
- Department of Otorhinolaryngology, Hainan General Hospital, Haikou, China
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Huang B, Han M, Wang G, Huang S, Zeng J, Yuan Y, Dai P. Genetic mutations in non-syndromic deafness patients in Hainan Province have a different mutational spectrum compared to patients from Mainland China. Int J Pediatr Otorhinolaryngol 2018; 108:49-54. [PMID: 29605365 DOI: 10.1016/j.ijporl.2018.02.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 01/18/2018] [Accepted: 02/11/2018] [Indexed: 10/18/2022]
Abstract
OBJECTIVES To provide appropriate genetic testing and counseling for non-syndromic hearing impairment patients in Hainan Province, an island in the South China Sea. METHODS 299 unrelated students with non-syndromic hearing loss who attended a special education school in Hainan Province were enrolled in this study. Three prominent deafness-related genes (GJB2, SLC26A4, and mtDNA 12S rRNA) were analyzed using Sanger sequencing. RESULTS GJB2 mutations were detected in 32.78% (98/299) of the entire cohort; however, only 5.69% (17/299) had two confirmed pathogenic mutations. The most common mutation observed in this population was c.109G > A in the GJB2 gene, with an allelic frequency of 15.05% (90/598), which is significantly higher than that reported in previous cohorts. A total of 16 patients had two confirmed pathogenic SLC26A4 gene mutations, and 16 patients had one. The IVS7-2A > G mutation was the most commonly observed, with an allelic frequency of 3.51% (21/598). Three patients had a m.1555A > G mutation in the mtDNA 12S rRNA gene. CONCLUSIONS These results reveal that genetic etiology occurred in 11.71% (35/299) of patients, suggesting that Hainan province have a different mutational spectrum compare to Mainland China in non-syndromic deafness patients, which provide useful information to genetic counseling in Hainan province.
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Affiliation(s)
- Bangqing Huang
- Department of Otorhinolaryngology, Hainan Branch of PLA General Hospital, Sanya 572013, PR China
| | - Mingyu Han
- Department of Otorhinolaryngology, Hainan Branch of PLA General Hospital, Sanya 572013, PR China; Department of Otolaryngology and Genetic Testing Center for Deafness, Chinese PLA General Hospital, Beijing 100853, PR China
| | - Guojian Wang
- Department of Otolaryngology and Genetic Testing Center for Deafness, Chinese PLA General Hospital, Beijing 100853, PR China
| | - ShaSha Huang
- Department of Otolaryngology and Genetic Testing Center for Deafness, Chinese PLA General Hospital, Beijing 100853, PR China
| | - Jialing Zeng
- Department of Otorhinolaryngology, Hainan Branch of PLA General Hospital, Sanya 572013, PR China
| | - Yongyi Yuan
- Department of Otolaryngology and Genetic Testing Center for Deafness, Chinese PLA General Hospital, Beijing 100853, PR China.
| | - Pu Dai
- Department of Otolaryngology and Genetic Testing Center for Deafness, Chinese PLA General Hospital, Beijing 100853, PR China.
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Large scale newborn deafness genetic screening of 142,417 neonates in Wuhan, China. PLoS One 2018; 13:e0195740. [PMID: 29634755 PMCID: PMC5892933 DOI: 10.1371/journal.pone.0195740] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 03/28/2018] [Indexed: 11/19/2022] Open
Abstract
Almost one third of the three million people in China suffering severe deafness are children, and 50% of these cases are believed to have genetic components to their etiology. Newborn hearing genetic screening can complement Universal Neonatal Hearing Screening for the diagnosis of congenital hearing loss as well as identifying children at risk for late-onset and progressive hearing impairment. The aim of this joint academic and Ministry of Health project was to prototype a cost effective newborn genetic screen in a community health setting on a city-wide level, and to ascertain the prevalence of variation at loci that have been associated with non-syndromic hearing loss. With the participation of 143 local hospitals in the city of Wuhan, China we screened 142,417 neonates born between May 2014 and Dec. 2015. The variants GJB2 c.235delC, SLC26A4 c.919-2A>G, and mitochondrial variants m.1555A>G and m.1494C>T were assayed using real time PCR. Newborns found to carry a variant were re-assayed by sequencing in duplicate. Within a subset of 707 newborns we assayed using real-time PCR and ARMS-PCR to compare cost, sensitivity and operating procedure. The most frequent hearing loss associated allele detected in this population was the 235delC variant in GJB2 gene. In total, 4289 (3.01%) newborns were found to carry at least one allele of either GJB2 c.235delC, SLC26A4 c.919-2A>G or two assayed MT-RNR1 variants. There was complete accordance between the real-time PCR and the ARMS PCR, though the real-time PCR had a much lower failure rate. Real-time PCR had a lower cost and operating time than ARMS PCR. Ongoing collaboration with the participating hospitals will determine the specificity and sensitivity of the association of the variants with hearing loss at birth and arising in early childhood, allowing an estimation of the benefits of newborn hearing genetic screening in a large-scale community setting.
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Yang SM, Liu Y, Liu C, Yin AH, Wu YF, Zheng XE, Yang HM, Yang J. Hearing-loss-associated gene detection in neonatal intensive care unit. J Matern Fetal Neonatal Med 2018; 31:284-288. [PMID: 28093008 DOI: 10.1080/14767058.2017.1282454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
OBJECTIVE To investigate the frequency and mutation spectrum of hearing loss-associated gene mutation in Neonatal Intensive Care Unit (NICU). METHODS Neonates (n=2305) admitted to NICU were enrolled in this study. Nine prominent hearing loss-associated genes, GJB2 (35 del G, 176 del 16,235 del C, 299 del AT), GJB3 (538 C > T), SLC26A4 (IVS7-2A > G, 2168 A > G) and mtDNA 12S rRNA(1555 A > G, 1494 C > T), were detected. RESULT There were 73 cases hearing-loss-associated gene mutation among 2305 cases, the mutation frequency was 3.1%, with 40 cases GJB2 (235del C) mutation (54.8%), 6 cases GJB2 (299 del AT) mutation (8.2%), 21 cases SLC26A4 (IVS 7-2 A > G) mutation (28.7%), 4 cases SLC26A4 (2168 A > G) mutation (5.5%), 2 cases of GJB2 (235del C) combined SLC26A4 (IVS 7-2 A > G, 2168 A > G) mutation (2.8%). Among 73 gene mutation cases, preterm neonates presented in 18 cases, accounting for 24.7% (18/73); hyperbilirubinemia in 13 cases, accounting for 17.8% (13/73); Torch Syndrome in 15 cases, with 12 cases CMV, 2 cases rubella, 1 case toxoplasm, respectively, totally accounting for 20.54% (15/73); neonatal pneumonia in 12 cases, accounting for 16.4% (12/73); birth asphyxia in 5 cases, accounting for 6.9% (5/73); sepsis in 5 cases, accounting for 6.9% (5/73); others in 5 cases, accounting for 6.8% (5/73) . CONCLUSIONS The frequency of hearing loss-associated gene mutation was higher in NICU.There were hearing loss-associated gene mutations in the NICU, suggesting this mutation may complicate with perinatal high-risk factors.
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Affiliation(s)
- S M Yang
- a Department of Neonatology , Guangdong Women and Children Hospital , Guangzhou , China
| | - Ying Liu
- a Department of Neonatology , Guangdong Women and Children Hospital , Guangzhou , China
| | - C Liu
- b Prenatal Diagnosis Centre, Guangdong Women and Children Hospital , Guangzhou , China
| | - A H Yin
- b Prenatal Diagnosis Centre, Guangdong Women and Children Hospital , Guangzhou , China
| | - Y F Wu
- c Department of ENT , Guangdong Women and Children Hospital , Guangzhou , China
| | - X E Zheng
- a Department of Neonatology , Guangdong Women and Children Hospital , Guangzhou , China
| | - H M Yang
- a Department of Neonatology , Guangdong Women and Children Hospital , Guangzhou , China
| | - J Yang
- a Department of Neonatology , Guangdong Women and Children Hospital , Guangzhou , China
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Shaikh H, Waryah AM, Narsani AK, Iqbal M, Shahzad M, Waryah YM, Shaikh N, Mahmood A. Genetic Testing of Non-familial Deaf Patients for CIB2 and GJB2 Mutations: Phenotype and Genetic Counselling. Biochem Genet 2017; 55:410-420. [PMID: 29086887 DOI: 10.1007/s10528-017-9828-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 09/19/2017] [Indexed: 02/02/2023]
Abstract
CIB2 and GJB2 genes variants contribute significantly in familial cases of prelingual recessive hearing loss (HL). This study was aimed to determine the CIB2 and GJB2 variants and associated phenotype in 150 non-familial individuals with HL. After getting informed consent, 150 non-familial deaf patients were enrolled and blood samples were obtained for DNA extraction. Pure tone air conduction audiometry was performed. Coding exons of CIB2 and GJB2 genes were Sanger sequenced. A tetra primer ARMS assay was developed for recurrent CIB2 variant. Four bi-allelic GJB2 variants, c.71G>A p.(Trp24*), c.231G>A p.(Trp77*), c.235delC p.(Leu79Cysfs3*) and c.35delG p.(Gly11Leufs24*), were found in nine hearing impaired individuals. We also found four homozygotes and five carriers of c.380G>A p. (Arg127His) variant of controversial clinical significance. CIB2 sequencing revealed single recurrent variant c.272T>C p. (Phe91Ser) segregating with HL in ten individuals. Among our patients, c.71G>A (p.Trp24*) was the most common variant, accounted for 45% of GJB2 variants. Two known GJB2 variants, c.235delC p. (Leu79Cysfs3*) and c.310del14 p. (Lys105Argfs2*), are reported here for the first time in Pakistani population. Our data further support the benign nature of c.380G>A p. (Arg127His) variant. For CIB2, c.272T>C p. (Phe91Ser) is the second common cause of HL among our sporadic cases. Phenotypically, in our patients, individuals homozygous for GJB2 variants had profound HL, whereas CIB2 homozygotes had severe to profound prelingual HL. Our results suggest that GJB2 and CIB2 are common cause of HL in different Pakistani ethnicities.
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Affiliation(s)
- Hina Shaikh
- Molecular Biology and Genetics Department, Medical Research Center, Liaquat University of Medical and Health Sciences, Jamshoro, Pakistan
| | - Ali M Waryah
- Molecular Biology and Genetics Department, Medical Research Center, Liaquat University of Medical and Health Sciences, Jamshoro, Pakistan.
| | - Ashok K Narsani
- Institute of Ophthalmology, Liaquat University of Medical and Health Sciences, Jamshoro, Pakistan
| | - Muhammad Iqbal
- Department of Biochemistry and Biotechnology, Islamia University, Bahawalpur, Pakistan
| | - Mohsin Shahzad
- Department of Molecular Biology, Shaheed Zulfiqar Ali Bhutto Medical University, Islamabad, Pakistan
| | - Yar M Waryah
- Molecular Biology and Genetics Department, Medical Research Center, Liaquat University of Medical and Health Sciences, Jamshoro, Pakistan
| | - Naila Shaikh
- Molecular Biology and Genetics Department, Medical Research Center, Liaquat University of Medical and Health Sciences, Jamshoro, Pakistan
| | - Amber Mahmood
- Molecular Biology and Genetics Department, Medical Research Center, Liaquat University of Medical and Health Sciences, Jamshoro, Pakistan
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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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