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Guan J, Wu X, Zhang J, Li J, Wang H, Wang Q. Global research landscape on the contribution of de novo mutations to human genetic diseases over the past 20 years: bibliometric analysis. J Neurogenet 2024:1-10. [PMID: 38647210 DOI: 10.1080/01677063.2024.2335171] [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: 01/12/2024] [Accepted: 03/21/2024] [Indexed: 04/25/2024]
Abstract
As the contribution of de novo mutations (DNMs) to human genetic diseases has been gradually uncovered, analyzing the global research landscape over the past 20 years is essential. Because of the large and rapidly increasing number of publications in this field, understanding the current landscape of the contribution of DNMs in the human genome to genetic diseases remains a challenge. Bibliometric analysis provides an approach for visualizing these studies using information in published records in a specific field. This study aimed to illustrate the current global research status and explore trends in the field of DNMs underlying genetic diseases. Bibliometric analyses were performed using the Bibliometrix Package based on the R language version 4.1.3 and CiteSpace version 6.1.R2 software for publications from 2000 to 2021 indexed under the Web of Science Core Collection (WoSCC) about DNMs underlying genetic diseases on 17 September 2022. We identified 3435 records, which were published in 731 journals by 26,538 authors from 6052 institutes in 66 countries. There was an upward trend in the number of publications since 2013. The USA, China, and Germany contributed the majority of the records included. The University of Washington, Columbia University, and Baylor College of Medicine were the top-producing institutions. Evan E Eichler of the University of Washington, Stephan J Sanders of the Yale University School of Medicine, and Ingrid E Scheffer of the University of Melbourne were the most high-ranked authors. Keyword co-occurrence analysis suggested that DNMs in neurodevelopmental disorders and intellectual disabilities were research hotspots and trends. In conclusion, our data show that DNMs have a significant effect on human genetic diseases, with a noticeable increase in annual publications over the last 5 years. Furthermore, potential hotspots are shifting toward understanding the causative role and clinical interpretation of newly identified or low-frequency DNMs observed in patients.
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Affiliation(s)
- Jing Guan
- Senior Department of Otolaryngology-Head & Neck Surgery, the Sixth Medical Center of PLA General Hospital, Beijing, PR China
- National Clinical Research Center for Otolaryngologic Diseases, Beijing, PR China
- State Key Laboratory of Hearing and Balance Science, Beijing, PR China
| | - Xiaonan Wu
- Senior Department of Otolaryngology-Head & Neck Surgery, the Sixth Medical Center of PLA General Hospital, Beijing, PR China
- National Clinical Research Center for Otolaryngologic Diseases, Beijing, PR China
- State Key Laboratory of Hearing and Balance Science, Beijing, PR China
| | - Jiao Zhang
- Senior Department of Otolaryngology-Head & Neck Surgery, the Sixth Medical Center of PLA General Hospital, Beijing, PR China
- National Clinical Research Center for Otolaryngologic Diseases, Beijing, PR China
- State Key Laboratory of Hearing and Balance Science, Beijing, PR China
| | - Jin Li
- Senior Department of Otolaryngology-Head & Neck Surgery, the Sixth Medical Center of PLA General Hospital, Beijing, PR China
- National Clinical Research Center for Otolaryngologic Diseases, Beijing, PR China
- State Key Laboratory of Hearing and Balance Science, Beijing, PR China
| | - Hongyang Wang
- Senior Department of Otolaryngology-Head & Neck Surgery, the Sixth Medical Center of PLA General Hospital, Beijing, PR China
- National Clinical Research Center for Otolaryngologic Diseases, Beijing, PR China
- State Key Laboratory of Hearing and Balance Science, Beijing, PR China
| | - Qiuju Wang
- Senior Department of Otolaryngology-Head & Neck Surgery, the Sixth Medical Center of PLA General Hospital, Beijing, PR China
- National Clinical Research Center for Otolaryngologic Diseases, Beijing, PR China
- State Key Laboratory of Hearing and Balance Science, Beijing, PR China
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Reda Del Barrio S, García Fernández A, Quesada-Espinosa JF, Sánchez-Calvín MT, Gómez-Manjón I, Sierra-Tomillo O, Juárez-Rufián A, de Vergas Gutiérrez J. Genetic diagnosis of childhood sensorineural hearing loss. ACTA OTORRINOLARINGOLOGICA ESPANOLA 2024; 75:83-93. [PMID: 38224868 DOI: 10.1016/j.otoeng.2023.07.002] [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: 03/24/2023] [Accepted: 07/03/2023] [Indexed: 01/17/2024]
Abstract
INTRODUCTION Congenital/early-onset sensorineural hearing loss (SNHL) is one of the most common hereditary disorders in our environment. There is increasing awareness of the importance of an etiologic diagnosis, and genetic testing with next-generation sequencing (NGS) has the highest diagnostic yield. Our study shows the genetic results obtained in a cohort of patients with bilateral congenital/early-onset SNHL. MATERIALS AND METHODS We included 105 children with bilateral SNHL that received genetic testing between 2019 and 2022. Genetic tests were performed with whole exome sequencing, analyzing genes related to hearing loss (virtual panel with 244 genes). RESULTS 48% (50/105) of patients were genetically diagnosed. We identified pathogenic and likely pathogenic variants in 26 different genes, and the most frequently mutated genes were GJB2, USH2A and STRC. 52% (26/50) of variants identified produced non-syndromic hearing loss, 40% (20/50) produced syndromic hearing loss, and the resting 8% (4/50) could produce both non-syndromic and syndromic hearing loss. CONCLUSIONS Genetic testing plays a vital role in the etiologic diagnosis of bilateral SNHL. Our cohort shows that genetic testing with NGS has a high diagnostic yield and can provide useful information for the clinical workup of patients.
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Affiliation(s)
- Sara Reda Del Barrio
- Servicio de Otorrinolaringología, Hospital Universitario 12 de Octubre, Madrid, Spain.
| | | | | | | | - Irene Gómez-Manjón
- Servicio de Genética, Hospital Universitario 12 de Octubre, Madrid, Spain
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Wang L, Liu G, Ma D, Zeng H, Wang Y, Luo C, Zhang J, Xu Z. Next-generation sequencing for genetic testing of hearing loss populations. Clin Chim Acta 2024; 552:117693. [PMID: 38056549 DOI: 10.1016/j.cca.2023.117693] [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: 07/14/2023] [Revised: 12/03/2023] [Accepted: 12/03/2023] [Indexed: 12/08/2023]
Abstract
BACKGROUND AND AIMS Hearing loss is a common sensorineural disease with genetic heterogeneity. More than 140 genes are known to cause hereditary hearing loss. We aim to uncover the etiologies of hearing loss and provide patients with reasonable reproductive choices. MATERIALS AND METHODS Total 825 participants were recruited, including 74 individuals, 47 couples, and 219 families, to identify the molecular etiologies of hearing loss using next-generation sequencing (NGS). Novel mutations were verified with a minigene splicing assay and the construction of three-dimensional protein models. RESULTS A positive molecular diagnosis was obtained for 244 patients, a rate of 63.05 %. Total 470 mutations were identified in 18 causative genes in positive patients. The most common genes mutated were GJB2 and SLC26A4. 47 novel mutations were identified. Further analysis predicted that two splicing mutations would cause abnormal mRNA splicing and three missense mutations would affect the protein structure. The results of prenatal diagnosis showed that the genotypes of 15 fetuses were the same as the probands. CONCLUSION Our findings expand the mutation spectrum of hearing loss and highlight the importance of genetic diagnosis and prenatal diagnosis to allow accurate and personalized guidance for those at high risk of deafness.
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Affiliation(s)
- Lulu Wang
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing 210004, Jiangsu, China
| | - Gang Liu
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing 210004, Jiangsu, China
| | - Dingyuan Ma
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing 210004, Jiangsu, China
| | - Huasha Zeng
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing 210004, Jiangsu, China
| | - Yuguo Wang
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing 210004, Jiangsu, China
| | - Chunyu Luo
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing 210004, Jiangsu, China
| | - Jingjing Zhang
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing 210004, Jiangsu, China.
| | - Zhengfeng Xu
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing 210004, Jiangsu, China.
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李 丹, 王 洪, 王 秋. [Splicing mutations of GSDME cause late-onset non-syndromic hearing loss]. LIN CHUANG ER BI YAN HOU TOU JING WAI KE ZA ZHI = JOURNAL OF CLINICAL OTORHINOLARYNGOLOGY, HEAD, AND NECK SURGERY 2024; 38:30-37. [PMID: 38297846 PMCID: PMC11116152 DOI: 10.13201/j.issn.2096-7993.2024.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Indexed: 02/02/2024]
Abstract
Objective:To dentify the genetic and audiological characteristics of families affected by late-onset hearing loss due to GSDMEgene mutations, aiming to explore clinical characteristics and pathogenic mechanisms for providing genetic counseling and intervention guidance. Methods:Six families with late-onset hearing loss from the Chinese Deafness Genome Project were included. Audiological tests, including pure-tone audiometry, acoustic immittance, speech recognition scores, auditory brainstem response, and distortion product otoacoustic emission, were applied to evaluate the hearing levels of patients. Combining with medical history and physical examination to analyze the phenotypic differences between the probands and their family members. Next-generation sequencing was used to identify pathogenic genes in probands, and validations were performed on their relatives by Sanger sequencing. Pathogenicity analysis was performed according to the American College of Medical Genetics and Genomics Guidelines. Meanwhile, the pathogenic mechanisms of GSDME-related hearing loss were explored combining with domestic and international research progress. Results:Among the six families with late-onset hearing loss, a total of 30 individuals performed hearing loss. The onset of hearing loss in these families ranged from 10 to 50 years(mean age: 27.88±9.74 years). In the study, four splicing mutations of the GSDME were identified, including two novel variants: c. 991-7C>G and c. 1183+1G>T. Significantly, the c. 991-7C>G was a de novo variant. The others were previously reported variants: c. 991-1G>C and c. 991-15_991-13del, the latter was identified in three families. Genotype-phenotype correlation analysis revealed that probands with the c. 991-7C>G and c. 1183+1G>T performed a predominantly high-frequency hearing loss. The three families carrying the same mutation exhibited varying degrees of hearing loss, with an annual rate of hearing deterioration exceeding 0.94 dB HL/year. Furthermore, follow-up of interventions showed that four of six probands received intervention(66.67%), but the results of intervention varied. Conclusion:The study analyzed six families with late-onset non-syndromic hearing loss linked to GSDME mutations, identifying four splicing variants. Notably, c. 991-7C>G is the first reported de novo variant of GSDME globally. Audiological analysis revealed that the age of onset generally exceeded 10 years,with variable effectiveness of interventions.
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Affiliation(s)
- 丹阳 李
- 中国人民解放军总医院第六医学中心耳鼻咽喉头颈外科医学部耳鼻咽喉内科解放军医学院(北京,100853)Department of Audiology and Vestibular Medicine, College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Beijing, 100853, China
- 南开大学医学院Nankai University School of Medicine
- 国家耳鼻咽喉疾病临床医学研究中心National Clinical Research Center for Otolaryngologic Diseases
| | - 洪阳 王
- 中国人民解放军总医院第六医学中心耳鼻咽喉头颈外科医学部耳鼻咽喉内科解放军医学院(北京,100853)Department of Audiology and Vestibular Medicine, College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Beijing, 100853, China
- 国家耳鼻咽喉疾病临床医学研究中心National Clinical Research Center for Otolaryngologic Diseases
| | - 秋菊 王
- 中国人民解放军总医院第六医学中心耳鼻咽喉头颈外科医学部耳鼻咽喉内科解放军医学院(北京,100853)Department of Audiology and Vestibular Medicine, College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Beijing, 100853, China
- 南开大学医学院Nankai University School of Medicine
- 国家耳鼻咽喉疾病临床医学研究中心National Clinical Research Center for Otolaryngologic Diseases
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周 睿, 关 静, 王 秋. [Genetic characteristic analysis of slight-to-moderate sensorineural hearing loss in children]. LIN CHUANG ER BI YAN HOU TOU JING WAI KE ZA ZHI = JOURNAL OF CLINICAL OTORHINOLARYNGOLOGY, HEAD, AND NECK SURGERY 2024; 38:18-22. [PMID: 38297844 PMCID: PMC11116154 DOI: 10.13201/j.issn.2096-7993.2024.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Indexed: 02/02/2024]
Abstract
Objective:To analyze genetic factors and phenotype characteristics in pediatric population with slight-to-moderate sensorineural hearing loss. Methods:Children with slight-to-moderate sensorineural hearing loss of and their parents, enrolled from the Chinese Deafness Genome Project, were studied. Hearing levels were assessed using pure tone audiometry, behavioral audiometry, auditory steady state response(ASSR), auditory brainstem response(ABR) thresholds, and deformed partial otoacoustic emission(DPOAE). Classification of hearing loss is according to the 2022 American College of Medical Genetics and Genomics(ACMG) Clinical Practice Guidelines for Hearing Loss. Whole exome sequencing(WES) and deafness gene Panel testing were performed on peripheral venous blood from probands and validations were performed on their parents by Sanger sequencing. Results:All 134 patients had childhood onset, exhibiting bilateral symmetrical slight-to-moderate sensorineural hearing loss, as indicated by audiological examinations. Of the 134 patients, 29(21.6%) had a family history of hearing loss, and the rest were sporadic patients. Genetic causative genes were identified in 66(49.3%) patients. A total of 11 causative genes were detected, of which GJB2 was causative in 34 cases(51.5%), STRC in 10 cases(15.1%), MPZL2 gene in six cases(9.1%), and USH2A in five cases(7.6%).The most common gene detected in slight-to-moderate hearing loss was GJB2, with c. 109G>A homozygous mutation found in 16 cases(47.1%) and c. 109G>A compound heterozygous mutation in 9 cases(26.5%). Conclusion:This study provides a crucial genetic theory reference for early screening and detection of mild to moderate hearing loss in children, highlighting the predominance of recessive inheritance and the significance of gene like GJB2, STRC, MPZL2, USH2A.
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Affiliation(s)
- 睿 周
- 中国人民解放军总医院第六医学中心耳鼻咽喉头颈外科医学部耳鼻咽喉内科解放军医学院(北京,100853)Department of Audiology and Vestibular Medicine, College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital; Chinese PLA Medical School, Beijing, 100853, China
- 国家耳鼻咽喉疾病临床医学研究中心National Clinical Research Center for Otolaryngologic Diseases
| | - 静 关
- 中国人民解放军总医院第六医学中心耳鼻咽喉头颈外科医学部耳鼻咽喉内科解放军医学院(北京,100853)Department of Audiology and Vestibular Medicine, College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital; Chinese PLA Medical School, Beijing, 100853, China
- 国家耳鼻咽喉疾病临床医学研究中心National Clinical Research Center for Otolaryngologic Diseases
| | - 秋菊 王
- 中国人民解放军总医院第六医学中心耳鼻咽喉头颈外科医学部耳鼻咽喉内科解放军医学院(北京,100853)Department of Audiology and Vestibular Medicine, College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital; Chinese PLA Medical School, Beijing, 100853, China
- 国家耳鼻咽喉疾病临床医学研究中心National Clinical Research Center for Otolaryngologic Diseases
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Ramzan M, Duman D, Hendricks LCP, Guo S, Mutlu A, Kalcioglu MT, Seyhan S, Carranza C, Bonyadi M, Mahdieh N, Yildirim-Baylan M, Figueroa-Ildefonso E, Alper O, Atik T, Ayral A, Bozan N, Balta B, Rivas C, Manzoli GN, Huesca-Hernandez F, Kuchay RAH, Durgut M, Bademci G, Tekin M. Genome sequencing identifies coding and non-coding variants for non-syndromic hearing loss. J Hum Genet 2023; 68:657-669. [PMID: 37217689 DOI: 10.1038/s10038-023-01159-9] [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: 10/10/2022] [Revised: 04/27/2023] [Accepted: 05/05/2023] [Indexed: 05/24/2023]
Abstract
Hearing loss (HL) is a common heterogeneous trait that involves variants in more than 200 genes. In this study, we utilized exome (ES) and genome sequencing (GS) to effectively identify the genetic cause of presumably non-syndromic HL in 322 families from South and West Asia and Latin America. Biallelic GJB2 variants were identified in 58 probands at the time of enrollment these probands were excluded. In addition, upon review of phenotypic findings, 38/322 probands were excluded based on syndromic findings at the time of ascertainment and no further evaluation was performed on those samples. We performed ES as a primary diagnostic tool on one or two affected individuals from 212/226 families. Via ES we detected a total of 78 variants in 30 genes and showed their co-segregation with HL in 71 affected families. Most of the variants were frameshift or missense and affected individuals were either homozygous or compound heterozygous in their respective families. We employed GS as a primary test on a subset of 14 families and a secondary tool on 22 families which were unsolved by ES. Although the cumulative detection rate of causal variants by ES and GS is 40% (89/226), GS alone has led to a molecular diagnosis in 7 of 14 families as the primary tool and 5 of 22 families as the secondary test. GS successfully identified variants present in deep intronic or complex regions not detectable by ES.
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Affiliation(s)
- Memoona Ramzan
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Duygu Duman
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
- Division of Genetics, Department of Pediatrics, Ankara University School of Medicine, Ankara, Turkey
| | - LeShon Chere Peart Hendricks
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Shengru Guo
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Ahmet Mutlu
- Department of Otorhinolaryngology, Istanbul Medeniyet University Faculty of Medicine, Istanbul, Turkey
- Goztepe Prof. Dr. Suleyman Yalcin City Hospital, Istanbul, Turkey
| | - Mahmut Tayyar Kalcioglu
- Department of Otorhinolaryngology, Istanbul Medeniyet University Faculty of Medicine, Istanbul, Turkey
- Goztepe Prof. Dr. Suleyman Yalcin City Hospital, Istanbul, Turkey
| | - Serhat Seyhan
- Department of Medical Genetics, Faculty of Medicine, Uskudar University, Istanbul, Turkey
| | - Claudia Carranza
- Institute for Research on Genetic and Metabolic Diseases, INVEGEM, Guatemala City, Guatemala
| | - Murtaza Bonyadi
- Faculty of Natural Sciences, Center of Excellence for Biodiversity, University of Tabriz, Tabriz, Iran
| | - Nejat Mahdieh
- Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
| | | | - Erick Figueroa-Ildefonso
- Neurogenetics Research Center, Instituto Nacional de Ciencias Neurológicas, Lima, Peru
- Universidad Peruana Cayetano Heredia, Lima, 15102, Peru
| | - Ozgul Alper
- Department of Medical Biology and Genetics, Faculty of Medicine, Akdeniz University, Antalya, Turkey
| | - Tahir Atik
- Division of Pediatric Genetics, Department of Pediatrics, School of Medicine, Ege University, Izmir, Turkey
| | - Abdurrahman Ayral
- Department of Otolaryngology, Faculty of Medicine, Yuzuncu Yıl University, Van, Turkey
| | - Nazim Bozan
- Department of Otolaryngology, Faculty of Medicine, Yuzuncu Yıl University, Van, Turkey
| | - Burhan Balta
- Department of Medical Genetics, Kayseri Training and Research Hospital, Kayseri, Turkey
| | | | - Gabrielle N Manzoli
- Gonçalo Moniz Research Center (CPqGM), Oswaldo Cruz Foundation (FIOCRUZ), Salvador, Bahia, Brazil
| | - Fabiola Huesca-Hernandez
- Genetics and Genomic Medicine Service. National Institute of Rehabilitation, Mexico City, Mexico
| | - Raja A H Kuchay
- Department of Biotechnology, Baba Ghulam Shah Badshah University, Rajouri, J&K, India
| | - Merve Durgut
- Kocaeli University Otorhinolaryngology Department- Audiology Unit, İzmit, Turkey
| | - Guney Bademci
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Mustafa Tekin
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA.
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA.
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Imizcoz T, Prieto-Matos C, Manrique-Huarte R, Calavia D, Huarte A, Pruneda PC, Ordoñez GR, Cañada-Higueras E, Patiño-García A, Alkorta-Aranburu G, Manrique Rodríguez M. Next-generation sequencing improves precision medicine in hearing loss. Front Genet 2023; 14:1264899. [PMID: 37811145 PMCID: PMC10557071 DOI: 10.3389/fgene.2023.1264899] [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: 07/21/2023] [Accepted: 08/23/2023] [Indexed: 10/10/2023] Open
Abstract
Background: An early etiological diagnosis of hearing loss positively impacts children's quality of life including language and cognitive development. Even though hearing loss associates with extremely high genetic and allelic heterogeneity, several studies have proven that Next-Generation Sequencing (NGS)-based gene panel testing significantly reduces the time between onset and diagnosis. Methods: In order to assess the clinical utility of our custom NGS GHELP panel, the prevalence of pathogenic single nucleotide variants, indels or copy number variants was assessed by sequencing 171 nuclear and 8 mitochondrial genes in 155 Spanish individuals with hearing loss. Results: A genetic diagnosis of hearing loss was achieved in 34% (52/155) of the individuals (5 out of 52 were syndromic). Among the diagnosed cases, 87% (45/52) and 12% (6/52) associated with autosomal recessive and dominant inheritance patterns respectively; remarkably, 2% (1/52) associated with mitochondrial inheritance pattern. Although the most frequently mutated genes in this cohort were consistent with those described in the literature (GJB2, OTOF or MYO7A), causative variants in less frequent genes such as TMC1, FGF3 or mitCOX1 were also identified. Moreover, 5% of the diagnosed cases (3/52) were associated with pathogenic copy number variants. Conclusion: The clinical utility of NGS panels that allows identification of different types of pathogenic variants-not only single nucleotide variants/indels in both nuclear and mitochondrial genes but also copy number variants-has been demonstrated to reduce the clinical diagnostic odyssey in hearing loss. Thus, clinical implementation of genomic strategies within the regular clinical practice, and, more significantly, within the newborn screening protocols, is warranted.
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Affiliation(s)
- T. Imizcoz
- CIMA LAB Diagnostics, University of Navarra, Pamplona, Spain
| | - C. Prieto-Matos
- Department of Otorhinolaryngology, University Clinic of Navarra, Pamplona, Spain
| | - R. Manrique-Huarte
- Department of Otorhinolaryngology, University Clinic of Navarra, Pamplona, Spain
| | - D. Calavia
- Department of Otorhinolaryngology, University Clinic of Navarra, Pamplona, Spain
| | - A. Huarte
- Department of Otorhinolaryngology, University Clinic of Navarra, Pamplona, Spain
| | | | | | | | - A. Patiño-García
- CIMA LAB Diagnostics, University of Navarra, Pamplona, Spain
- Department of Pediatrics and Medical Genomics Unit, University Clinic of Navarra, Pamplona, Spain
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Bernardinelli E, Huber F, Roesch S, Dossena S. Clinical and Molecular Aspects Associated with Defects in the Transcription Factor POU3F4: A Review. Biomedicines 2023; 11:1695. [PMID: 37371790 DOI: 10.3390/biomedicines11061695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 06/07/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023] Open
Abstract
X-linked deafness (DFNX) is estimated to account for up to 2% of cases of hereditary hearing loss and occurs in both syndromic and non-syndromic forms. POU3F4 is the gene most commonly associated with X-linked deafness (DFNX2, DFN3) and accounts for about 50% of the cases of X-linked non-syndromic hearing loss. This gene codes for a transcription factor of the POU family that plays a major role in the development of the middle and inner ear. The clinical features of POU3F4-related hearing loss include a pathognomonic malformation of the inner ear defined as incomplete partition of the cochlea type 3 (IP-III). Often, a perilymphatic gusher is observed upon stapedectomy during surgery, possibly as a consequence of an incomplete separation of the cochlea from the internal auditory canal. Here we present an overview of the pathogenic gene variants of POU3F4 reported in the literature and discuss the associated clinical features, including hearing loss combined with additional phenotypes such as cognitive and motor developmental delays. Research on the transcriptional targets of POU3F4 in the ear and brain is in its early stages and is expected to greatly advance our understanding of the pathophysiology of POU3F4-linked hearing loss.
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Affiliation(s)
- Emanuele Bernardinelli
- Institute of Pharmacology and Toxicology, Paracelsus Medical University, 5020 Salzburg, Austria
| | - Florian Huber
- Institute of Pharmacology and Toxicology, Paracelsus Medical University, 5020 Salzburg, Austria
| | - Sebastian Roesch
- Department of Otorhinolaryngology, Head and Neck Surgery, Paracelsus Medical University, 5020 Salzburg, Austria
| | - Silvia Dossena
- Institute of Pharmacology and Toxicology, Paracelsus Medical University, 5020 Salzburg, Austria
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Jonard L, Brotto D, Moreno-Pelayo MA, Del Castillo I, Kremer H, Pennings R, Caria H, Fialho G, Boudewyns A, Van Camp G, Ołdak M, Oziębło D, Deggouj N, De Siati RD, Gasparini P, Girotto G, Verstreken M, Dossena S, Roesch S, Battelino S, Trebušak Podkrajšek K, Warnecke A, Lenarz T, Lesinski-Schiedat A, Mondain M, Roux AF, Denoyelle F, Loundon N, Serey Gaut M, Trevisi P, Rubinato E, Martini A, Marlin S. Genetic Evaluation of Prelingual Hearing Impairment: Recommendations of an European Network for Genetic Hearing Impairment. Audiol Res 2023; 13:341-346. [PMID: 37218840 DOI: 10.3390/audiolres13030029] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 02/23/2023] [Accepted: 03/03/2023] [Indexed: 05/24/2023] Open
Abstract
The cause of childhood hearing impairment (excluding infectious pathology of the middle ear) can be extrinsic (embryofoetopathy, meningitis, trauma, drug ototoxicity, noise trauma, etc [...].
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Affiliation(s)
- Laurence Jonard
- Centre de Référence «Surdités Génétiques», Fédération de Génétique, Centre de Recherche en Audiologie (CREA), Hôpital Necker-Enfants Malades, Assistance Publique Hôpitaux de Paris, 75015 Paris, France
| | - Davide Brotto
- ENT Unit, Neurosciences Department, University of Padova, 35122 Padova, Italy
| | - Miguel A Moreno-Pelayo
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto Ramón y Cajal deInvestigaciones Sani-tarias (IRYCIS), Genetics Department, University hospital Ramón y Cajal, 28034 Madrid, Spain
| | - Ignacio Del Castillo
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto Ramón y Cajal deInvestigaciones Sani-tarias (IRYCIS), Genetics Department, University hospital Ramón y Cajal, 28034 Madrid, Spain
| | - Hannie Kremer
- Department of Otorhinolaryngology and Department of Human Genetics, Hearing & Genes, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behaviour, Radboud University, 6525 XZ Nijmegen, The Netherlands
| | - Ronald Pennings
- Department of Otorhinolaryngology and Department of Human Genetics, Hearing & Genes, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behaviour, Radboud University, 6525 XZ Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, 6525 XZ Nijmegen, The Netherlands
| | - Helena Caria
- BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1649-004 Lisboa, Portugal
- Biomedical Sciences Department, CIIAS-School of Health, Polytechnic Institute of Setubal, 2914-503 Setubal, Portugal
| | - Graça Fialho
- BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1649-004 Lisboa, Portugal
| | - An Boudewyns
- Department of Otorhinolaryngology, Head and Neck Surgery, Antwerp University Hospital, University of Antwerp, 2000 Edegem, Belgium
| | - Guy Van Camp
- Center for Medical Genetics, University of Antwerp, 2000 Antwerp, Belgium
| | - Monika Ołdak
- Department of Genetics, Institute of Physiology and Pathology of Hearing, 02-042 Warsaw, Poland
| | - Dominika Oziębło
- Department of Genetics, Institute of Physiology and Pathology of Hearing, 02-042 Warsaw, Poland
| | - Naïma Deggouj
- ENT Department, UCLouvain, Academic Hospital Saint-Luc-Brussels, 1200 Bruxelles, Belgium
| | | | - Paolo Gasparini
- Medical Genetics, Institute for Ma-ternal and Child Health (IRCCS) "Burlo Garofolo", Department of Medical, Surgery and Health Sciences, University of Trieste, 34127 Trieste, Italy
| | - Giorgia Girotto
- Medical Genetics, Institute for Ma-ternal and Child Health (IRCCS) "Burlo Garofolo", Department of Medical, Surgery and Health Sciences, University of Trieste, 34127 Trieste, Italy
| | | | - Silvia Dossena
- Institute of Pharmacology and Toxicology, Paracelsus Medical University, 5020 Salzburg, Austria
| | - Sebastian Roesch
- Department of Otorhinolaryngology, Head and Neck Surgery, Paracelsus Medical University, 5020 Salzburg, Austria
| | - Saba Battelino
- Department of Otorhinolaryngology and Cervicofacial Surgery, University Medical Centre Ljubljana, Medical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Katarina Trebušak Podkrajšek
- Institute of Biochemistry and Molecular Genetics, Medical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Athanasia Warnecke
- Department of Otorhinolaryngology-Head and Neck Surgery, Hannover Medical School, D-30625 Hannover, Germany
- Cluster of Excellence Hearing4all, German Research Foundation, Oldenburg 26129, Germany
| | - Thomas Lenarz
- Department of Otorhinolaryngology-Head and Neck Surgery, Hannover Medical School, D-30625 Hannover, Germany
- Cluster of Excellence Hearing4all, German Research Foundation, Oldenburg 26129, Germany
| | - Anke Lesinski-Schiedat
- Medical Head German Hearing Center, Department of Otorhinolaryngology, Medical University of Hannover, D-30625 Hannover, Germany
| | - Michel Mondain
- ENT Department, CHU Montpellier, Université de Montpellier, 34090 Montpellier, France
| | - Anne-Françoise Roux
- Laboratoire de Génétique Moléculaire, CHU de Montpellier, Université de Montpellier, 34090 Montpellier, France
| | - Françoise Denoyelle
- Service d'ORL Pédiatrique et de Chirurgie Cervico-Faciale, INSERM UMR 1120, Hôpital Necker-Enfants Malades, Assistance Publique Hôpitaux de Paris, 75015 Paris, France
| | - Natalie Loundon
- Centre de Référence «Surdités Génétiques», Fédération de Génétique, Centre de Recherche en Audiologie (CREA), Hôpital Necker-Enfants Malades, Assistance Publique Hôpitaux de Paris, 75015 Paris, France
- Service d'ORL Pédiatrique et de Chirurgie Cervico-Faciale, INSERM UMR 1120, Hôpital Necker-Enfants Malades, Assistance Publique Hôpitaux de Paris, 75015 Paris, France
| | - Margaux Serey Gaut
- Centre de Référence «Surdités Génétiques», Fédération de Génétique, Centre de Recherche en Audiologie (CREA), Hôpital Necker-Enfants Malades, Assistance Publique Hôpitaux de Paris, 75015 Paris, France
| | - Patrizia Trevisi
- ENT Unit, Neurosciences Department, University of Padova, 35122 Padova, Italy
| | - Elisa Rubinato
- Medical Genetics, Institute for Ma-ternal and Child Health (IRCCS) "Burlo Garofolo", Department of Medical, Surgery and Health Sciences, University of Trieste, 34127 Trieste, Italy
| | - Alessandro Martini
- ENT Unit, Neurosciences Department, University of Padova, 35122 Padova, Italy
| | - Sandrine Marlin
- Centre de Référence «Surdités Génétiques», Fédération de Génétique, Centre de Recherche en Audiologie (CREA), Hôpital Necker-Enfants Malades, Assistance Publique Hôpitaux de Paris, 75015 Paris, France
- Laboratory of Embryology and Genetics of Malformations, Imagine Institute, INSERM UMR 1163, Université de Paris, 75015 Paris, France
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10
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Bi Q, Huang S, Wang H, Gao X, Ma M, Han M, Lu S, Kang D, Nourbakhsh A, Yan D, Blanton S, Liu X, Yuan Y, Yao Y, Dai P. Preimplantation genetic testing for hereditary hearing loss in Chinese population. J Assist Reprod Genet 2023:10.1007/s10815-023-02753-8. [PMID: 37017887 PMCID: PMC10352472 DOI: 10.1007/s10815-023-02753-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 02/13/2023] [Indexed: 04/06/2023] Open
Abstract
PURPOSE To evaluate the clinical validity of preimplantation genetic testing (PGT) to prevent hereditary hearing loss (HL) in Chinese population. METHODS A PGT procedure combining multiple annealing and looping-based amplification cycles (MALBAC) and single-nucleotide polymorphisms (SNPs) linkage analyses with a single low-depth next-generation sequencing run was implemented. Forty-three couples carried pathogenic variants in autosomal recessive non-syndromic HL genes, GJB2 and SLC26A4, and four couples carried pathogenic variants in rare HL genes: KCNQ4, PTPN11, PAX3, and USH2A were enrolled. RESULTS Fifty-four in vitro fertilization (IVF) cycles were implemented, 340 blastocysts were cultured, and 303 (89.1%) of these received a definite diagnosis of a disease-causing variant testing, linkage analysis and chromosome screening. A clinical pregnancy of 38 implanted was achieved, and 34 babies were born with normal hearing. The live birth rate was 61.1%. CONCLUSIONS AND RELEVANCE In both the HL population and in hearing individuals at risk of giving birth to offspring with HL in China, there is a practical need for PGT. The whole genome amplification combined with NGS can simplify the PGT process, and the efficiency of PGT process can be improved by establishing a universal SNP bank of common disease-causing gene in particular regions and nationalities. This PGT procedure was demonstrated to be effective and lead to satisfactory clinical outcomes.
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Affiliation(s)
- Qingling Bi
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, National Clinical Research Center for Otolaryngologic Diseases, Key Lab of Hearing Impairment Science of Ministry of Education, Key Lab of Hearing Impairment Prevention and Treatment of Beijing, #28 Fuxing Road, Beijing, 100853, China
- Departments of Otolaryngology Head & Neck Surgery, China-Japan Friendship Hospital, 2#Yinghua Road, Beijing, 100029, China
| | - Shasha Huang
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, National Clinical Research Center for Otolaryngologic Diseases, Key Lab of Hearing Impairment Science of Ministry of Education, Key Lab of Hearing Impairment Prevention and Treatment of Beijing, #28 Fuxing Road, Beijing, 100853, China
| | - Hui Wang
- Reproductive Center, Chinese PLA General Hospital, 28#Fuxing Road, Beijing, 100853, China
| | - Xue Gao
- Department of Otolaryngology, PLA Rocket Force Characteristic Medical Center, 16# XinWai Da Jie, Beijing, 100088, China
| | - Minyue Ma
- Reproductive Center, Chinese PLA General Hospital, 28#Fuxing Road, Beijing, 100853, China
| | - Mingyu Han
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, National Clinical Research Center for Otolaryngologic Diseases, Key Lab of Hearing Impairment Science of Ministry of Education, Key Lab of Hearing Impairment Prevention and Treatment of Beijing, #28 Fuxing Road, Beijing, 100853, China
| | - Sijia Lu
- Department of Clinical Research, Yikon Genomics, 1698 Wangyuan Road, Fengxian District Shanghai, 201400, China
| | - Dongyang Kang
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, National Clinical Research Center for Otolaryngologic Diseases, Key Lab of Hearing Impairment Science of Ministry of Education, Key Lab of Hearing Impairment Prevention and Treatment of Beijing, #28 Fuxing Road, Beijing, 100853, China
| | - Aida Nourbakhsh
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Denise Yan
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Susan Blanton
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Xuezhong Liu
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Yongyi Yuan
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, National Clinical Research Center for Otolaryngologic Diseases, Key Lab of Hearing Impairment Science of Ministry of Education, Key Lab of Hearing Impairment Prevention and Treatment of Beijing, #28 Fuxing Road, Beijing, 100853, China.
| | - Yuanqing Yao
- Reproductive Center, Chinese PLA General Hospital, 28#Fuxing Road, Beijing, 100853, China.
| | - Pu Dai
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, National Clinical Research Center for Otolaryngologic Diseases, Key Lab of Hearing Impairment Science of Ministry of Education, Key Lab of Hearing Impairment Prevention and Treatment of Beijing, #28 Fuxing Road, Beijing, 100853, China.
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11
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Riza AL, Alkhzouz C, Farcaș M, Pîrvu A, Miclea D, Mihuț G, Pleșea RM, Ștefan D, Drodar M, Lazăr C, Study OBOTHINT, Study OBOTFUSE, Ioana M, Popp R. Non-Syndromic Hearing Loss in a Romanian Population: Carrier Status and Frequent Variants in the GJB2 Gene. Genes (Basel) 2022; 14:69. [PMID: 36672810 PMCID: PMC9858611 DOI: 10.3390/genes14010069] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 12/16/2022] [Accepted: 12/22/2022] [Indexed: 12/28/2022] Open
Abstract
The genetic causes of autosomal recessive nonsyndromic hearing loss (ARNSHL) are heterogeneous and highly ethnic-specific. We describe GJB2 (connexin 26) variants and carrier frequencies as part of our study and summarize previously reported ones for the Romanian population. In total, 284 unrelated children with bilateral congenital NSHL were enrolled between 2009 and 2018 in northwestern Romania. A tiered diagnostic approach was used: all subjects were tested for c.35delG, c.71G>A and deletions in GJB6 (connexin 30) using PCR-based methods. Furthermore, 124 cases undiagnosed at this stage were analyzed by multiplex-ligation-dependent probe amplifications (MLPA), probe mix P163, and sequencing of GJB2 exon 2. Targeted allele-specific PCR/restriction fragment length polymorphism (RFLP) established definite ethio-pathogenical diagnosis for 72/284 (25.35%) of the cohort. Out of the 124 further analyzed, in 12 cases (9.67%), we found compound heterozygous point mutations in GJB2. We identified one case of deletion of exon 1 of the WFS1 (wolframin) gene. Carrier status evaluation used Illumina Infinium Global Screening Array (GSA) genotyping: the HINT cohort-416 individuals in northwest Romania, and the FUSE cohort-472 individuals in southwest Romania. GSA variants yielded a cumulated risk allele presence of 0.0284. A tiered diagnostic approach may be efficient in diagnosing ARNSHL. The summarized contributions to Romanian descriptive epidemiology of ARNSHL shows that pathogenic variants in the GJB2 gene are frequent among NSHL cases and have high carrier rates, especially for c.35delG and c.71G>A. These findings may serve in health strategy development.
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Affiliation(s)
- Anca-Lelia Riza
- Regional Centre of Medical Genetics Dolj, Emergency County Hospital Craiova, 200642 Craiova, Romania
- Laboratory of Human Genomics, University of Medicine and Pharmacy of Craiova, 200638 Craiova, Romania
| | - Camelia Alkhzouz
- First Pediatric Department, “Iuliu Hatieganu” University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania
- Clinical Emergency Hospital for Children, 400394 Cluj-Napoca, Romania
| | - Marius Farcaș
- Molecular Sciences Department, “Iuliu Hatieganu” University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania
| | - Andrei Pîrvu
- Regional Centre of Medical Genetics Dolj, Emergency County Hospital Craiova, 200642 Craiova, Romania
- Laboratory of Human Genomics, University of Medicine and Pharmacy of Craiova, 200638 Craiova, Romania
| | - Diana Miclea
- First Pediatric Department, “Iuliu Hatieganu” University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania
- Clinical Emergency Hospital for Children, 400394 Cluj-Napoca, Romania
| | - Gheorghe Mihuț
- ENT Department, Clinical Emergency Hospital for Children, 400394 Cluj-Napoca, Romania
| | - Răzvan-Mihail Pleșea
- Regional Centre of Medical Genetics Dolj, Emergency County Hospital Craiova, 200642 Craiova, Romania
- Laboratory of Human Genomics, University of Medicine and Pharmacy of Craiova, 200638 Craiova, Romania
| | - Delia Ștefan
- Molecular Sciences Department, “Iuliu Hatieganu” University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania
| | - Mihaela Drodar
- Laboratory of Human Genomics, University of Medicine and Pharmacy of Craiova, 200638 Craiova, Romania
| | - Călin Lazăr
- First Pediatric Department, “Iuliu Hatieganu” University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania
- Clinical Emergency Hospital for Children, 400394 Cluj-Napoca, Romania
| | | | | | - Mihai Ioana
- Regional Centre of Medical Genetics Dolj, Emergency County Hospital Craiova, 200642 Craiova, Romania
- Laboratory of Human Genomics, University of Medicine and Pharmacy of Craiova, 200638 Craiova, Romania
| | - Radu Popp
- Molecular Sciences Department, “Iuliu Hatieganu” University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania
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12
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Klimara MJ, Nishimura C, Wang D, Kolbe DL, Schaefer AM, Walls WD, Frees KL, Smith RJH, Azaiez H. De novo variants are a common cause of genetic hearing loss. Genet Med 2022; 24:2555-2567. [PMID: 36194208 PMCID: PMC9729384 DOI: 10.1016/j.gim.2022.08.028] [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: 06/29/2022] [Revised: 08/25/2022] [Accepted: 08/26/2022] [Indexed: 11/06/2022] Open
Abstract
PURPOSE De novo variants (DNVs) are a well-recognized cause of genetic disorders. The contribution of DNVs to hearing loss (HL) is poorly characterized. We aimed to evaluate the rate of DNVs in HL-associated genes and assess their contribution to HL. METHODS Targeted genomic enrichment and massively parallel sequencing were used for molecular testing of all exons and flanking intronic sequences of known HL-associated genes, with no exclusions on the basis of type of HL or clinical features. Segregation analysis was performed, and previous reports of DNVs in PubMed and ClinVar were reviewed to characterize the rate, distribution, and spectrum of DNVs in HL. RESULTS DNVs were detected in 10% (24/238) of trios for whom segregation analysis was performed. Overall, DNVs were causative in at least ∼1% of probands for whom a genetic diagnosis was resolved, with marked variability based on inheritance mode and phenotype. DNVs of MITF were most common (21% of DNVs), followed by GATA3 (13%), STRC (13%), and ACTG1 (8%). Review of reported DNVs revealed gene-specific variability in contribution of DNV to the mutational spectrum of HL-associated genes. CONCLUSION DNVs are a relatively common cause of genetic HL and must be considered in all cases of sporadic HL.
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Affiliation(s)
- Miles J Klimara
- Molecular Otolaryngology and Renal Research Laboratories, Department of Otolaryngology-Head and Neck Surgery, Roy J. and Lucille A. Carver College of Medicine University of Iowa, Iowa City, IA
| | - Carla Nishimura
- Molecular Otolaryngology and Renal Research Laboratories, Department of Otolaryngology-Head and Neck Surgery, Roy J. and Lucille A. Carver College of Medicine University of Iowa, Iowa City, IA
| | - Donghong Wang
- Molecular Otolaryngology and Renal Research Laboratories, Department of Otolaryngology-Head and Neck Surgery, Roy J. and Lucille A. Carver College of Medicine University of Iowa, Iowa City, IA
| | - Diana L Kolbe
- Molecular Otolaryngology and Renal Research Laboratories, Department of Otolaryngology-Head and Neck Surgery, Roy J. and Lucille A. Carver College of Medicine University of Iowa, Iowa City, IA
| | - Amanda M Schaefer
- Molecular Otolaryngology and Renal Research Laboratories, Department of Otolaryngology-Head and Neck Surgery, Roy J. and Lucille A. Carver College of Medicine University of Iowa, Iowa City, IA
| | - William D Walls
- Molecular Otolaryngology and Renal Research Laboratories, Department of Otolaryngology-Head and Neck Surgery, Roy J. and Lucille A. Carver College of Medicine University of Iowa, Iowa City, IA
| | - Kathy L Frees
- Molecular Otolaryngology and Renal Research Laboratories, Department of Otolaryngology-Head and Neck Surgery, Roy J. and Lucille A. Carver College of Medicine University of Iowa, Iowa City, IA
| | - Richard J H Smith
- Molecular Otolaryngology and Renal Research Laboratories, Department of Otolaryngology-Head and Neck Surgery, Roy J. and Lucille A. Carver College of Medicine University of Iowa, Iowa City, IA.
| | - Hela Azaiez
- Molecular Otolaryngology and Renal Research Laboratories, Department of Otolaryngology-Head and Neck Surgery, Roy J. and Lucille A. Carver College of Medicine University of Iowa, Iowa City, IA.
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13
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Corriols-Noval P, López Simón EC, Cadiñanos J, Diñeiro M, Capín R, González Aguado R, Costales Marcos M, Morales Angulo C, Cabanillas Farpón R. Clinical Impact of Genetic Diagnosis of Sensorineural Hearing Loss in Adults. Otol Neurotol 2022; 43:1125-1136. [PMID: 36190904 DOI: 10.1097/mao.0000000000003706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
HYPOTHESIS Adult genetic sensorineural hearing loss (SNHL) may be underestimated. BACKGROUND The diagnosis of genetic hearing loss is challenging, given its extreme genetic and phenotypic heterogeneity, particularly in adulthood. This study evaluated the utility of next-generation sequencing (NGS) in the etiological diagnosis of adult-onset SNHL. MATERIALS AND METHODS Adults (>16 yr old) with SNHL were recruited at the Otolaryngology Department at Marqués de Valdecilla University Hospital (Spain). Environmental factors, acoustic trauma, endolymphatic hydrops, and age-related hearing loss were excluding criteria. An NGS gene panel was used, including 196 genes (OTOgenics v3) or 229 genes (OTOgenics v4) related to syndromic and nonsyndromic hearing loss. RESULTS Sixty-five patients were included in the study (average age at the onset of SNHL, 41 yr). Fifteen pathogenic/likely pathogenic variants considered to be causative were found in 15 patients (23% diagnostic yield) in TECTA (4), KCNQ4 (3), GJB2 (2), ACTG1 (1), COL2A1 (1), COCH (1), COCH/COL2A1 (1), STRC (1), and ABHD12 (1). Three patients had syndromic associations (20% of patients with genetic diagnosis) that had not been previously diagnosed (two Stickler type I and one polyneuropathy, hearing loss, ataxia, retinitis pigmentosa, cataract syndrome). Seven variants of unknown significance were found in COL11A1 (1), GSMDE (2), DNTM1 (1), SOX10 (1), EYA4 (1), and TECTA (1). CONCLUSION NGS gene panels can provide diagnostic yields greater than 20% for adult SNHL, with a significant proportion of variant of unknown significance that could potentially contribute to increasing diagnostic output. Identifying a genetic cause enables genetic counseling, provides prognostic information and can reveal unrecognized syndromes contributing to an accurate management of their associated manifestations.
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Affiliation(s)
- Patricia Corriols-Noval
- Department of Otolaryngology-Head and Neck Surgery, Marques de Valdecilla University Hospital, Santander, Spain
| | - Eugenia Carmela López Simón
- Department of Otolaryngology-Head and Neck Surgery, Marques de Valdecilla University Hospital, Santander, Spain
| | - Juan Cadiñanos
- Institute of Oncological and Molecular Medicine of Asturias
| | - Marta Diñeiro
- Institute of Oncological and Molecular Medicine of Asturias
| | - Raquel Capín
- Institute of Oncological and Molecular Medicine of Asturias
| | - Rocío González Aguado
- Department of Otolaryngology-Head and Neck Surgery, Marques de Valdecilla University Hospital, Santander, Spain
| | - María Costales Marcos
- Department of Otolaryngology-Head and Neck Surgery, Central University Hospital of Asturias, Asturias, Spain
| | - Carmelo Morales Angulo
- Department of Otolaryngology-Head and Neck Surgery, Marques de Valdecilla University Hospital, Santander, Spain
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14
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Yang JY, Wang WQ, Han MY, Huang SS, Wang GJ, Su Y, Xu JC, Fu Y, Kang DY, Yang K, Zhang X, Liu X, Gao X, Yuan YY, Dai P. Addition of an affected family member to a previously ascertained autosomal recessive nonsyndromic hearing loss pedigree and systematic phenotype-genotype analysis of splice-site variants in MYO15A. BMC Med Genomics 2022; 15:241. [PMCID: PMC9673454 DOI: 10.1186/s12920-022-01368-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 09/29/2022] [Indexed: 11/19/2022] Open
Abstract
Pathogenic variants in MYO15A are known to cause autosomal recessive nonsyndromic hearing loss (ARNSHL), DFNB3. We have previously reported on one ARNSHL family including two affected siblings and identified MYO15A c.5964+3G > A and c.8375 T > C (p.Val2792Ala) as the possible deafness-causing variants. Eight year follow up identified one new affected individual in this family, who also showed congenital, severe to profound sensorineural hearing loss. By whole exome sequencing, we identified a new splice-site variant c.5531+1G > C (maternal allele), in a compound heterozygote with previously identified missense variant c.8375 T > C (p.Val2792Ala) (paternal allele) in MYO15A as the disease-causing variants. The new affected individual underwent unilateral cochlear implantation at the age of 1 year, and 5 year follow-up showed satisfactory speech and language outcomes. Our results further indicate that MYO15A-associated hearing loss is good candidates for cochlear implantation, which is in accordance with previous report. In light of our findings and review of the literatures, 58 splice-site variants in MYO15A are correlated with a severe deafness phenotype, composed of 46 canonical splice-site variants and 12 non-canonical splice-site variants.
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Affiliation(s)
- Jin-Yuan Yang
- grid.488137.10000 0001 2267 2324College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, 28 Fuxing Road, Beijing, 100853 People’s Republic of China ,grid.419897.a0000 0004 0369 313XNational Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, People’s Republic of China ,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, People’s Republic of China
| | - Wei-Qian Wang
- grid.488137.10000 0001 2267 2324College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, 28 Fuxing Road, Beijing, 100853 People’s Republic of China ,grid.419897.a0000 0004 0369 313XNational Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, People’s Republic of China ,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, People’s Republic of China ,grid.488137.10000 0001 2267 2324Department of Otolaryngology, PLA Rocket Force Characteristic Medical Center, 16# XinWai Da Jie, Beijing, 100088 People’s Republic of China
| | - Ming-Yu Han
- grid.488137.10000 0001 2267 2324College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, 28 Fuxing Road, Beijing, 100853 People’s Republic of China ,grid.419897.a0000 0004 0369 313XNational Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, People’s Republic of China ,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, People’s Republic of China
| | - Sha-Sha Huang
- grid.488137.10000 0001 2267 2324College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, 28 Fuxing Road, Beijing, 100853 People’s Republic of China ,grid.419897.a0000 0004 0369 313XNational Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, People’s Republic of China ,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, People’s Republic of China
| | - Guo-Jian Wang
- grid.488137.10000 0001 2267 2324College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, 28 Fuxing Road, Beijing, 100853 People’s Republic of China ,grid.419897.a0000 0004 0369 313XNational Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, People’s Republic of China ,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, People’s Republic of China
| | - Yu Su
- Department of Otolaryngology, Head and Neck Surgery, Chinese PLA General Hospital Affiliated Hainan Hospital, Jianglin Road, Sanya, 572013 People’s Republic of China ,Hainan Province Clinical Research Center for Otolaryngologic and Head and Neck Diseases, Jianglin Road, Sanya, 572013 People’s Republic of China
| | - Jin-Cao Xu
- grid.488137.10000 0001 2267 2324Department of Otolaryngology, PLA Rocket Force Characteristic Medical Center, 16# XinWai Da Jie, Beijing, 100088 People’s Republic of China
| | - Ying Fu
- grid.27255.370000 0004 1761 1174Department of Otorhinolaryngology, Qilu Hospital (Qingdao), Cheeloo College of Medicine, Shandong University, 758 Hefei Road, Qingdao, 266035 Shandong People’s Republic of China
| | - Dong-Yang Kang
- grid.488137.10000 0001 2267 2324College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, 28 Fuxing Road, Beijing, 100853 People’s Republic of China ,grid.419897.a0000 0004 0369 313XNational Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, People’s Republic of China ,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, People’s Republic of China
| | - Kun Yang
- grid.488137.10000 0001 2267 2324Postgraduate Training Base of Jinzhou Medical University, The PLA Rocket Force Characteristic Medical Center, 16# XinWai Da Jie, Beijing, 100088 People’s Republic of China
| | - Xin Zhang
- grid.488137.10000 0001 2267 2324College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, 28 Fuxing Road, Beijing, 100853 People’s Republic of China ,grid.419897.a0000 0004 0369 313XNational Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, People’s Republic of China ,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, People’s Republic of China
| | - Xing Liu
- grid.488137.10000 0001 2267 2324Department of Otolaryngology, PLA Rocket Force Characteristic Medical Center, 16# XinWai Da Jie, Beijing, 100088 People’s Republic of China
| | - Xue Gao
- grid.488137.10000 0001 2267 2324College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, 28 Fuxing Road, Beijing, 100853 People’s Republic of China ,grid.419897.a0000 0004 0369 313XNational Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, People’s Republic of China ,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, People’s Republic of China ,grid.488137.10000 0001 2267 2324Department of Otolaryngology, PLA Rocket Force Characteristic Medical Center, 16# XinWai Da Jie, Beijing, 100088 People’s Republic of China
| | - Yong-Yi Yuan
- grid.488137.10000 0001 2267 2324College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, 28 Fuxing Road, Beijing, 100853 People’s Republic of China ,grid.419897.a0000 0004 0369 313XNational Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, People’s Republic of China ,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, People’s Republic of China
| | - Pu Dai
- grid.488137.10000 0001 2267 2324College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, 28 Fuxing Road, Beijing, 100853 People’s Republic of China ,grid.419897.a0000 0004 0369 313XNational Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, People’s Republic of China ,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, People’s Republic of China
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15
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Five years' experience of the clinical exome sequencing in a Spanish single center. Sci Rep 2022; 12:19209. [PMID: 36357507 PMCID: PMC9649665 DOI: 10.1038/s41598-022-23786-6] [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: 05/19/2022] [Accepted: 11/04/2022] [Indexed: 11/12/2022] Open
Abstract
Nowadays, exome sequencing is a robust and cost-efficient genetic diagnostic tool already implemented in many clinical laboratories. Despite it has undoubtedly improved our diagnostic capacity and has allowed the discovery of many new Mendelian-disease genes, it only provides a molecular diagnosis in up to 25-30% of cases. Here, we comprehensively evaluate the results of a large sample set of 4974 clinical exomes performed in our laboratory over a period of 5 years, showing a global diagnostic rate of 24.62% (1391/4974). For the evaluation we establish different groups of diseases and demonstrate how the diagnostic rate is not only dependent on the analyzed group of diseases (43.12% in ophthalmological cases vs 16.61% in neurological cases) but on the specific disorder (47.49% in retinal dystrophies vs 24.02% in optic atrophy; 18.88% in neuropathies/paraparesias vs 11.43% in dementias). We also detail the most frequent mutated genes within each group of disorders and discuss, on our experience, further investigations and directions needed for the benefit of patients.
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16
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Santos DF, Molina Thurin LJ, Gustavo Vargas J, Izquierdo NJ, Oliver A. A Genotype-Phenotype Analysis of Usher Syndrome in Puerto Rico: A Case Series. Cureus 2022; 14:e28213. [PMID: 36003347 PMCID: PMC9392863 DOI: 10.7759/cureus.28213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/18/2022] [Indexed: 11/15/2022] Open
Abstract
Introduction Patients with Usher syndrome (USH) have retinitis pigmentosa (RP) and hearing loss inherited as an autosomal recessive (ar) trait. Mutations in the USH2A gene are the most common cause of Usher syndrome. We report the genotype-phenotype correlation in 10 patients with Usher syndrome from Puerto Rico (PR). This is the first genotype-phenotype analysis of patients with the syndrome in PR. Methods We conducted a chart review of patients who carried an Usher syndrome diagnosis. They underwent a comprehensive ophthalmic evaluation by at least one of the authors. This included best corrected visual acuity (BCVA), visual field mean deviation (VF MD), pattern standard deviation (PSD), and macular optical coherence tomography (mOCT) average volume and thickness. Genotyping was done using the Invitae Inherited Retinal Disease (IRD) Panel. Results Three patients had a logMAR BCVA of 1.0 or worse. The median VF MD was -29.7 dB and -29.2 dB in the OD and OS, respectively. The median PSD was 5.5 dB and 5.7 dB in the OD and OS, respectively. Upon macular OCT, patients had a median volume of 8.4 μm3 and 8 μm3 in the OD and OS, respectively. The median thickness was 235 μm and 223 μm in the OD and OS, respectively. All patients had pathogenic USH2A variants, and eight of these were compound heterozygotes. The most common variants were p.Cys575Tyr and p.Glu767Serfs*21, each present in four patients. Patients with the p.Cys759Phe variant had the worst phenotype with the worst BCVA, largest VF MD, and slimmer macular thickness. Conclusion Our findings are compatible with previously reported pathogenic mutations in the USH2A gene. However, the p.Cys759Phe variant has previously been correlated with a mild phenotype. In our study, the p.Cys759Phe variant correlated with the most severe phenotype. This variant has a high prevalence in the Spanish population, and PR was a Spanish colony for 400 years. The presence of this variant could be traced back to Spain. Genotyping patients with Usher syndrome is of utmost importance. Further studies to evaluate the common founder effect of patients with the syndrome in PR are warranted.
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17
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Elander J, Ullmark T, Ehrencrona H, Jonson T, Piccinelli P, Samuelsson S, Löwgren K, Falkenius-Schmidt K, Ehinger J, Stenfeldt K, Värendh M. Extended genetic diagnostics for children with profound sensorineural hearing loss by implementing massive parallel sequencing. Diagnostic outcome, family experience and clinical implementation. Int J Pediatr Otorhinolaryngol 2022; 159:111218. [PMID: 35779349 DOI: 10.1016/j.ijporl.2022.111218] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 06/12/2022] [Accepted: 06/22/2022] [Indexed: 10/17/2022]
Abstract
OBJECTIVES The aim of this study was to investigate genetic outcomes, analyze the family experience, and describe the process of implementing genetic sequencing for children with profound sensorineural hearing loss (SNHL) at a tertial audiological center in southern Sweden. DESIGN This is a prospective pilot study including eleven children with profound bilateral SNHL who underwent cochlear implant surgery. Genetic diagnostic investigation was performed with whole exome sequencing (WES) complemented with XON-array to identify copy number variants, using a manually curated gene panel incorporating 179 genes associated with non-syndromic and syndromic SNHL. Mitochondrial DNA (mtDNA) from blood was examined separately. A patient reported experience measures (PREM) questionnaire was used to evaluate parental experience. We also describe here the process of implementing WES in an audiology department. RESULTS Six female and five male children (mean 3.4 years, SD 3.5 years), with profound bilateral SNHL were included. Genetic variants of interest were found in six subjects (55%), where three (27%) could be classified as pathogenic or likely pathogenic. Among the six cases, one child was found to have a homozygous pathogenic variant in MYO7A and two children had homozygous likely pathogenic variants in SLC26A4 and PCDH15, respectively. One was carrying a compound heterozygote frameshift variant of uncertain significance (VUS) on one allele and in trans, a likely pathogenic deletion on the other allele in PCDH15. Two subjects had homozygous VUS in PCDH15 and ADGRV1, respectively. In five of the cases the variants were in genes associated with Usher syndrome. For one of the likely pathogenic variants, the finding was related to Pendred syndrome. No mtDNA variants related to SNHL were found. The PREM questionnaire revealed that the families had difficulty in fully understanding the results of the genetic analysis. However, the parents of all eleven (100%) subjects still recommended that other families with children with SNHL should undergo genetic testing. Specifically addressed referrals for prompt complementary clinical examination and more individualized care were possible, based on the genetic results. Close clinical collaboration between different specialists, including physicians of audiology, audiologists, clinical geneticists, ophthalmologists, pediatricians, otoneurologists, physiotherapists and hearing habilitation teams was initiated during the implementation of the new regime. For all professionals involved, a better knowledge of the diversity of the genetic background of hearing loss was achieved. CONCLUSIONS Whole exome sequencing and XON-array using a panel of genes associated with SNHL had a high diagnostic yield, added value to the families, and provided guidance for further examinations and habilitation for the child. Great care should be taken to thoroughly inform parents about the genetic test result. Collaborations between departments were intensified and knowledge of hearing genomics was increased among the staff.
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Affiliation(s)
- Johanna Elander
- Lund University, Skåne University Hospital, Department of Clinical Sciences Lund, Otorhinolaryngology, Head and Neck Surgery, 221 84, Lund, Sweden.
| | - Tove Ullmark
- Department of Clinical Genetics and Pathology, Office for Medical Services, Region Skåne, 221 85, Lund, Sweden
| | - Hans Ehrencrona
- Department of Clinical Genetics and Pathology, Office for Medical Services, Region Skåne, 221 85, Lund, Sweden; Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, 221 85, Lund, Sweden
| | - Tord Jonson
- Department of Clinical Genetics and Pathology, Office for Medical Services, Region Skåne, 221 85, Lund, Sweden
| | - Paul Piccinelli
- Department of Clinical Genetics and Pathology, Office for Medical Services, Region Skåne, 221 85, Lund, Sweden
| | - Sofie Samuelsson
- Department of Clinical Genetics and Pathology, Office for Medical Services, Region Skåne, 221 85, Lund, Sweden
| | - Karolina Löwgren
- Lund University, Skåne University Hospital, Department of Clinical Sciences Lund, Otorhinolaryngology, Head and Neck Surgery, 221 84, Lund, Sweden
| | - Karolina Falkenius-Schmidt
- Lund University, Skåne University Hospital, Department of Clinical Sciences Lund, Otorhinolaryngology, Head and Neck Surgery, 221 84, Lund, Sweden
| | - Johannes Ehinger
- Lund University, Skåne University Hospital, Department of Clinical Sciences Lund, Otorhinolaryngology, Head and Neck Surgery, 221 84, Lund, Sweden
| | - Karin Stenfeldt
- Lund University, Skåne University Hospital, Department of Clinical Sciences Lund, Otorhinolaryngology, Head and Neck Surgery, 221 84, Lund, Sweden; Lund University, Department of Clinical Sciences Lund, Logopedics, Phoniatrics and Audiology, 221 84, Lund, Sweden
| | - Maria Värendh
- Lund University, Skåne University Hospital, Department of Clinical Sciences Lund, Otorhinolaryngology, Head and Neck Surgery, 221 84, Lund, Sweden
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18
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Feng P, Xu Z, Chen J, Liu M, Zhao Y, Wang D, Han L, Wang L, Wan B, Xu X, Li D, Shu Y, Hua Y. Rescue of mis-splicing of a common SLC26A4 mutant associated with sensorineural hearing loss by antisense oligonucleotides. MOLECULAR THERAPY - NUCLEIC ACIDS 2022; 28:280-292. [PMID: 35433113 PMCID: PMC8987850 DOI: 10.1016/j.omtn.2022.03.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 03/18/2022] [Indexed: 11/11/2022]
Abstract
A wide spectrum of SLC26A4 mutations causes Pendred syndrome and enlarged vestibular aqueduct, both associated with sensorineural hearing loss (SNHL). A splice-site mutation, c.919-2A>G (A-2G), which is common in Asian populations, impairs the 3′ splice site of intron 7, resulting in exon 8 skipping during pre-mRNA splicing and a subsequent frameshift that creates a premature termination codon in the following exon. Currently, there is no effective drug treatment for SHNL. For A-2G-triggered SNHL, molecules that correct mis-splicing of the mutant hold promise to treat the disease. Antisense oligonucleotides (ASOs) can promote exon inclusion when targeting specific splicing silencers. Here, we systematically screened a large number of ASOs in a minigene system and identified a few that markedly repressed exon 8 skipping. A lead ASO, which targets a heterogeneous nuclear ribonucleoprotein (hnRNP) A1/A2 intronic splicing silencer (ISS) in intron 8, promoted efficient exon 8 inclusion in cultured peripheral blood mononuclear cells derived from two homozygous patients. In a partially humanized Slc26a4 A-2G mouse model, two subcutaneous injections of the ASO at 160 mg/kg significantly rescued exon 8 splicing in the liver. Our results demonstrate that the ISS-targeting ASO has therapeutic potential to treat genetic hearing loss caused by the A-2G mutation in SLC26A4.
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19
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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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20
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Identification of the First Single GSDME Exon 8 Structural Variants Associated with Autosomal Dominant Hearing Loss. Diagnostics (Basel) 2022; 12:diagnostics12010207. [PMID: 35054374 PMCID: PMC8774889 DOI: 10.3390/diagnostics12010207] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 01/12/2022] [Accepted: 01/13/2022] [Indexed: 02/04/2023] Open
Abstract
GSDME, also known as DFNA5, is a gene implicated in autosomal dominant nonsyndromic hearing loss (ADNSHL), affecting, at first, the high frequencies with a subsequent progression over all frequencies. To date, all the GSDME pathogenic variants associated with deafness lead to skipping of exon 8. In two families with apparent ADNSHL, massively parallel sequencing (MPS) integrating a coverage-based method for detection of copy number variations (CNVs) was applied, and it identified the first two causal GSDME structural variants affecting exon 8. The deleterious impact of the c.991-60_1095del variant, which includes the acceptor splice site sequence of exon 8, was confirmed by the study of the proband’s transcripts. The second mutational event is a complex rearrangement that deletes almost all of the exon 8 sequence. This study increases the mutational spectrum of the GSDME gene and highlights the crucial importance of MPS data for the detection of GSDME exon 8 deletions, even though the identification of a causal single-exon CNV by MPS analysis is still challenging.
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21
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De Novo ACTG1 Variant Expands the Phenotype and Genotype of Partial Deafness and Baraitser-Winter Syndrome. Int J Mol Sci 2022; 23:ijms23020692. [PMID: 35054877 PMCID: PMC8776155 DOI: 10.3390/ijms23020692] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/02/2022] [Accepted: 01/05/2022] [Indexed: 02/04/2023] Open
Abstract
Actin molecules are fundamental for embryonic structural and functional differentiation; γ-actin is specifically required for the maintenance and function of cytoskeletal structures in the ear, resulting in hearing. Baraitser–Winter Syndrome (B-WS, OMIM #243310, #614583) is a rare, multiple-anomaly genetic disorder caused by mutations in either cytoplasmically expressed actin gene, ACTB (β-actin) or ACTG1 (γ-actin). The resulting actinopathies cause characteristic cerebrofrontofacial and developmental traits, including progressive sensorineural deafness. Both ACTG1-related non-syndromic A20/A26 deafness and B-WS diagnoses are characterized by hypervariable penetrance in phenotype. Here, we identify a 28th patient worldwide carrying a mutated γ-actin ACTG1 allele, with mildly manifested cerebrofrontofacial B-WS traits, hypervariable penetrance of developmental traits and sensorineural hearing loss. This patient also displays brachycephaly and a complete absence of speech faculty, previously unreported for ACTG1-related B-WS or DFNA20/26 deafness, representing phenotypic expansion. The patient’s exome sequence analyses (ES) confirms a de novo ACTG1 variant previously unlinked to the pathology. Additional microarray analysis uncover no further mutational basis for dual molecular diagnosis in our patient. We conclude that γ-actin c.542C > T, p.Ala181Val is a dominant pathogenic variant, associated with mildly manifested facial and cerebral traits typical of B-WS, hypervariable penetrance of developmental traits and sensorineural deafness. We further posit and present argument and evidence suggesting ACTG1-related non-syndromic DFNA20/A26 deafness is a manifestation of undiagnosed ACTG1-related B-WS.
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22
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Pavlenkova Z, Varga L, Borecka S, Karhanek M, Huckova M, Skopkova M, Profant M, Gasperikova D. Comprehensive molecular-genetic analysis of mid-frequency sensorineural hearing loss. Sci Rep 2021; 11:22488. [PMID: 34795337 PMCID: PMC8602250 DOI: 10.1038/s41598-021-01876-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 10/27/2021] [Indexed: 12/14/2022] Open
Abstract
The genetic heterogeneity of sensorineural hearing loss (SNHL) is a major hurdle to the detection of disease-causing variants. We aimed to identify underlying causal genes associated with mid-frequency hearing loss (HL), which contributes to less than about 1% of SNHL cases, by whole exome sequencing (WES). Thirty families segregating mid-frequency SNHL, in whom biallelic GJB2 mutations had been previously excluded, were selected from among 851 families in our DNA repository of SNHL. DNA samples from the probands were subjected to WES analysis and searched for candidate variants associated with SNHL. We were able to identify the genetic aetiology in six probands (20%). In total, we found three pathogenic and three likely pathogenic variants in four genes (COL4A5, OTOGL, TECTA, TMPRSS3). One more proband was a compound heterozygote for a pathogenic variant and a variant of uncertain significance (VUS) in MYO15A gene. To date, MYO15A and TMPRSS3 have not yet been described in association with mid-frequency SNHL. In eight additional probands, eight candidate VUS variants were detected in five genes (DIAPH1, MYO7A, TECTA, TMC1, TSPEAR). Seven of these 16 variants have not yet been published or mentioned in the available databases. The most prevalent gene was TECTA, identified in 23% of all tested families. Furthermore, we confirmed the hypothesis that a substantive portion of cases with this conspicuous audiogram shape is a consequence of a genetic disorder.
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Affiliation(s)
- Zuzana Pavlenkova
- Department of Otorhinolaryngology-Head and Neck Surgery, Faculty of Medicine and University Hospital, Comenius University, Bratislava, Slovakia.,DIABGENE Laboratory, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Lukas Varga
- Department of Otorhinolaryngology-Head and Neck Surgery, Faculty of Medicine and University Hospital, Comenius University, Bratislava, Slovakia. .,DIABGENE Laboratory, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia.
| | - Silvia Borecka
- DIABGENE Laboratory, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Miloslav Karhanek
- Laboratory of Bioinformatics, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Miloslava Huckova
- DIABGENE Laboratory, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Martina Skopkova
- DIABGENE Laboratory, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Milan Profant
- Department of Otorhinolaryngology-Head and Neck Surgery, Faculty of Medicine and University Hospital, Comenius University, Bratislava, Slovakia
| | - Daniela Gasperikova
- DIABGENE Laboratory, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia
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23
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Huang S, Zhao G, Wu J, Li K, Wang Q, Fu Y, Zhang H, Bi Q, Li X, Wang W, Guo C, Zhang D, Wu L, Li X, Xu H, Han M, Wang X, Lei C, Qiu X, Li Y, Li J, Dai P, Yuan Y. Gene4HL: An Integrated Genetic Database for Hearing Loss. Front Genet 2021; 12:773009. [PMID: 34733322 PMCID: PMC8558372 DOI: 10.3389/fgene.2021.773009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 09/28/2021] [Indexed: 11/18/2022] Open
Abstract
Hearing loss (HL) is one of the most common disabilities in the world. In industrialized countries, HL occurs in 1–2/1,000 newborns, and approximately 60% of HL is caused by genetic factors. Next generation sequencing (NGS) has been widely used to identify many candidate genes and variants in patients with HL, but the data are scattered in multitudinous studies. It is a challenge for scientists, clinicians, and biologists to easily obtain and analyze HL genes and variant data from these studies. Thus, we developed a one-stop database of HL-related genes and variants, Gene4HL (http://www.genemed.tech/gene4hl/), making it easy to catalog, search, browse and analyze the genetic data. Gene4HL integrates the detailed genetic and clinical data of 326 HL-related genes from 1,608 published studies, along with 62 popular genetic data sources to provide comprehensive knowledge of candidate genes and variants associated with HL. Additionally, Gene4HL supports the users to analyze their own genetic engineering network data, performs comprehensive annotation, and prioritizes candidate genes and variations using custom parameters. Thus, Gene4HL can help users explain the function of HL genes and the clinical significance of variants by correlating the genotypes and phenotypes in humans.
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Affiliation(s)
- Shasha Huang
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, Beijing, China.,National Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, China.,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, China
| | - Guihu Zhao
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, China.,Center for Medical Genetics & Hunan Key Laboratory, School of Life Sciences, Central South University, Changsha, China
| | - Jie Wu
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, Beijing, China.,National Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, China.,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, China
| | - Kuokuo Li
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, China.,Center for Medical Genetics & Hunan Key Laboratory, School of Life Sciences, Central South University, Changsha, China
| | - Qiuquan Wang
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, Beijing, China.,National Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, China.,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, China
| | - Ying Fu
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, Beijing, China.,National Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, China.,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, China
| | - Honglei Zhang
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, Beijing, China.,National Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, China.,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, China
| | - Qingling Bi
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, Beijing, China.,National Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, China.,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, China
| | - Xiaohong Li
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, Beijing, China.,National Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, China.,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, China
| | - Weiqian Wang
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, Beijing, China.,National Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, China.,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, China
| | - Chang Guo
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, Beijing, China.,National Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, China.,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, China
| | - Dejun Zhang
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, Beijing, China.,National Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, China.,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, China
| | - Lihua Wu
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, Beijing, China.,National Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, China.,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, China
| | - Xiaoge Li
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, Beijing, China.,National Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, China.,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, China
| | - Huiyan Xu
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, Beijing, China.,National Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, China.,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, China
| | - Mingyu Han
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, Beijing, China.,National Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, China.,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, China
| | - Xin Wang
- Angen Gene Medicine Technology Co., Ltd., Beijing, China
| | - Chen Lei
- Angen Gene Medicine Technology Co., Ltd., Beijing, China
| | - Xiaofang Qiu
- Angen Gene Medicine Technology Co., Ltd., Beijing, China
| | - Yang Li
- Angen Gene Medicine Technology Co., Ltd., Beijing, China
| | - Jinchen Li
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, China.,Center for Medical Genetics & Hunan Key Laboratory, School of Life Sciences, Central South University, Changsha, China
| | - Pu Dai
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, Beijing, China.,National Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, China.,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, China
| | - Yongyi Yuan
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, Beijing, China.,National Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, China.,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, China
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24
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Comprehensive functional network analysis and screening of deleterious pathogenic variants in non-syndromic hearing loss causative genes. Biosci Rep 2021; 41:230001. [PMID: 34714320 PMCID: PMC8559308 DOI: 10.1042/bsr20211865] [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: 08/05/2021] [Revised: 10/12/2021] [Accepted: 10/15/2021] [Indexed: 11/17/2022] Open
Abstract
Hearing loss (HL) is a significant public health problem and causes the most frequent congenital disability in developed societies. The genetic analysis of non-syndromic hearing loss (NSHL) may be considered as a complement to the existent plethora of diagnostic modalities available. The present study focuses on exploring more target genes with respective non-synonymous single nucleotide polymorphisms (nsSNPs) involved in the development of NSHL. The functional network analysis and variant study have successfully been carried out from the gene pool retrieved from reported research articles of the last decade. The analyses have been done through STRING. According to predicted biological processes, various variant analysis tools have successfully classified the NSHL causative genes and identified the deleterious nsSNPs, respectively. Among the predicted pathogenic nsSNPs with rsIDs rs80356586 (I515T), rs80356596 (L1011P), rs80356606 (P1987R) in OTOF have been reported in NSHL earlier. The rs121909642 (P722S), rs267606805 (P722H) in FGFR1, rs121918506 (E565A) and rs121918509 (A628T, A629T) in FGFR2 have not been reported in NSHL yet, which should be clinically experimented in NSHL. This also indicates this variant's novelty as its association in NSHL. The findings and the analyzed data have delivered some vibrant genetic pathogenesis of NSHL. These data might be used in the diagnostic and prognostic purposes in non-syndromic congenitally deaf children.
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25
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DFNA20/26 and Other ACTG1-Associated Phenotypes: A Case Report and Review of the Literature. Audiol Res 2021; 11:582-593. [PMID: 34698053 PMCID: PMC8544197 DOI: 10.3390/audiolres11040052] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 10/10/2021] [Accepted: 10/13/2021] [Indexed: 02/08/2023] Open
Abstract
Since the early 2000s, an ever-increasing subset of missense pathogenic variants in the ACTG1 gene has been associated with an autosomal-dominant, progressive, typically post-lingual non-syndromic hearing loss (NSHL) condition designed as DFNA20/26. ACTG1 gene encodes gamma actin, the predominant actin protein in the cytoskeleton of auditory hair cells; its normal expression and function are essential for the stereocilia maintenance. Different gain-of-function pathogenic variants of ACTG1 have been associated with two major phenotypes: DFNA20/26 and Baraitser-Winter syndrome, a multiple congenital anomaly disorder. Here, we report a novel ACTG1 variant [c.625G>A (p. Val209Met)] in an adult patient with moderate-severe NSHL characterized by a downsloping audiogram. The patient, who had a clinical history of slowly progressive NSHL and tinnitus, was referred to our laboratory for the analysis of a large panel of NSHL-associated genes by next generation sequencing. An extensive review of previously reported ACTG1 variants and their associated phenotypes was also performed.
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26
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Booth KT, Hirsch Y, Vardaro AC, Ekstein J, Yefet D, Quint A, Weiden T, Corey DP. Identification of Novel and Recurrent Variants in MYO15A in Ashkenazi Jewish Patients With Autosomal Recessive Nonsyndromic Hearing Loss. Front Genet 2021; 12:737782. [PMID: 34733312 PMCID: PMC8558392 DOI: 10.3389/fgene.2021.737782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 09/21/2021] [Indexed: 12/02/2022] Open
Abstract
Hearing loss is a genetically and phenotypically heterogeneous disorder. The purpose of this study was to determine the genetic cause underlying hearing loss in four Ashkenazi Jewish families. We screened probands from each family using a combination of targeted mutation screening and exome sequencing to identifiy the genetic cause of hearing loss in each family. We identified four variants in MYO15A, two novel variants never previously linked to deafness (c.7212+5G>A and p.Leu2532ArgfsTer37) and two recurrent variants (p.Tyr2684His and p.Gly3287Gly). One family showed locus heterogeneity, segregrating two genetic forms of hearing loss. Mini-gene assays revealed the c.7212+5G>A variant results in abnormal splicing and is most likely a null allele. We show that families segregrating the p.Gly3287Gly variant show both inter and intra-familial phenotypic differences. These results add to the list of MYO15A deafness-causing variants, further confirm the pathogenicity of the p.Gly3287Gly variant and shed further light on the genetic etiology of hearing loss in the Ashkenazi Jewish population.
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Affiliation(s)
- Kevin T. Booth
- Department of Neurobiology, Harvard Medical School, Boston, MA, United States
| | - Yoel Hirsch
- Dor Yeshorim, Committee for Prevention of Jewish Genetic Diseases, Brooklyn, NY, United States
| | - Anna C. Vardaro
- Department of Neurobiology, Harvard Medical School, Boston, MA, United States
| | - Josef Ekstein
- Dor Yeshorim, Committee for Prevention of Jewish Genetic Diseases, Brooklyn, NY, United States
| | - Devorah Yefet
- Dor Yeshorim, Committee for Prevention of Jewish Genetic Diseases, Jerusalem, Israel
| | - Adina Quint
- Dor Yeshorim, Committee for Prevention of Jewish Genetic Diseases, Jerusalem, Israel
| | - Tzvi Weiden
- Dor Yeshorim, Committee for Prevention of Jewish Genetic Diseases, Jerusalem, Israel
| | - David P. Corey
- Department of Neurobiology, Harvard Medical School, Boston, MA, United States
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27
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Han S, Zhang D, Guo Y, Fu Z, Guan G. Prevalence and Characteristics of STRC Gene Mutations (DFNB16): A Systematic Review and Meta-Analysis. Front Genet 2021; 12:707845. [PMID: 34621290 PMCID: PMC8491653 DOI: 10.3389/fgene.2021.707845] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 08/13/2021] [Indexed: 11/13/2022] Open
Abstract
Background: Mutations in the STRC (MIM 606440) gene, inducing DFNB16, are considered a major cause of mild–moderate autosomal recessive non-syndromic hearing loss (ARNSHL). We conducted a systematic review and meta-analysis to determine the global prevalence and characteristics of STRC variations, important information required for genetic counseling. Methods: PubMed, Google Scholar, Medline, Embase, and Web of Science were searched for relevant articles published before January 2021. Results: The pooled prevalence of DFNB16 in GJB2-negative patients with hearing loss was 4.08% (95% CI: 0.0289–0.0573), and the proportion of STRC variants in the mild–moderate hearing loss group was 14.36%. Monoallelic mutations of STRC were 4.84% (95% CI: 0.0343–0.0680) in patients with deafness (non-GJB2) and 1.36% (95% CI: 0.0025–0.0696) in people with normal hearing. The DFNB16 prevalence in genetically confirmed patients (non-GJB2) was 11.10% (95% CI: 0.0716–0.1682). Overall pooled prevalence of deafness–infertility syndrome (DIS) was 36.75% (95% CI: 0.2122–0.5563) in DFNB16. The prevalence of biallelic deletions in STRC gene mutations was 70.85% (95% CI: 0.5824–0.8213). Conclusion: Variants in the STRC gene significantly contribute to mild–moderate hearing impairment. Moreover, biallelic deletions are a main feature of STRC mutations. Copy number variations associated with infertility should be seriously considered when investigating DFNB16.
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Affiliation(s)
- Shuang Han
- Department of Otolaryngology Head and Neck Surgery, The Second Hospital of Jilin University, Changchun, China
| | - Dejun Zhang
- Department of Otolaryngology Head and Neck Surgery, The Second Hospital of Jilin University, Changchun, China
| | - Yingyuan Guo
- Department of Otolaryngology Head and Neck Surgery, The Second Hospital of Jilin University, Changchun, China
| | - Zeming Fu
- Department of Otolaryngology Head and Neck Surgery, The Second Hospital of Jilin University, Changchun, China
| | - Guofang Guan
- Department of Otolaryngology Head and Neck Surgery, The Second Hospital of Jilin University, Changchun, China
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28
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Kılıç S, Bouzaher MH, Cohen MS, Lieu JEC, Kenna M, Anne S. Comprehensive medical evaluation of pediatric bilateral sensorineural hearing loss. Laryngoscope Investig Otolaryngol 2021; 6:1196-1207. [PMID: 34667865 PMCID: PMC8513426 DOI: 10.1002/lio2.657] [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: 07/04/2021] [Revised: 08/30/2021] [Accepted: 08/31/2021] [Indexed: 11/08/2022] Open
Abstract
Children with bilateral sensorineural hearing loss (SNHL) should undergo a comprehensive medical evaluation to determine the underlying etiology and help guide treatment and counseling. In this article, we review the indications and rationale for medical evaluation of pediatric bilateral SNHL, including history and physical examination, imaging, genetic testing, specialist referrals, cytomegalovirus (CMV) testing, and other laboratory tests. Workup begins with a history and physical examination, which can provide clues to the etiology of SNHL, particularly with syndromic causes. If SNHL is diagnosed within the first 3 weeks of life, CMV testing should be performed to identify patients that may benefit from antiviral treatment. If SNHL is diagnosed after 3 weeks, testing can be done using dried blood spots samples, if testing capability is available. Genetic testing is oftentimes successful in identifying causes of hearing loss as a result of recent technological advances in testing and an ever-increasing number of identified genes and genetic mutations. Therefore, where available, genetic testing should be performed, ideally with next generation sequencing techniques. Ophthalmological evaluation must be done on all children with SNHL. Imaging (high-resolution computed tomography and/or magnetic resonance imaging) should be performed to assess for anatomic causes of hearing loss and to determine candidacy for cochlear implantation when indicated. Laboratory testing is indicated for certain etiologies, but should not be ordered indiscriminately since the yield overall is low.
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Affiliation(s)
- Suat Kılıç
- Head and Neck InstituteCleveland ClinicClevelandOhioUSA
| | | | - Michael S. Cohen
- Department of Otolaryngology, Head and Neck SurgeryHarvard Medical SchoolBostonMassachusettsUSA
| | - Judith E. C. Lieu
- Department of Otolaryngology‐Head and Neck SurgeryWashington University in St. LouisSt. LouisMissouriUSA
| | - Margaret Kenna
- Department of Otolaryngology and Communication EnhancementBoston Children's HospitalBostonMassachusettsUSA
| | - Samantha Anne
- Head and Neck InstituteCleveland ClinicClevelandOhioUSA
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29
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Usami SI, Nishio SY. The genetic etiology of hearing loss in Japan revealed by the social health insurance-based genetic testing of 10K patients. Hum Genet 2021; 141:665-681. [PMID: 34599366 PMCID: PMC9035015 DOI: 10.1007/s00439-021-02371-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 09/14/2021] [Indexed: 11/28/2022]
Abstract
Etiological studies have shown genetic disorders to be a major cause of sensorineural hearing loss, but there are a limited number of comprehensive etiological reports based on genetic analysis. In the present study, the same platform using a diagnostic DNA panel carrying 63 deafness genes and the same filtering algorithm were applied to 10,047 samples obtained from social health insurance-based genetic testing of hearing loss. The most remarkable result obtained in this comprehensive study was that the data first clarified the genetic epidemiology from congenital/early-onset deafness to late-onset hearing loss. The overall diagnostic rate was 38.8%, with the rate differing for each age group; 48.6% for the congenital/early-onset group (~5y.o.), 33.5% for the juvenile/young adult-onset group, and 18.0% for the 40+ y.o. group. Interestingly, each group showed a different kind of causative gene. With regard to the mutational spectra, there are certain recurrent variants that may be due to founder effects or hot spots. A series of haplotype studies have shown many recurrent variants are due to founder effects, which is compatible with human migration. It should be noted that, regardless of differences in the mutational spectrum, the clinical characteristics caused by particular genes can be considered universal. This comprehensive review clarified the detailed clinical characteristics (onset age, severity, progressiveness, etc.) of hearing loss caused by each gene, and will provide useful information for future clinical application, including genetic counseling and selection of appropriate interventions.
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Affiliation(s)
- Shin-Ichi Usami
- Department of Hearing Implant Sciences, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, 390-8621, Japan.
| | - Shin-Ya Nishio
- Department of Hearing Implant Sciences, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, 390-8621, Japan
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30
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Núñez-Batalla F, Jáudenes-Casaubón C, Sequí-Canet JM, Vivanco-Allende A, Zubicaray-Ugarteche J, Olleta Lascarro I. New-born Hearing Screening Programmes in 2020: CODEPEH Recommendations. ACTA OTORRINOLARINGOLOGICA ESPANOLA 2021; 72:312-323. [PMID: 34535222 DOI: 10.1016/j.otoeng.2020.06.009] [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: 06/10/2020] [Accepted: 06/18/2020] [Indexed: 10/20/2022]
Abstract
Programmes for early detection of congenital hearing loss have been successfully implemented mainly in developed countries, after overcoming some conceptual errors argued against their implementation and some criticism of their efficacy. However, some difficulties and weaknesses are still identified in these programmes: the detection of late-onset hearing loss and the percentage of children who did not pass the screening and did not complete the process of diagnosis and treatment, these being cases that are lost in the process. The purpose of this Document is to analyse these problems to determine areas for improvement and to emphasize one of the basic principles for the success of the programmes: continuous training for the interdisciplinary team. The result of the review process carried out by CODEPEH has been drafted as Recommendations for updating the Programmes with the evidence of the last decade, including advances in screening technology, the impact of the present knowledge on congenital infection by cytomegalovirus, genetic hearing loss research and control systems of lost to follow-up cases, treatment and follow up.
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31
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Núñez-Batalla F, Jáudenes-Casaubón C, Sequí-Canet JM, Vivanco-Allende A, Zubicaray-Ugarteche J, Olleta Lascarro I. Programas de cribado de la hipoacusia congénita en 2020: recomendaciones CODEPEH. ACTA OTORRINOLARINGOLOGICA ESPANOLA 2021. [DOI: 10.1016/j.otorri.2020.06.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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32
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Lezirovitz K, Vieira-Silva GA, Batissoco AC, Levy D, Kitajima JP, Trouillet A, Ouyang E, Zebarjadi N, Sampaio-Silva J, Pedroso-Campos V, Nascimento LR, Sonoda CY, Borges VM, Vasconcelos LG, Beck RMO, Grasel SS, Jagger DJ, Grillet N, Bento RF, Mingroni-Netto RC, Oiticica J. A rare genomic duplication in 2p14 underlies autosomal dominant hearing loss DFNA58. Hum Mol Genet 2021; 29:1520-1536. [PMID: 32337552 DOI: 10.1093/hmg/ddaa075] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 04/02/2020] [Accepted: 04/20/2020] [Indexed: 02/07/2023] Open
Abstract
Here we define a ~200 Kb genomic duplication in 2p14 as the genetic signature that segregates with postlingual progressive sensorineural autosomal dominant hearing loss (HL) in 20 affected individuals from the DFNA58 family, first reported in 2009. The duplication includes two entire genes, PLEK and CNRIP1, and the first exon of PPP3R1 (protein coding), in addition to four uncharacterized long non-coding (lnc) RNA genes and part of a novel protein-coding gene. Quantitative analysis of mRNA expression in blood samples revealed selective overexpression of CNRIP1 and of two lncRNA genes (LOC107985892 and LOC102724389) in all affected members tested, but not in unaffected ones. Qualitative analysis of mRNA expression identified also fusion transcripts involving parts of PPP3R1, CNRIP1 and an intergenic region between PLEK and CNRIP1, in the blood of all carriers of the duplication, but were heterogeneous in nature. By in situ hybridization and immunofluorescence, we showed that Cnrip1, Plek and Ppp3r1 genes are all expressed in the adult mouse cochlea including the spiral ganglion neurons, suggesting changes in expression levels of these genes in the hearing organ could underlie the DFNA58 form of deafness. Our study highlights the value of studying rare genomic events leading to HL, such as copy number variations. Further studies will be required to determine which of these genes, either coding proteins or non-coding RNAs, is or are responsible for DFNA58 HL.
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Affiliation(s)
- Karina Lezirovitz
- Otorhinolaryngology/LIM32, Hospital das Clínicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo 01246-000, Brazil.,Departamento de Otorrinolaringologia, Faculdade de Medicina FMUSP, Universidade de São Paulo, São Paulo 05403-000, Brazil
| | - Gleiciele A Vieira-Silva
- Otorhinolaryngology/LIM32, Hospital das Clínicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo 01246-000, Brazil.,Departamento de Otorrinolaringologia, Faculdade de Medicina FMUSP, Universidade de São Paulo, São Paulo 05403-000, Brazil
| | - Ana C Batissoco
- Otorhinolaryngology/LIM32, Hospital das Clínicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo 01246-000, Brazil.,Departamento de Otorrinolaringologia, Faculdade de Medicina FMUSP, Universidade de São Paulo, São Paulo 05403-000, Brazil
| | - Débora Levy
- Lipids, Oxidation, and Cell Biology Group, Head, Laboratory of Immunology (LIM19), Heart Institute (InCor), Hospital das Clínicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo 05403-900, Brazil
| | | | - Alix Trouillet
- Department of Otolaryngology - Head and Neck Surgery, Stanford University, Stanford, CA 94305, USA
| | - Ellen Ouyang
- Department of Otolaryngology - Head and Neck Surgery, Stanford University, Stanford, CA 94305, USA
| | - Navid Zebarjadi
- Department of Otolaryngology - Head and Neck Surgery, Stanford University, Stanford, CA 94305, USA
| | - Juliana Sampaio-Silva
- Otorhinolaryngology/LIM32, Hospital das Clínicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo 01246-000, Brazil
| | - Vinicius Pedroso-Campos
- Otorhinolaryngology/LIM32, Hospital das Clínicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo 01246-000, Brazil
| | - Larissa R Nascimento
- Otorhinolaryngology/LIM32, Hospital das Clínicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo 01246-000, Brazil.,Departamento de Otorrinolaringologia, Faculdade de Medicina FMUSP, Universidade de São Paulo, São Paulo 05403-000, Brazil
| | - Cindy Y Sonoda
- Otorhinolaryngology/LIM32, Hospital das Clínicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo 01246-000, Brazil
| | - Vinícius M Borges
- Centro de Pesquisas sobre o Genoma Humano e Células-Tronco, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo 05508-900, Brazil
| | - Laura G Vasconcelos
- Departamento de Otorrinolaringologia, Faculdade de Medicina FMUSP, Universidade de São Paulo, São Paulo 05403-000, Brazil
| | - Roberto M O Beck
- Departamento de Otorrinolaringologia, Faculdade de Medicina FMUSP, Universidade de São Paulo, São Paulo 05403-000, Brazil
| | - Signe S Grasel
- Departamento de Otorrinolaringologia, Faculdade de Medicina FMUSP, Universidade de São Paulo, São Paulo 05403-000, Brazil
| | - Daniel J Jagger
- UCL Ear Institute, University College London, London WC1E 6BT, UK
| | - Nicolas Grillet
- Department of Otolaryngology - Head and Neck Surgery, Stanford University, Stanford, CA 94305, USA
| | - Ricardo F Bento
- Otorhinolaryngology/LIM32, Hospital das Clínicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo 01246-000, Brazil.,Departamento de Otorrinolaringologia, Faculdade de Medicina FMUSP, Universidade de São Paulo, São Paulo 05403-000, Brazil
| | - Regina C Mingroni-Netto
- Centro de Pesquisas sobre o Genoma Humano e Células-Tronco, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo 05508-900, Brazil
| | - Jeanne Oiticica
- Otorhinolaryngology/LIM32, Hospital das Clínicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo 01246-000, Brazil.,Departamento de Otorrinolaringologia, Faculdade de Medicina FMUSP, Universidade de São Paulo, São Paulo 05403-000, Brazil
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33
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Hearing Screening Combined with Target Gene Panel Testing Increased Etiological Diagnostic Yield in Deaf Children. Neural Plast 2021; 2021:6151973. [PMID: 34335733 PMCID: PMC8324351 DOI: 10.1155/2021/6151973] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 06/09/2021] [Accepted: 07/11/2021] [Indexed: 12/16/2022] Open
Abstract
Genetic testing is the gold standard for exploring the etiology of congenital hearing loss. Here, we enrolled 137 Chinese patients with congenital hearing loss to describe the molecular epidemiology by using 127 gene panel testing or 159 variant testing. Sixty-three deaf children received 127 gene panel testing, while seventy-four patients received 159 variant testing. By use of 127 gene panel testing, more mutant genes and variants were identified. The most frequent mutant genes were GJB2, SLC26A4, MYO15A, CDH23, and OTOF. By analyzing the patients who received 127 gene panel testing, we found that 51 deaf children carried variants which were not included in 159 variant testing. Therefore, a large number of patients would be misdiagnosed if only 159 variant testing is used. This study highlights the advantage of 127 gene panel testing, and it suggests that broader genetic testing should be done to identify the genetic etiology of congenital hearing loss.
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34
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Hirsch Y, Tangshewinsirikul C, Booth KT, Azaiez H, Yefet D, Quint A, Weiden T, Brownstein Z, Macarov M, Davidov B, Pappas J, Rabin R, Kenna MA, Oza AM, Lafferty K, Amr SS, Rehm HL, Kolbe DL, Frees K, Nishimura C, Luo M, Farra C, Morton CC, Scher SY, Ekstein J, Avraham KB, Smith RJH, Shen J. A synonymous variant in MYO15A enriched in the Ashkenazi Jewish population causes autosomal recessive hearing loss due to abnormal splicing. Eur J Hum Genet 2021; 29:988-997. [PMID: 33398081 PMCID: PMC8187401 DOI: 10.1038/s41431-020-00790-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 11/04/2020] [Accepted: 11/25/2020] [Indexed: 11/09/2022] Open
Abstract
Nonsyndromic hearing loss is genetically heterogeneous. Despite comprehensive genetic testing, many cases remain unsolved because the clinical significance of identified variants is uncertain or because biallelic pathogenic variants are not identified for presumed autosomal recessive cases. Common synonymous variants are often disregarded. Determining the pathogenicity of synonymous variants may improve genetic diagnosis. We report a synonymous variant c.9861 C > T/p.(Gly3287=) in MYO15A in homozygosity or compound heterozygosity with another pathogenic or likely pathogenic MYO15A variant in 10 unrelated families with nonsyndromic sensorineural hearing loss. Biallelic variants in MYO15A were identified in 21 affected and were absent in 22 unaffected siblings. A mini-gene assay confirms that the synonymous variant leads to abnormal splicing. The variant is enriched in the Ashkenazi Jewish population. Individuals carrying biallelic variants involving c.9861 C > T often exhibit progressive post-lingual hearing loss distinct from the congenital profound deafness typically associated with biallelic loss-of-function MYO15A variants. This study establishes the pathogenicity of the c.9861 C > T variant in MYO15A and expands the phenotypic spectrum of MYO15A-related hearing loss. Our work also highlights the importance of multicenter collaboration and data sharing to establish the pathogenicity of a relatively common synonymous variant for improved diagnosis and management of hearing loss.
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Affiliation(s)
- Yoel Hirsch
- Dor Yeshorim, Committee for Prevention of Jewish Genetic Diseases, Brooklyn, NY, 11211, USA
| | - Chayada Tangshewinsirikul
- Division of Maternal Fetal Medicine, Department of Obstetrics and Gynecology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, 10400, Thailand
- Department of Obstetrics and Gynecology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Kevin T Booth
- Molecular Otolaryngology and Renal Research Laboratories, The University of Iowa, Iowa City, IA, 52242, USA
- Department of Neurobiology, Harvard Medical School, Boston, MA, 02215, USA
| | - Hela Azaiez
- Molecular Otolaryngology and Renal Research Laboratories, The University of Iowa, Iowa City, IA, 52242, USA
| | - Devorah Yefet
- Dor Yeshorim, Committee for Prevention of Jewish Genetic Diseases, Jerusalem, 91506, Israel
| | - Adina Quint
- Dor Yeshorim, Committee for Prevention of Jewish Genetic Diseases, Jerusalem, 91506, Israel
| | - Tzvi Weiden
- Dor Yeshorim, Committee for Prevention of Jewish Genetic Diseases, Jerusalem, 91506, Israel
| | - Zippora Brownstein
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Michal Macarov
- Department of Genetics and Metabolic Diseases, Hadassah Medical Center, Jerusalem, 91120, Israel
| | - Bella Davidov
- Department of Medical Genetics, Rabin Medical Center, Petah Tikva, 49100, Israel
| | - John Pappas
- Department of Pediatrics, New York University School of Medicine, New York, NY, 10016, USA
| | - Rachel Rabin
- Department of Pediatrics, New York University School of Medicine, New York, NY, 10016, USA
| | - Margaret A Kenna
- Department of Otolaryngology and Communication Enhancement, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Harvard Medical School Center for Hereditary Deafness, Boston, MA, 02115, USA
| | - Andrea M Oza
- Department of Otolaryngology and Communication Enhancement, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, Cambridge, MA, 02139, USA
| | - Katherine Lafferty
- Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, Cambridge, MA, 02139, USA
- Maine Medical Center, Scarborough, ME, 04074, USA
| | - Sami S Amr
- Harvard Medical School Center for Hereditary Deafness, Boston, MA, 02115, USA
- Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, Cambridge, MA, 02139, USA
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Heidi L Rehm
- Harvard Medical School Center for Hereditary Deafness, Boston, MA, 02115, USA
- Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, Cambridge, MA, 02139, USA
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Diana L Kolbe
- Molecular Otolaryngology and Renal Research Laboratories, The University of Iowa, Iowa City, IA, 52242, USA
| | - Kathy Frees
- Molecular Otolaryngology and Renal Research Laboratories, The University of Iowa, Iowa City, IA, 52242, USA
| | - Carla Nishimura
- Molecular Otolaryngology and Renal Research Laboratories, The University of Iowa, Iowa City, IA, 52242, USA
| | - Minjie Luo
- The Children's Hospital of Philadelphia, The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Chantal Farra
- Medical Genetics Unit, American University of Beirut Medical Center, AUBMC, 1107 2020, Beirut, Lebanon
| | - Cynthia C Morton
- Department of Obstetrics and Gynecology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Harvard Medical School Center for Hereditary Deafness, Boston, MA, 02115, USA
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Manchester Centre for Audiology and Deafness, School of Health Sciences, The University of Manchester, Manchester, M13 9PL, UK
| | - Sholem Y Scher
- Dor Yeshorim, Committee for Prevention of Jewish Genetic Diseases, Brooklyn, NY, 11211, USA
| | - Josef Ekstein
- Dor Yeshorim, Committee for Prevention of Jewish Genetic Diseases, Brooklyn, NY, 11211, USA
| | - Karen B Avraham
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, 6997801, Israel.
| | - Richard J H Smith
- Molecular Otolaryngology and Renal Research Laboratories, The University of Iowa, Iowa City, IA, 52242, USA.
| | - Jun Shen
- Harvard Medical School Center for Hereditary Deafness, Boston, MA, 02115, USA.
- Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, Cambridge, MA, 02139, USA.
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA.
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Innovative Artificial Intelligence Approach for Hearing-Loss Symptoms Identification Model Using Machine Learning Techniques. SUSTAINABILITY 2021. [DOI: 10.3390/su13105406] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Physicians depend on their insight and experience and on a fundamentally indicative or symptomatic approach to decide on the possible ailment of a patient. However, numerous phases of problem identification and longer strategies can prompt a longer time for consulting and can subsequently cause other patients that require attention to wait for longer. This can bring about pressure and tension concerning those patients. In this study, we focus on developing a decision-support system for diagnosing the symptoms as a result of hearing loss. The model is implemented by utilizing machine learning techniques. The Frequent Pattern Growth (FP-Growth) algorithm is used as a feature transformation method and the multivariate Bernoulli naïve Bayes classification model as the classifier. To find the correlation that exists between the hearing thresholds and symptoms of hearing loss, the FP-Growth and association rule algorithms were first used to experiment with small sample and large sample datasets. The result of these two experiments showed the existence of this relationship, and that the performance of the hybrid of the FP-Growth and naïve Bayes algorithms in identifying hearing-loss symptoms was found to be efficient, with a very small error rate. The average accuracy rate and average error rate for the multivariate Bernoulli model with FP-Growth feature transformation, using five training sets, are 98.25% and 1.73%, respectively.
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Lee JH, Hwang YJ, Li H, Kim H, Suh MW, Han D, Oh SH. In-depth proteome of perilymph in guinea pig model. Proteomics 2021; 21:e2000138. [PMID: 33459488 DOI: 10.1002/pmic.202000138] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 11/13/2020] [Accepted: 12/07/2020] [Indexed: 01/10/2023]
Abstract
The vast majority of sensorineural hearing loss is caused by impairment of the inner ear cells. Proteomic analysis of perilymph may therefore improve our understanding of inner ear diseases and hearing loss. However, the investigation of the human perilymph proteome was limited due to technical difficulties in perilymph sampling. The guinea pig (Cavia porcellus) is frequently used as an experimental model in preclinical hearing research. In this study, we analyzed samples of perilymph collected from 12 guinea pigs to overcome limited experimental information regarding its proteome. We identified a total of 1413 proteins, establishing a greatly expanded proteome of the previously inferred guinea pig perilymph. This provides a comprehensive proteomic resource for the research community, which will facilitate future molecular-phenotypic studies using the guinea pig as an experimental model of relevance to human inner ear biology.
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Affiliation(s)
- Jung Hun Lee
- Proteomics Core Facility, Biomedical Research Institute, Seoul National University Hospital, Seoul, Korea
| | - Yu-Jung Hwang
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Hospital, Seoul, South Korea
| | - Hui Li
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Hospital, Seoul, South Korea
| | - Hyeyoon Kim
- Proteomics Core Facility, Biomedical Research Institute, Seoul National University Hospital, Seoul, Korea
| | - Myung-Whan Suh
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Hospital, Seoul, South Korea
| | - Dohyun Han
- Proteomics Core Facility, Biomedical Research Institute, Seoul National University Hospital, Seoul, Korea
| | - Seung-Ha Oh
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Hospital, Seoul, South Korea
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Biological and clinical significance of dysplastic hematopoiesis in patients with newly diagnosed multiple myeloma. Blood 2021; 135:2375-2387. [PMID: 32299093 DOI: 10.1182/blood.2019003382] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 03/15/2020] [Indexed: 02/07/2023] Open
Abstract
Risk of developing myelodysplastic syndrome (MDS) is significantly increased in both multiple myeloma (MM) and monoclonal gammopathy of undetermined significance, suggesting that it is therapy independent. However, the incidence and sequelae of dysplastic hematopoiesis at diagnosis are unknown. Here, we used multidimensional flow cytometry (MFC) to prospectively screen for the presence of MDS-associated phenotypic alterations (MDS-PA) in the bone marrow of 285 patients with MM enrolled in the PETHEMA/GEM2012MENOS65 trial (#NCT01916252). We investigated the clinical significance of monocytic MDS-PA in a larger series of 1252 patients enrolled in 4 PETHEMA/GEM protocols. At diagnosis, 33 (11.6%) of 285 cases displayed MDS-PA. Bulk and single-cell-targeted sequencing of MDS recurrently mutated genes in CD34+ progenitors (and dysplastic lineages) from 67 patients revealed clonal hematopoiesis in 13 (50%) of 26 cases with MDS-PA vs 9 (22%) of 41 without MDS-PA; TET2 and NRAS were the most frequently mutated genes. Dynamics of MDS-PA at diagnosis and after autologous transplant were evaluated in 86 of 285 patients and showed that in most cases (69 of 86 [80%]), MDS-PA either persisted or remained absent in patients with or without MDS-PA at diagnosis, respectively. Noteworthy, MDS-associated mutations infrequently emerged after high-dose therapy. Based on MFC profiling, patients with MDS-PA have altered hematopoiesis and T regulatory cell distribution in the tumor microenvironment. Importantly, the presence of monocytic MDS-PA at diagnosis anticipated greater risk of hematologic toxicity and was independently associated with inferior progression-free survival (hazard ratio, 1.5; P = .02) and overall survival (hazard ratio, 1.7; P = .01). This study reveals the biological and clinical significance of dysplastic hematopoiesis in newly diagnosed MM, which can be screened with moderate sensitivity using cost-effective MFC.
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Sánchez-Fernández P, Riobello C, Costales M, Vivanco B, Cabal VN, García-Marín R, Suárez-Fernández L, López F, Cabanillas R, Hermsen MA, Llorente JL. Next-generation sequencing for identification of actionable gene mutations in intestinal-type sinonasal adenocarcinoma. Sci Rep 2021; 11:2247. [PMID: 33500480 PMCID: PMC7838394 DOI: 10.1038/s41598-020-80242-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 11/26/2020] [Indexed: 01/30/2023] Open
Abstract
Intestinal-type sinonasal adenocarcinoma (ITAC) is a rare tumor carrying poor prognosis and needing new treatment options. The aim of this study was to identify actionable gene mutations that can guide new personalized target-specific therapies in ITAC patients. A series of 48 tumor and 27 corresponding germline DNA samples were analyzed by next generation sequencing using a panel of 120 genes. In total, 223 sequence variants were found in 70 genes. Matched tumor/germline comparison in 27 cases revealed that 57% were in fact germline variants. In 20 of these 27 cases, 58 somatic variants in 33 different genes were identified, the most frequent being PIK3CA (5 cases), APC and ATM (4 cases), and KRAS, NF1, LRP1B and BRCA1 (3 cases). Many of the somatic gene variants affected PI3K, MAPK/ERK, WNT and DNA repair signaling pathways, although not in a mutually exclusive manner. None of the alterations were related to histological ITAC subtype, tumor stage or survival. Our data showed that thorough interpretation of somatic mutations requires sequencing analysis of the corresponding germline DNA. Potentially actionable somatic mutations were found in 20 of 27 cases, 8 of which being biomarkers of FDA-approved targeted therapies. Our data implicate new possibilities for personalized treatment of ITAC patients.
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Affiliation(s)
- Paula Sánchez-Fernández
- grid.411052.30000 0001 2176 9028Department Otolaryngology, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - Cristina Riobello
- grid.10863.3c0000 0001 2164 6351Department Head and Neck Oncology, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Centro de Investigación Biomédica en Red (CIBER-ONC), Edf. FINBA, N-1 F49, C/ Avenida de Roma s/n, 33011 Oviedo, Spain
| | - María Costales
- grid.411052.30000 0001 2176 9028Department Otolaryngology, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - Blanca Vivanco
- grid.411052.30000 0001 2176 9028Department Pathology, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - Virginia N. Cabal
- grid.10863.3c0000 0001 2164 6351Department Head and Neck Oncology, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Centro de Investigación Biomédica en Red (CIBER-ONC), Edf. FINBA, N-1 F49, C/ Avenida de Roma s/n, 33011 Oviedo, Spain
| | - Rocío García-Marín
- grid.10863.3c0000 0001 2164 6351Department Head and Neck Oncology, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Centro de Investigación Biomédica en Red (CIBER-ONC), Edf. FINBA, N-1 F49, C/ Avenida de Roma s/n, 33011 Oviedo, Spain
| | - Laura Suárez-Fernández
- grid.10863.3c0000 0001 2164 6351Department Head and Neck Oncology, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Centro de Investigación Biomédica en Red (CIBER-ONC), Edf. FINBA, N-1 F49, C/ Avenida de Roma s/n, 33011 Oviedo, Spain
| | - Fernando López
- grid.411052.30000 0001 2176 9028Department Otolaryngology, Hospital Universitario Central de Asturias, Oviedo, Spain
| | | | - Mario A. Hermsen
- grid.10863.3c0000 0001 2164 6351Department Head and Neck Oncology, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Centro de Investigación Biomédica en Red (CIBER-ONC), Edf. FINBA, N-1 F49, C/ Avenida de Roma s/n, 33011 Oviedo, Spain
| | - José Luis Llorente
- grid.411052.30000 0001 2176 9028Department Otolaryngology, Hospital Universitario Central de Asturias, Oviedo, Spain
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Downie L, Amor DJ, Halliday J, Lewis S, Martyn M, Goranitis I. Exome Sequencing for Isolated Congenital Hearing Loss: A Cost-Effectiveness Analysis. Laryngoscope 2020; 131:E2371-E2377. [PMID: 33382469 DOI: 10.1002/lary.29356] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 12/14/2020] [Accepted: 12/15/2020] [Indexed: 12/19/2022]
Abstract
OBJECTIVES/HYPOTHESIS To assess the relative cost-effectiveness of exome sequencing for isolated congenital deafness compared with standard care. STUDY DESIGN Incremental cost-effectiveness and cost-benefit analyses were undertaken from the perspective of the Australian healthcare system using an 18-year time horizon. METHODS A decision tree was used to model the costs and outcomes associated with exome sequencing and standard care for infants presenting with isolated congenital deafness. RESULTS Exome sequencing resulted in an incremental cost of AU$1,000 per child and an additional 30 diagnoses per 100 children tested. The incremental cost-effectiveness ratio was AU$3,333 per additional diagnosis. The mean societal willingness to pay for exome sequencing was estimated at AU$4,600 per child tested relative to standard care, resulting in a positive net benefit of AU$3,600. Deterministic and probabilistic sensitivity analyses confirmed the cost-effectiveness of exome sequencing. CONCLUSIONS Our findings demonstrate the cost-effectiveness of exome sequencing in congenital hearing loss, through increased diagnostic rate and consequent improved process of care by reducing or ceasing diagnostic investigation or facilitating targeted further investigation. We recommend equitable funding for exome sequencing in infants presenting with isolated congenital hearing loss. LEVEL OF EVIDENCE N/A. Laryngoscope, 131:E2371-E2377, 2021.
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Affiliation(s)
- Lilian Downie
- Victorian Clinical Genetics Services, Melbourne, Victoria, Australia.,Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Royal Children's Hospital, Melbourne, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
| | - David J Amor
- Victorian Clinical Genetics Services, Melbourne, Victoria, Australia.,Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Royal Children's Hospital, Melbourne, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
| | - Jane Halliday
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
| | - Sharon Lewis
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
| | - Melissa Martyn
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia.,Melbourne Genomics Health Alliance, Melbourne, Victoria, Australia
| | - Ilias Goranitis
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Centre for Health Policy, University of Melbourne, Melbourne, Victoria, Australia.,Australian Genomics Health Alliance, Melbourne, Victoria, Australia
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40
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Radixin modulates the function of outer hair cell stereocilia. Commun Biol 2020; 3:792. [PMID: 33361775 PMCID: PMC7758333 DOI: 10.1038/s42003-020-01506-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 11/18/2020] [Indexed: 01/07/2023] Open
Abstract
The stereocilia of the inner ear sensory cells contain the actin-binding protein radixin, encoded by RDX. Radixin is important for hearing but remains functionally obscure. To determine how radixin influences hearing sensitivity, we used a custom rapid imaging technique to visualize stereocilia motion while measuring electrical potential amplitudes during acoustic stimulation. Radixin inhibition decreased sound-evoked electrical potentials. Other functional measures, including electrically induced sensory cell motility and sound-evoked stereocilia deflections, showed a minor amplitude increase. These unique functional alterations demonstrate radixin as necessary for conversion of sound into electrical signals at acoustic rates. We identified patients with RDX variants with normal hearing at birth who showed rapidly deteriorating hearing during the first months of life. This may be overlooked by newborn hearing screening and explained by multiple disturbances in postnatal sensory cells. We conclude radixin is necessary for ensuring normal conversion of sound to electrical signals in the inner ear. Sonal Prasad et al. identify several mutations in the radixin (RDX) gene that are associated with early-life hearing loss. Using a guinea pig model, they propose that radixin helps convert sound into electrical signals in the mature inner ear.
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Puusepp S, Reinson K, Pajusalu S, van Kuilenburg ABP, Dobritzsch D, Roelofsen J, Stenzel W, Õunap K. Atypical presentation of Arts syndrome due to a novel hemizygous loss-of-function variant in the PRPS1 gene. Mol Genet Metab Rep 2020; 25:100677. [PMID: 33294372 PMCID: PMC7689168 DOI: 10.1016/j.ymgmr.2020.100677] [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: 08/17/2020] [Revised: 11/06/2020] [Accepted: 11/07/2020] [Indexed: 11/30/2022] Open
Abstract
The PRPS1 gene, located on Xq22.3, encodes phosphoribosyl-pyrophosphate synthetase (PRPS), a key enzyme in de novo purine synthesis. Three clinical phenotypes are associated with loss-of-function PRPS1 variants and decreased PRPS activity: Arts syndrome (OMIM: 301835), Charcot–Marie–Tooth disease type 5 (CMTX5, OMIM: 311070), and nonsyndromic X-linked deafness (DFN2, OMIM: 304500). Hearing loss is present in all cases. CMTX5 patients also show peripheral neuropathy and optic atrophy. Arts syndrome includes developmental delay, intellectual disability, ataxia, and susceptibility to infections, in addition to the above three features. Gain-of-function PRPS1 variants result in PRPS superactivity (OMIM: 300661) with hyperuricemia and gout. We report a 6-year-old boy who presented with marked generalized muscular hypotonia, global developmental delay, lack of speech, trunk instability, exercise intolerance, hypomimic face with open mouth, oropharyngeal dysphagia, dysarthria, and frequent upper respiratory tract infections. However, his nerve conduction velocity, audiologic, and funduscopic investigations were normal. A novel hemizygous variant, c.130A > G p.(Ile44Val), was found in the PRPS1 gene by panel sequencing. PRPS activity in erythrocytes was markedly reduced, confirming the pathogenicity of the variant. Serum uric acid and urinary purine and pyrimidine metabolite levels were normal. In conclusion, we present a novel PRPS1 loss-of-function variant in a patient with some clinical features of Arts syndrome, but lacking a major attribute, hearing loss, which is congenital/early-onset in all other reported Arts syndrome patients. In addition, it is important to acknowledge that normal levels of serum and urinary purine and pyrimidine metabolites do not exclude PRPS1-related disorders. We describe a male patient with atypical presentation of Arts syndrome. Our patient harbors a novel loss-of-function variant in the PRPS1 gene. The purine and pyrimidine levels can be normal in patients with decreased PRPS activity.
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Affiliation(s)
- Sanna Puusepp
- Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia.,Department of Clinical Genetics, Institute of Clinical Medicine, Faculty of Medicine, University of Tartu, Tartu, Estonia
| | - Karit Reinson
- Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia.,Department of Clinical Genetics, Institute of Clinical Medicine, Faculty of Medicine, University of Tartu, Tartu, Estonia
| | - Sander Pajusalu
- Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia.,Department of Clinical Genetics, Institute of Clinical Medicine, Faculty of Medicine, University of Tartu, Tartu, Estonia.,Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - André B P van Kuilenburg
- Department of Clinical Chemistry, Cancer Center Amsterdam, Amsterdam Gastroenterology & Metabolism, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | | | - Jeroen Roelofsen
- Department of Clinical Chemistry, Cancer Center Amsterdam, Amsterdam Gastroenterology & Metabolism, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Werner Stenzel
- Department of Neuropathology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.,Leibniz Science Campus Chronic Inflammation, Berlin, Germany
| | - Katrin Õunap
- Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia.,Department of Clinical Genetics, Institute of Clinical Medicine, Faculty of Medicine, University of Tartu, Tartu, Estonia
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Improving the Management of Patients with Hearing Loss by the Implementation of an NGS Panel in Clinical Practice. Genes (Basel) 2020; 11:genes11121467. [PMID: 33297549 PMCID: PMC7762334 DOI: 10.3390/genes11121467] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 12/02/2020] [Accepted: 12/03/2020] [Indexed: 12/15/2022] Open
Abstract
A cohort of 128 patients from 118 families diagnosed with non-syndromic or syndromic hearing loss (HL) underwent an exhaustive clinical evaluation. Molecular analysis was performed using targeted next-generation sequencing (NGS) with a custom panel that included 59 genes associated with non-syndromic HL or syndromic HL. Variants were prioritized according to the minimum allele frequency and classified according to the American College of Medical Genetics and Genomics guidelines. Variant(s) responsible for the disease were detected in a 40% of families including autosomal recessive (AR), autosomal dominant (AD) and X-linked patterns of inheritance. We identified pathogenic or likely pathogenic variants in 26 different genes, 15 with AR inheritance pattern, 9 with AD and 2 that are X-linked. Fourteen of the found variants are novel. This study highlights the clinical utility of targeted NGS for sensorineural hearing loss. The optimal panel for HL must be designed according to the spectrum of the most represented genes in a given population and the laboratory capabilities considering the pressure on healthcare.
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Diñeiro M, Capín R, Cifuentes GÁ, Fernández‐Vega B, Villota E, Otero A, Santiago A, Pruneda PC, Castillo D, Viejo‐Díaz M, Hernando I, Durán NS, Álvarez R, Lago CG, Ordóñez GR, Fernández‐Vega Á, Cabanillas R, Cadiñanos J. Comprehensive genomic diagnosis of inherited retinal and optical nerve disorders reveals hidden syndromes and personalized therapeutic options. Acta Ophthalmol 2020; 98:e1034-e1048. [PMID: 32483926 PMCID: PMC7754416 DOI: 10.1111/aos.14479] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 04/29/2020] [Indexed: 01/14/2023]
Abstract
PURPOSE In the era of precision medicine, genomic characterization of blind patients is critical. Here, we evaluate the effects of comprehensive genetic analysis on the etiologic diagnosis of potentially hereditary vision loss and its impact on clinical management. METHODS We studied 100 non-syndromic and syndromic Spanish patients with a clinical diagnosis of blindness caused by alterations on the retina, choroid, vitreous and/or optic nerve. We used a next-generation sequencing (NGS) panel (OFTALMOgenics™), developed and validated within this study, including up to 362 genes previously associated with these conditions. RESULTS We identified the genetic cause of blindness in 45% of patients (45/100). A total of 28.9% of genetically diagnosed cases (13/45) were syndromic and, of those, in 30.8% (4/13) extraophthalmic features had been overlooked and/or not related to visual impairment before genetic testing, including cases with Mainzer-Saldino, Bardet-Biedl, mucolipidosis and MLCRD syndromes. In two additional cases-syndromic blindness had been proposed before, but not specifically diagnosed, and one patient with Heimler syndrome had been misdiagnosed as an Usher case before testing. 33.3% of the genetically diagnosed patients (15/45) had causative variants in genes targeted by clinical trials exploring the curative potential of gene therapy approaches. CONCLUSION Comprehensive genomic testing provided clinically relevant insights in a large proportion of blind patients, identifying potential therapeutic opportunities or previously undiagnosed syndromes in 42.2% of the genetically diagnosed cases (19/45).
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Affiliation(s)
- Marta Diñeiro
- Instituto de Medicina Oncológica y Molecular de Asturias (IMOMA) S. A.OviedoSpain
| | - Raquel Capín
- Instituto de Medicina Oncológica y Molecular de Asturias (IMOMA) S. A.OviedoSpain
| | | | | | - Eva Villota
- Instituto Oftalmológico Fernández‐Vega (IOFV)OviedoSpain
| | - Andrea Otero
- Instituto de Medicina Oncológica y Molecular de Asturias (IMOMA) S. A.OviedoSpain
| | - Adrián Santiago
- Instituto de Medicina Oncológica y Molecular de Asturias (IMOMA) S. A.OviedoSpain
| | | | - David Castillo
- Disease Research And Medicine (DREAMgenics) S. L.OviedoSpain
| | | | - Inés Hernando
- Hospital Universitario Central de AsturiasOviedoSpain
| | - Noelia S. Durán
- Instituto de Medicina Oncológica y Molecular de Asturias (IMOMA) S. A.OviedoSpain
| | - Rebeca Álvarez
- Instituto de Medicina Oncológica y Molecular de Asturias (IMOMA) S. A.OviedoSpain
| | - Claudia G. Lago
- Instituto de Medicina Oncológica y Molecular de Asturias (IMOMA) S. A.OviedoSpain
| | | | | | - Rubén Cabanillas
- Instituto de Medicina Oncológica y Molecular de Asturias (IMOMA) S. A.OviedoSpain
| | - Juan Cadiñanos
- Instituto de Medicina Oncológica y Molecular de Asturias (IMOMA) S. A.OviedoSpain
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Morgan A, Lenarduzzi S, Spedicati B, Cattaruzzi E, Murru FM, Pelliccione G, Mazzà D, Zollino M, Graziano C, Ambrosetti U, Seri M, Faletra F, Girotto G. Lights and Shadows in the Genetics of Syndromic and Non-Syndromic Hearing Loss in the Italian Population. Genes (Basel) 2020; 11:genes11111237. [PMID: 33105617 PMCID: PMC7690429 DOI: 10.3390/genes11111237] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 10/15/2020] [Accepted: 10/20/2020] [Indexed: 11/16/2022] Open
Abstract
Hearing loss (HL), both syndromic (SHL) and non-syndromic (NSHL), is the most common sensory disorder, affecting ~460 million people worldwide. More than 50% of the congenital/childhood cases are attributable to genetic causes, highlighting the importance of genetic testing in this class of disorders. Here we applied a multi-step strategy for the molecular diagnosis of HL in 125 patients, which included: (1) an accurate clinical evaluation, (2) the analysis of GJB2, GJB6, and MT-RNR1 genes, (3) the evaluation STRC-CATSPER2 and OTOA deletions via Multiplex Ligation Probe Amplification (MLPA), (4) Whole Exome Sequencing (WES) in patients negative to steps 2 and 3. Our approach led to the characterization of 50% of the NSHL cases, confirming both the relevant role of the GJB2 (20% of cases) and STRC deletions (6% of cases), and the high genetic heterogeneity of NSHL. Moreover, due to the genetic findings, 4% of apparent NSHL patients have been re-diagnosed as SHL. Finally, WES characterized 86% of SHL patients, supporting the role of already know disease-genes. Overall, our approach proved to be efficient in identifying the molecular cause of HL, providing essential information for the patients’ future management.
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Affiliation(s)
- Anna Morgan
- Institute for Maternal and Child Health–IRCCS “Burlo Garofolo”, 34137 Trieste, Italy; (S.L.); (B.S.); (E.C.); (F.M.M.); (G.P.); (D.M.); (F.F.); (G.G.)
- Correspondence:
| | - Stefania Lenarduzzi
- Institute for Maternal and Child Health–IRCCS “Burlo Garofolo”, 34137 Trieste, Italy; (S.L.); (B.S.); (E.C.); (F.M.M.); (G.P.); (D.M.); (F.F.); (G.G.)
| | - Beatrice Spedicati
- Institute for Maternal and Child Health–IRCCS “Burlo Garofolo”, 34137 Trieste, Italy; (S.L.); (B.S.); (E.C.); (F.M.M.); (G.P.); (D.M.); (F.F.); (G.G.)
- Department of Medicine, Surgery and Health Sciences, University of Trieste, 34125 Trieste, Italy
| | - Elisabetta Cattaruzzi
- Institute for Maternal and Child Health–IRCCS “Burlo Garofolo”, 34137 Trieste, Italy; (S.L.); (B.S.); (E.C.); (F.M.M.); (G.P.); (D.M.); (F.F.); (G.G.)
| | - Flora Maria Murru
- Institute for Maternal and Child Health–IRCCS “Burlo Garofolo”, 34137 Trieste, Italy; (S.L.); (B.S.); (E.C.); (F.M.M.); (G.P.); (D.M.); (F.F.); (G.G.)
| | - Giulia Pelliccione
- Institute for Maternal and Child Health–IRCCS “Burlo Garofolo”, 34137 Trieste, Italy; (S.L.); (B.S.); (E.C.); (F.M.M.); (G.P.); (D.M.); (F.F.); (G.G.)
| | - Daniela Mazzà
- Institute for Maternal and Child Health–IRCCS “Burlo Garofolo”, 34137 Trieste, Italy; (S.L.); (B.S.); (E.C.); (F.M.M.); (G.P.); (D.M.); (F.F.); (G.G.)
| | - Marcella Zollino
- Fondazione Policlinico Universitario A. Gemelli, IRCCS, UOC Genetica, 00168 Rome, Italy;
- Istituto di Medicina Genomica, Università Cattolica Sacro Cuore, 00168 Rome, Italy
| | - Claudio Graziano
- Unit of Medical Genetics, S. Orsola-Malpighi Hospital, 40138 Bologna, Italy; (C.G.); (M.S.)
| | - Umberto Ambrosetti
- Audiology and audiophonology, University of Milano/Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, 20122 Milano, Italy;
| | - Marco Seri
- Unit of Medical Genetics, S. Orsola-Malpighi Hospital, 40138 Bologna, Italy; (C.G.); (M.S.)
| | - Flavio Faletra
- Institute for Maternal and Child Health–IRCCS “Burlo Garofolo”, 34137 Trieste, Italy; (S.L.); (B.S.); (E.C.); (F.M.M.); (G.P.); (D.M.); (F.F.); (G.G.)
| | - Giorgia Girotto
- Institute for Maternal and Child Health–IRCCS “Burlo Garofolo”, 34137 Trieste, Italy; (S.L.); (B.S.); (E.C.); (F.M.M.); (G.P.); (D.M.); (F.F.); (G.G.)
- Department of Medicine, Surgery and Health Sciences, University of Trieste, 34125 Trieste, Italy
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Vona B, Doll J, Hofrichter MA, Haaf T. Non-syndromic hearing loss: clinical and diagnostic challenges. MED GENET-BERLIN 2020. [DOI: 10.1515/medgen-2020-2022] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Abstract
Hereditary hearing loss is clinically and genetically heterogeneous. There are presently over 120 genes that have been associated with non-syndromic hearing loss and many more that are associated with syndromic forms. Despite an increasing number of genes that have been implemented into routine molecular genetic diagnostic testing, the diagnostic yield from European patient cohorts with hereditary hearing loss remains around the 50 % mark. This attests to the many gaps of knowledge the field is currently working toward resolving. It can be expected that many more genes await identification. However, it can also be expected, for example, that the mutational signatures of the known genes are still unclear, especially variants in non-coding or regulatory regions influencing gene expression. This review summarizes several challenges in the clinical and diagnostic setting for hereditary hearing loss with emphasis on syndromes that mimic non-syndromic forms of hearing loss in young children and other factors that heavily influence diagnostic rates. A molecular genetic diagnosis for patients with hearing loss opens several additional avenues, such as patient tailored selection of the best currently available treatment modalities, an understanding of the prognosis, and supporting family planning decisions. In the near future, a genetic diagnosis may enable patients to engage in preclinical trials for the development of therapeutics.
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Affiliation(s)
- Barbara Vona
- Tübingen Hearing Research Centre, Department of Otolaryngology – Head & Neck Surgery , Eberhard Karls University , Elfriede-Aulhorn-Strasse 5 , Tübingen , Germany
| | - Julia Doll
- Institute of Human Genetics , Julius Maximilians University , Würzburg , Germany
| | | | - Thomas Haaf
- Institute of Human Genetics , Julius-Maximilians University Würzburg , Biozentrum, Am Hubland , Würzburg , Germany
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MITF variants cause nonsyndromic sensorineural hearing loss with autosomal recessive inheritance. Sci Rep 2020; 10:12712. [PMID: 32728090 PMCID: PMC7391749 DOI: 10.1038/s41598-020-69633-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 07/15/2020] [Indexed: 11/18/2022] Open
Abstract
MITF is a known gene underlying autosomal dominant hearing loss, Waardenburg syndrome (WS). Biallelic MITF mutations have been found associated with a rare hearing loss syndrome consisting eye abnormalities and albinism; and a more severe type of WS whose heterozygous parents were affected with classic WS in both cases. The aims of this study were to identify a new candidate gene causing autosomal recessive nonsyndromic hearing loss (ARNSHL) and confirm its causation by finding additional families affected with the candidate gene and supporting evidences from functional analyses. By using whole exome sequencing, we identified a homozygous c.1022G>A: p.Arg341His variant of MITF, which co-segregated with the hearing loss in five affected children of a consanguineous hearing couple. Targeted exome sequencing in a cohort of 130 NSHL individuals, using our in-house gene panel revealed a second family with c.1021C>T: p.Arg341Cys MITF variant. Functional studies confirmed that the Arg341His and Arg341Cys alleles yielded a normal sized MITF protein, with aberrant cytosolic localization as supported by the molecular model and the reporter assay. In conclusion, we demonstrate MITF as a new cause of ARNSHL, with heterozygous individuals free of symptoms. MITF should be included in clinical testing for NSHL, though it is rare.
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Targeted Next-Generation Sequencing Identified Compound Heterozygous Mutations in MYO15A as the Probable Cause of Nonsyndromic Deafness in a Chinese Han Family. Neural Plast 2020; 2020:6350479. [PMID: 32617096 PMCID: PMC7313121 DOI: 10.1155/2020/6350479] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 05/10/2020] [Accepted: 05/29/2020] [Indexed: 12/02/2022] Open
Abstract
Hearing loss is a highly heterogeneous disorder, with more than 60% of congenital cases caused by genetic factors. This study is aimed at identifying the genetic cause of congenital hearing loss in a Chinese Han family. Auditory evaluation before and after cochlear implantation and targeted next-generation sequencing of 140 deafness-related genes were performed for the deaf proband. Compound heterozygous mutations c.3658_3662del (p. E1221Wfs∗23) and c.6177+1G>T were identified in MYO15A as the only candidate pathogenic mutations cosegregated with the hearing loss in this family. These two variants were absent in 200 normal-hearing Chinese Hans and were classified as likely pathogenic and pathogenic, respectively, based on the ACMG guideline. Our study further expanded the mutation spectrum of MYO15A as the c.3658_3662del mutation is novel and confirmed that deaf patients with recessive MYO15A mutations have a good outcome for cochlear implantation.
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Lemos MC, Thakker RV. Hypoparathyroidism, deafness, and renal dysplasia syndrome: 20 Years after the identification of the first GATA3 mutations. Hum Mutat 2020; 41:1341-1350. [PMID: 32442337 DOI: 10.1002/humu.24052] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 04/28/2020] [Accepted: 05/16/2020] [Indexed: 12/12/2022]
Abstract
The hypoparathyroidism, deafness, and renal dysplasia (HDR) syndrome is an autosomal dominant disorder caused by heterozygous mutations of the GATA3 gene. In the last 20 years, since the identification of the genetic cause of the HDR syndrome, GATA3 mutations have been reported in 124 families (177 patients). The clinical aspects and molecular genetics of the HDR syndrome are reviewed here together with the reported mutations and phenotypes. Reported mutations consist of 40% frameshift deletions or insertions, 23% missense mutations, 14% nonsense mutations, 6% splice-site mutations, 1% in-frame deletions or insertions, 15% whole-gene deletions, and 1% whole-gene duplication. Missense mutations were found to cluster in the regions encoding the two GATA3 zinc-finger domains. Patients showed great clinical variability and the penetrance of each HDR defect increased with age. The most frequently observed abnormality was deafness (93%), followed by hypoparathyroidism (87%) and renal defects (61%). The mean age of diagnosis of HDR was 15.3, 7.5, and 14.0 years, respectively. However, patients with whole-gene deletions and protein-truncating mutations were diagnosed earlier than patients with missense mutations.
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Affiliation(s)
- Manuel C Lemos
- CICS-UBI, Health Sciences Research Centre, University of Beira Interior, Covilhã, Portugal
| | - Rajesh V Thakker
- Academic Endocrine Unit, Nuffield Department of Clinical Medicine, Oxford Centre for Diabetes, Endocrinology and Metabolism (OCDEM), Churchill Hospital, University of Oxford, Oxford, UK
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Rodrigo L, Campos-Asensio C, Rodríguez MÁ, Crespo I, Olmedillas H. Role of nutrition in the development and prevention of age-related hearing loss: A scoping review. J Formos Med Assoc 2020; 120:107-120. [PMID: 32473863 DOI: 10.1016/j.jfma.2020.05.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Revised: 05/07/2020] [Accepted: 05/08/2020] [Indexed: 11/18/2022] Open
Abstract
Age-related hearing loss (ARHL) is a major and increasingly prevalent health problem worldwide, causing disability and social isolation in the people who present it. This impairment is caused by genetic and environmental factors. Nutritional status has been identified as a related risk associated with hearing loss (HL). This scoping review aimed to characterize the links between HL and nutritional status. PubMed, Embase, Cochrane and Scopus databases were searched up to December 2019. Studies examining the relation between nutrition and dietary habits and HL were included. After screening 3510 citations, 22 publications were selected for inclusion in the current review, all of which were published between 2010 and 2019. Diets rich in saturated fats and cholesterol have deleterious effects on hearing that could be prevented by lower consumption. Conversely, greater consumption of fruit and vegetables, and of polyunsaturated fatty acids (omega-3) and anti-oxidants in the form of vitamins A, C, and E, prevent the development of ARHL. The current literature suggests a possible association between nutritional status and hearing loss. More studies are needed to better characterize the clinical consequences of this association.
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Affiliation(s)
- Luis Rodrigo
- Gastroenterology Unit, Hospital Universitario Central de Asturias (HUCA), Oviedo, Spain
| | | | | | - Irene Crespo
- Department of Functional Biology, University of Oviedo, Oviedo, Spain; Institute of Biomedicine, University of León, León, Spain
| | - Hugo Olmedillas
- Department of Functional Biology, University of Oviedo, Oviedo, Spain; Health Research Institute of the Principality of Asturias (ISPA), Oviedo, Spain.
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Congenital hearing impairment associated with peripheral cochlear nerve dysmyelination in glycosylation-deficient muscular dystrophy. PLoS Genet 2020; 16:e1008826. [PMID: 32453729 PMCID: PMC7274486 DOI: 10.1371/journal.pgen.1008826] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 06/05/2020] [Accepted: 05/04/2020] [Indexed: 02/06/2023] Open
Abstract
Hearing loss (HL) is one of the most common sensory impairments and etiologically and genetically heterogeneous disorders in humans. Muscular dystrophies (MDs) are neuromuscular disorders characterized by progressive degeneration of skeletal muscle accompanied by non-muscular symptoms. Aberrant glycosylation of α-dystroglycan causes at least eighteen subtypes of MD, now categorized as MD-dystroglycanopathy (MD-DG), with a wide spectrum of non-muscular symptoms. Despite a growing number of MD-DG subtypes and increasing evidence regarding their molecular pathogeneses, no comprehensive study has investigated sensorineural HL (SNHL) in MD-DG. Here, we found that two mouse models of MD-DG, Largemyd/myd and POMGnT1-KO mice, exhibited congenital, non-progressive, and mild-to-moderate SNHL in auditory brainstem response (ABR) accompanied by extended latency of wave I. Profoundly abnormal myelination was found at the peripheral segment of the cochlear nerve, which is rich in the glycosylated α-dystroglycan–laminin complex and demarcated by “the glial dome.” In addition, patients with Fukuyama congenital MD, a type of MD-DG, also had latent SNHL with extended latency of wave I in ABR. Collectively, these findings indicate that hearing impairment associated with impaired Schwann cell-mediated myelination at the peripheral segment of the cochlear nerve is a notable symptom of MD-DG. Hearing loss (HL) is one of the most common sensory impairments and heterogeneous disorders in humans. Up to 60% of HL cases are caused by genetic factors, and approximately 30% of genetic HL cases are syndromic. Although 400–700 genetic syndromes are associated with sensorineural HL (SNHL), caused due to problems in the nerve pathways from the cochlea to the brain, only about 45 genes are known to be associated with syndromic HL. Muscular dystrophies (MDs) are neuromuscular disorders characterized by progressive degeneration of skeletal muscle accompanied by non-muscular symptoms. MD-dystroglycanopathy (MD-DG), caused by aberrant glycosylation of α-dystroglycan, is an MD subtype with a wide spectrum of non-muscular symptoms. Despite a growing number of MD-DG subtypes (at least 18), no comprehensive study has investigated SNHL in MD-DG. Here, we found that hearing impairment was associated with abnormal myelination of the peripheral segment of the cochlear nerve caused by impaired dystrophin–dystroglycan complex in two mouse models (type 3 and 6) of MD-DG and in patients (type 4) with MD-DG. This is the first comprehensive study investigating SNHL in MD-DG. Our findings may provide new insights into understanding the pathogenic characteristics and mechanisms underlying inherited syndromic hearing impairment.
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