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Lin L, Zhang Y, Pan H, Wang J, Qi Y, Ma Y. Inconsistencies between prenatal diagnostic and genetic testing laboratories on variant validation of rare monogenic diseases. Prenat Diagn 2024; 44:1053-1061. [PMID: 38898598 DOI: 10.1002/pd.6628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 05/14/2024] [Accepted: 06/10/2024] [Indexed: 06/21/2024]
Abstract
BACKGROUND The advent of next-generation sequencing (NGS) has enhanced the diagnostic efficacy for monogenic diseases, while presenting challenges in achieving consistent diagnoses. METHOD We retrospectively analyzed the concordance rate and reasons for the inconsistency between the original diagnostic result from the genetic testing laboratory and the variant validation result from the prenatal diagnostic center. The validation procedure comprised three stages: validation of variant detection, reevaluation of variant classification, and assessment of recurrence risk, which involved verifying the mode of inheritance and parental carriage. RESULT In total, 17 (6%) of the 286 families affected by rare monogenic diseases showed different results during the variant validation procedure. These cases comprised four (23.5%) with variant detection errors, 12 (70.5%) with inconsistent interpretation, and one (6%) with non-Mendelian inheritance patterns. False-positive NGS results confirmed by Sanger sequencing were related to pseudogenes and GC-rich regions. The classification of the 17 variants was altered in the 12 cases owing to various factors. The case with an atypical inheritance pattern was originally considered autosomal recessive inheritance, but was diagnosed as maternal uniparental disomy after additional genetic analysis. CONCLUSION We underscored the significance of variant validation by prenatal diagnostic centers. Families affected by monogenic diseases with reproductive plans should be referred to prenatal genetic centers as early as possible to avoid different results that may postpone subsequent prenatal diagnosis.
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Affiliation(s)
- Liling Lin
- Department of Central Laboratory, Peking University First Hospital, Beijing, China
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Beijing, China
| | - Ying Zhang
- Department of Central Laboratory, Peking University First Hospital, Beijing, China
| | - Hong Pan
- Department of Central Laboratory, Peking University First Hospital, Beijing, China
| | - Jingmin Wang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Yu Qi
- Department of Central Laboratory, Peking University First Hospital, Beijing, China
| | - Yinan Ma
- Department of Central Laboratory, Peking University First Hospital, Beijing, China
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2
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Ford CL, Riggs WJ, Quigley T, Keifer OP, Whitton JP, Valayannopoulos V. The natural history, clinical outcomes, and genotype-phenotype relationship of otoferlin-related hearing loss: a systematic, quantitative literature review. Hum Genet 2023; 142:1429-1449. [PMID: 37679651 PMCID: PMC10511631 DOI: 10.1007/s00439-023-02595-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 08/09/2023] [Indexed: 09/09/2023]
Abstract
Congenital hearing loss affects one in 500 newborns. Sequence variations in OTOF, which encodes the calcium-binding protein otoferlin, are responsible for 1-8% of congenital, nonsyndromic hearing loss and are the leading cause of auditory neuropathy spectrum disorders. The natural history of otoferlin-related hearing loss, the relationship between OTOF genotype and hearing loss phenotype, and the outcomes of clinical practices in patients with this genetic disorder are incompletely understood because most analyses have reported on small numbers of cases with homogeneous OTOF genotypes. Here, we present the first systematic, quantitative literature review of otoferlin-related hearing loss, which analyzes patient-specific data from 422 individuals across 61 publications. While most patients display a typical phenotype of severe-to-profound hearing loss with prelingual onset, 10-15% of patients display atypical phenotypes, including mild-to-moderate, progressive, and temperature-sensitive hearing loss. Patients' phenotypic presentations appear to depend on their specific genotypes. For example, non-truncating variants located in and immediately downstream of the C2E calcium-binding domain are more likely to produce atypical phenotypes. Additionally, the prevalence of certain sequence variants and their associated phenotypes varies between populations due to evolutionary founder effects. Our analyses also suggest otoacoustic emissions are less common in older patients and those with two truncating OTOF variants. Critically, our review has implications for the application and limitations of clinical practices, including newborn hearing screenings, hearing aid trials, cochlear implants, and upcoming gene therapy clinical trials. We conclude by discussing the limitations of available research and recommendations for future studies on this genetic cause of hearing loss.
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Kim SY, Lee S, Seo GH, Kim BJ, Oh DY, Han JH, Park MK, Lee SM, Kim B, Yi N, Kim NJ, Koh DH, Hwang S, Keum C, Choi BY. Powerful use of automated prioritization of candidate variants in genetic hearing loss with extreme etiologic heterogeneity. Sci Rep 2021; 11:19476. [PMID: 34593925 PMCID: PMC8484668 DOI: 10.1038/s41598-021-99007-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 08/17/2021] [Indexed: 01/02/2023] Open
Abstract
Variant prioritization of exome sequencing (ES) data for molecular diagnosis of sensorineural hearing loss (SNHL) with extreme etiologic heterogeneity poses a significant challenge. This study used an automated variant prioritization system (“EVIDENCE”) to analyze SNHL patient data and assess its diagnostic accuracy. We performed ES of 263 probands manifesting mild to moderate or higher degrees of SNHL. Candidate variants were classified according to the 2015 American College of Medical Genetics guidelines, and we compared the accuracy, call rates, and efficiency of variant prioritizations performed manually by humans or using EVIDENCE. In our in silico panel, 21 synthetic cases were successfully analyzed by EVIDENCE. In our cohort, the ES diagnostic yield for SNHL by manual analysis was 50.19% (132/263) and 50.95% (134/263) by EVIDENCE. EVIDENCE processed ES data 24-fold faster than humans, and the concordant call rate between humans and EVIDENCE was 97.72% (257/263). Additionally, EVIDENCE outperformed human accuracy, especially at discovering causative variants of rare syndromic deafness, whereas flexible interpretations that required predefined specific genotype–phenotype correlations were possible only by manual prioritization. The automated variant prioritization system remarkably facilitated the molecular diagnosis of hearing loss with high accuracy and efficiency, fostering the popularization of molecular genetic diagnosis of SNHL.
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Affiliation(s)
- So Young Kim
- Department of Otorhinolaryngology-Head and Neck Surgery, CHA Bundang Medical Center, CHA University, Seongnam, Republic of Korea
| | - Seungmin Lee
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Bundang Hospital, Seongnam, Republic of Korea.,R&D Center, ENCell Co. Ltd, Seoul, Republic of Korea
| | - Go Hun Seo
- 3billion, Inc., Seoul, Republic of Korea
| | - Bong Jik Kim
- Department of Otolaryngology-Head and Neck Surgery, Chungnam National University Sejong Hospital, College of Medicine, Chungnam National University, Daejeon, Republic of Korea
| | - Doo Yi Oh
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
| | - Jin Hee Han
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
| | - Moo Kyun Park
- Department of Otorhinolaryngology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - So Min Lee
- Department of Otorhinolaryngology-Head and Neck Surgery, CHA Bundang Medical Center, CHA University, Seongnam, Republic of Korea
| | - Bonggi Kim
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
| | - Nayoung Yi
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
| | - Namju Justin Kim
- Department of Biological Sciences, Vanderbilt University, Nashville, USA
| | - Doo Hyun Koh
- Department of Biomedical Science, The Graduate School, CHA University, Seongnam, Republic of Korea
| | - Sohyun Hwang
- Department of Biomedical Science, The Graduate School, CHA University, Seongnam, Republic of Korea.,Department of Pathology, CHA University, CHA Bundang Medical Center, Seongnam, Republic of Korea
| | | | - Byung Yoon Choi
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Bundang Hospital, Seongnam, Republic of Korea.
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4
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Xiang YB, Xu CY, Xu YZ, Li HZ, Zhou LL, Xu XQ, Chen ZH, Tang SH. Next-generation sequencing identifies rare pathogenic and novel candidate variants in a cohort of Chinese patients with syndromic or nonsyndromic hearing loss. Mol Genet Genomic Med 2020; 8:e1539. [PMID: 33095980 PMCID: PMC7767562 DOI: 10.1002/mgg3.1539] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 09/27/2020] [Accepted: 10/02/2020] [Indexed: 11/15/2022] Open
Abstract
Background Hearing loss (HL) is a common sensory disorder in humans characterized by extreme clinical and genetic heterogeneity. In recent years, next‐generation sequencing (NGS) technologies have proven to be highly effective and powerful tools for population genetic studies of HL. Here, we analyzed clinical and molecular data from 21 Chinese deaf families who did not have hotspot mutations in the common deafness genes GJB2, SLC26A4, GJB3, and MT‐RNR1. Method Targeted next‐generation sequencing (TGS) of 127 known deafness genes was performed in probands of 12 families, while whole‐exome sequencing (WES) or trio‐WES was used for the remaining nine families. Results Potential pathogenic mutations in a total of 12 deafness genes were identified in 13 probands; the mutations were observed in GJB2, CDH23, EDNRB, MYO15A, OTOA, OTOF, TBC1D24, SALL1, TMC1, TWNK, USH1C, and USH1G, with eight of the identified mutations being novel. Further, a copy number variant (CNV) was detected in one proband with heterozygous deletion of chromosome 4p16.3‐4p15.32. Thus, the total diagnostic rate using NGS in our deafness patients reached 66.67% (14/21). Conclusions These results expand the mutation spectrum of deafness‐causing genes and provide support for the use of NGS detection technologies for routine molecular diagnosis in Chinese deaf populations.
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Affiliation(s)
- Yan-Bao Xiang
- 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
| | - Yun-Zhi Xu
- Key Laboratory of Birth Defects, Department of Genetics, Wenzhou Central Hospital, Wenzhou, China
| | - Huan-Zheng Li
- Key Laboratory of Birth Defects, Department of Genetics, Wenzhou Central Hospital, Wenzhou, China
| | - Li-Li Zhou
- Key Laboratory of Birth Defects, Department of Genetics, Wenzhou Central Hospital, Wenzhou, China
| | - Xue-Qin Xu
- Key Laboratory of Birth Defects, Department of Genetics, Wenzhou Central Hospital, Wenzhou, China
| | - Zi-Hui Chen
- Key laboratory of Medical Genetic, School of Laboratory Medicine and Life Science, Wenzhou Medical University, 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
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Yawn RJ, Nassiri AM, Rivas A. Auditory Neuropathy: Bridging the Gap Between Hearing Aids and Cochlear Implants. Otolaryngol Clin North Am 2019; 52:349-355. [PMID: 30765091 DOI: 10.1016/j.otc.2018.11.016] [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: 10/27/2022]
Abstract
Auditory neuropathy spectrum disorder (ANSD) is a complex and heterogeneous disorder associated with altered neural synchrony with respect to auditory stimuli. Patients have characteristic auditory findings including normal otoacoustic emissions in the setting of abnormal auditory brainstem response. Patients with ANSD have a high incidence of comorbid developmental delay that may impact speech outcomes. Treatment options for ANSD include hearing amplification and cochlear implantation. The article highlights issues and controversies with the diagnosis and treatment of this complex disorder.
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Affiliation(s)
- Robert J Yawn
- The Otology Group of Vanderbilt, Department of Otolaryngology-Head and Neck Surgery, Vanderbilt University Medical Center, 7209 Medical Center East, South Tower 1215 21st Avenue South, Nashville, TN 37232-8605, USA
| | - Ashley M Nassiri
- The Otology Group of Vanderbilt, Department of Otolaryngology-Head and Neck Surgery, Vanderbilt University Medical Center, 7209 Medical Center East, South Tower 1215 21st Avenue South, Nashville, TN 37232-8605, USA
| | - Alejandro Rivas
- The Otology Group of Vanderbilt, Department of Otolaryngology-Head and Neck Surgery, Vanderbilt University Medical Center, 7209 Medical Center East, South Tower 1215 21st Avenue South, Nashville, TN 37232-8605, USA.
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6
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Pandey N, Rashid T, Jalvi R, Sharma M, Rangasayee R, Andrabi KI, Anand A. Mutations in OTOF, CLDN14 & SLC26A4 genes as major causes of hearing impairment in Dhadkai village, Jammu & Kashmir, India. Indian J Med Res 2018; 146:489-497. [PMID: 29434063 PMCID: PMC5819031 DOI: 10.4103/ijmr.ijmr_635_15] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Background & objectives: A high incidence of hearing impairment is reported from the village of Dhadkai in the State of Jammu and Kashmir, India. Prevalence of endogamy in this community suggested a common genetic basis for the disorder. A genetic study was undertaken to ascertain the basis for the high incidence of hearing impairment in this region. Methods: In a two-step approach to identify the causative mutation/s, a whole-genome-based linkage analysis of an extended family of 45 members was carried out, which included 23 affected and 22 unaffected members. Mutational analysis for the candidate deafness genes helped reveal causative mutations in the family. In addition, seven deafness-causing genes, Cx26, SLC26A4, CLDN14, TMPRSS3, TMC1, TMIE and USH1C, were analyzed in smaller families with hearing impairment. Results: In the 45-member extended family, the critical chromosomal region mapped to 2p24-p22. The c.2122C>T (p.R708X) mutation in OTOF in 2p24-p22was identified as being the causal change. Linkage to 2p24-p22 locus was not observed in a particular branch of this extended family. Analysis of seven known deafness-causing genes in this branch revealed a mutation, c.254T>A (p.V85D), in CLDN14. Among seven small families unrelated to the 45-member extended family, hearing loss was attributable to p.R708X in OTOF in three families and to p.V85D in CLDN14 in one family; a new mutation c.1668T>A (p.Y556X) SLC26A4 was identified in two families and the causative change could not be identified in one family. Interpretation & conclusions: This study suggested considerable genetic heterogeneity in the causation of hearing loss in Dhadkai. Recessive mutations were observed in at least three genes causing hearing loss: OTOF (p.R708X), SLC26A4 (p.Y556X) and CLDN14 (p.V85D). Mutation p.R708X appeared to be the major cause of hearing impairment in Dhadkai.
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Affiliation(s)
- Nishtha Pandey
- Molecular Biology & Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research; Centre for Human Genetics, Bengaluru, India
| | - Tabassum Rashid
- Department of Biotechnology, The University of Kashmir, Srinagar, India
| | - Rajeev Jalvi
- Department of Audiology, Ali Yavar Jung National Institute for the Hearing Handicapped, Mumbai, India
| | - Meenakshi Sharma
- Molecular Biology & Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, India
| | - Raghunath Rangasayee
- Department of Audiology, Ali Yavar Jung National Institute for the Hearing Handicapped, Mumbai, India
| | | | - Anuranjan Anand
- Molecular Biology & Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, India
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7
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Lang-Roth R, Fischer-Krall E, Kornblum C, Nürnberg G, Meschede D, Goebel I, Nürnberg P, Beutner D, Kubisch C, Walger M, Volk AE. AUNA2: A Novel Type of Non-Syndromic Slowly Progressive Auditory Synaptopathy/Auditory Neuropathy with Autosomal-Dominant Inheritance. Audiol Neurootol 2017; 22:30-40. [PMID: 28601886 DOI: 10.1159/000474929] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 03/31/2017] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Auditory synaptopathy/neuropathy (AS/AN) is a heterogeneous disorder, which may be caused by environmental factors like postnatal hyperbilirubinemia or by genetic factors. The genetic forms are subdivided into syndromic and non-syndromic types, and show different inheritance patterns with a strong preponderance of autosomal-recessive forms. To date, only a single locus for non-syndromic autosomal-dominant AS/AN (AUNA1) has been reported in a single family, in which a non-coding DIAPH3 mutation was subsequently described as causative. MATERIALS AND METHODS Here, we report detailed clinical data on a large German AS/AN family with slowly progressive postlingual hearing loss. Affected family members developed their first symptoms in their second decade. Moderate hearing loss in the fourth decade then progressed to profound hearing impairment in older family members. Comprehensive audiological and neurological tests were performed in the affected family members. Genetic testing comprised linkage analyses with polymorphic markers and a genome-wide linkage analysis using the Affymetrix GeneChip® Human Mapping 250K. RESULTS AND CONCLUSION We identified a large family with autosomal-dominant AS/AN. By means of linkage analyses, the AUNA1 locus was excluded, and putatively linked regions on chromosomal bands 12q24 and 13q34 were identified as likely carrying the second locus for autosomal-dominant AS/AN (AUNA2). AUNA2 is associated with a slowly progressive postlingual hearing loss without any evidence for additional symptoms in other organ systems.
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Affiliation(s)
- Ruth Lang-Roth
- Department of Otorhinolaryngology, Head and Neck Surgery, University of Cologne, Cologne, Germany
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8
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Zhang QJ, Han B, Lan L, Zong L, Shi W, Wang HY, Xie LY, Wang H, Zhao C, Zhang C, Yin ZF, Wang DY, Petit C, Guan J, Wang QJ. High frequency of OTOF mutations in Chinese infants with congenital auditory neuropathy spectrum disorder. Clin Genet 2016; 90:238-46. [PMID: 26818607 DOI: 10.1111/cge.12744] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2015] [Revised: 01/21/2016] [Accepted: 01/22/2016] [Indexed: 11/30/2022]
Abstract
Auditory neuropathy spectrum disorder (ANSD) is one of the most common diseases leading to hearing and speech communication barriers in infants and young children. The OTOF gene is the first gene identified for autosomal recessive non-syndromic ANSD, and patients with OTOF mutations have shown marked improvement of auditory functions from the cochlear implantation, but the true involvement of OTOF mutations in Chinese ANSD patients is still unknown which precludes the effective management of this disease. Here, we investigated the contribution of OTOF mutations to congenital ANSD patients in China. In all, 37 infants and young Children with ANSD were screened for all the exons of OTOF gene, of them 34 patients had no neonatal risk factors who were considered as congenital ANSD. The clinical manifestation and audiometric features were also investigated and compared in patients with and without OTOF mutations. In all, 14 of these subjects were shown to carry two or three mutant alleles of OTOF with the high frequency of 41.2% in congenital ANSD patients. In total, 15 novel pathogenic mutations and 10 reported mutations were identified. Our results confirmed that mutations in OTOF gene were a major cause of congenital ANSD in China. Identification of OTOF mutations can facilitate diagnosis, clinical intervention and counseling for congenital ANSD.
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Affiliation(s)
- Q-J Zhang
- Department of Otolaryngology/ Head and Neck Surgery, Chinese PLA Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, China
| | - B Han
- Department of Otolaryngology/ Head and Neck Surgery, Chinese PLA Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, China
| | - L Lan
- Department of Otolaryngology/ Head and Neck Surgery, Chinese PLA Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, China
| | - L Zong
- Department of Otolaryngology/ Head and Neck Surgery, Chinese PLA Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, China
| | - W Shi
- Department of Otolaryngology/ Head and Neck Surgery, Chinese PLA Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, China
| | - H-Y Wang
- Department of Otolaryngology/ Head and Neck Surgery, Chinese PLA Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, China
| | - L-Y Xie
- Department of Otolaryngology/ Head and Neck Surgery, Chinese PLA Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, China
| | - H Wang
- Department of Otolaryngology/ Head and Neck Surgery, Chinese PLA Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, China
| | - C Zhao
- Department of Otolaryngology/ Head and Neck Surgery, Chinese PLA Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, China
| | - C Zhang
- Department of Otolaryngology/ Head and Neck Surgery, Chinese PLA Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, China
| | - Z-F Yin
- Department of Otolaryngology/ Head and Neck Surgery, Chinese PLA Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, China
| | - D-Y Wang
- Department of Otolaryngology/ Head and Neck Surgery, Chinese PLA Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, China
| | - C Petit
- Unité de Génétique et Physiologie de l'Audition, Institut Pasteur, Collège de France, Paris, France
| | - J Guan
- Department of Otolaryngology/ Head and Neck Surgery, Chinese PLA Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, China
| | - Q-J Wang
- Department of Otolaryngology/ Head and Neck Surgery, Chinese PLA Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, China
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9
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Zhang LP, Chai YC, Yang T, Wu H. Identification of novel OTOF compound heterozygous mutations by targeted next-generation sequencing in a Chinese patient with auditory neuropathy spectrum disorder. Int J Pediatr Otorhinolaryngol 2013; 77:1749-52. [PMID: 24001616 DOI: 10.1016/j.ijporl.2013.08.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/04/2013] [Revised: 08/02/2013] [Accepted: 08/06/2013] [Indexed: 11/19/2022]
Abstract
OBJECTIVES The molecular causes of auditory neuropathy spectrum disorder (ANSD) are not well known. Identification of the pathogenic mutations underlying nonsyndromic ANSD is difficult because of its extremely heterogeneous trait. The aim of the present study was to identify the genetic etiology of a single Chinese patient diagnosed with congenital ANSD by targeted next-generation sequencing. METHODS Targeted next-generation sequencing of 79 known deafness genes was performed in a child that was clinically diagnosed with ANSD and received cochlear implantation. Candidate pathogenic variants were confirmed by Sanger sequencing. Post-implantation outcome were evaluated in a 40 months span. RESULTS Novel compound heterozygous mutations p.R1583H/p.Q1883X in OTOF were identified as the pathogenic cause of the patient, correlated with a good post-implantation outcome in terms of sound detection and communication skills. CONCLUSION Targeted next-generation sequencing is effective for molecular diagnosis of ANSD and may provide important information for clinical management of this disease.
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Affiliation(s)
- Lu-ping Zhang
- Department of Otolaryngology-Head and Neck Surgery, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200092, China; Ear Institute, Shanghai Jiaotong University, Shanghai 200092, China
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10
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Iwasa YI, Nishio SY, Yoshimura H, Kanda Y, Kumakawa K, Abe S, Naito Y, Nagai K, Usami SI. OTOF mutation screening in Japanese severe to profound recessive hearing loss patients. BMC MEDICAL GENETICS 2013; 14:95. [PMID: 24053799 PMCID: PMC3849620 DOI: 10.1186/1471-2350-14-95] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Accepted: 08/27/2013] [Indexed: 12/21/2022]
Abstract
BACKGROUND Auditory neuropathy spectrum disorder (ANSD) is a unique form of hearing loss that involves absence or severe abnormality of auditory brainstem response (ABR), but also the presence of otoacoustic emissions (OAEs). However, with age, the OAEs disappear, making it difficult to distinguish this condition from other nonsyndromic hearing loss. Therefore, the frequency of ANSD may be underestimated. The aim of this study was to determine what portion of nonsyndromic hearing loss is caused by mutations of OTOF, the major responsible gene for nonsyndromic ANSD. METHODS We screened 160 unrelated Japanese with severe to profound recessive nonsyndromic hearing loss (ARNSHL) without GJB2 or SLC26A4 mutations, and 192 controls with normal hearing. RESULTS We identified five pathogenic OTOF mutations (p.D398E, p.Y474X, p.N727S, p.R1856Q and p.R1939Q) and six novel, possibly pathogenic variants (p.D450E, p.W717X, p.S1368X, p.R1583H, p.V1778I, and p.E1803A). CONCLUSIONS The present study showed that OTOF mutations accounted for 3.2-7.3% of severe to profound ARNSHL patients in Japan. OTOF mutations are thus a frequent cause in the Japanese deafness population and mutation screening should be considered regardless of the presence/absence of OAEs.
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Affiliation(s)
- Yoh-ichiro Iwasa
- Department of Otorhinolaryngology, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, Nagano 390-8621, Japan.
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11
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Bae SH, Baek JI, Lee JD, Song MH, Kwon TJ, Oh SK, Jeong JY, Choi JY, Lee KY, Kim UK. Genetic analysis of auditory neuropathy spectrum disorder in the Korean population. Gene 2013; 522:65-9. [PMID: 23562982 DOI: 10.1016/j.gene.2013.02.057] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Revised: 02/19/2013] [Accepted: 02/21/2013] [Indexed: 10/27/2022]
Abstract
Auditory neuropathy spectrum disorder (ANSD) is caused by dys-synchronous auditory neural response as a result of impairment of the functions of the auditory nerve or inner hair cells, or synapses between inner hair cells and the auditory nerve. To identify a causative gene causing ANSD in the Korean population, we conducted gene screening of the OTOF, DIAPH3, and PJVK genes in 19 unrelated Korean patients with ANSD. A novel nonsense mutation (p.Y1064X) and a known pathogenic mutation (p.R1939Q) of the OTOF gene were identified in a patient as compound heterozygote. Pedigree analysis for these mutations showed co-segregation of mutation genotype and the disease in the family, and it supported that the p.Y1064X might be a novel genetic cause of autosomal recessive ANSD. A novel missense variant p.K1017R (c.3050A>G) in the DIAPH3 gene was also identified in the heterozygous state. In contrast, no mutation was detected in the PJVK gene. These results indicate that no major causative gene has been reported to date in the Korean population and that pathogenic mutations in undiscovered candidate genes may have an effect on ANSD.
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Affiliation(s)
- Seung-Hyun Bae
- Department of Biology, College of Natural Sciences, Kyungpook National University, Daegu, South Korea
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12
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Mahdieh N, Shirkavand A, Rabbani B, Tekin M, Akbari B, Akbari MT, Zeinali S. Screening of OTOF mutations in Iran: a novel mutation and review. Int J Pediatr Otorhinolaryngol 2012; 76:1610-5. [PMID: 22906306 DOI: 10.1016/j.ijporl.2012.07.030] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2012] [Revised: 07/21/2012] [Accepted: 07/27/2012] [Indexed: 10/28/2022]
Abstract
OBJECTIVE Mutations in OTOF have been reported to cause nonsyndromic hearing loss in different populations. The purpose of this study is screening of OTOF mutations in Iranian population. METHODS Thirty-eight consanguineous families affected with autosomal recessive nonsyndromic hearing loss (ARNSHL) and negative for GJB2 or GJB6 mutations were screened by autozygosity mapping and Sanger sequencing to find OTOF mutations. RESULTS A novel homozygous frameshift mutation (c.1981dupG) was found to cause hearing loss in one family and no other OTOF variants were detected in the remaining families. The affected individuals were homozygous forp. D661GfsX2 causing defect in long isoform of otoferlin. CONCLUSIONS We conclude that OTOF mutations are not the major cause of ARNSHL in the Iranian population but still may play an important role in HL; therefore evaluation the OTOF gene is of concern.
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Affiliation(s)
- Nejat Mahdieh
- Medical Genetic Group, Faculty of Medicine, Ilam University of Medical Sciences, Ilam, Iran.
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