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Alerasool M, Eslahi A, Vona B, Kahaei MS, Mojaver NK, Rajati M, Pasdar A, Ghasemi MM, Saburi E, Ardehaie RM, Aval MH, Tale MR, Nourizadeh N, Afzalzadeh MR, Niknezhad HT, Mojarrad M. Genetic landscape of hearing loss in prelingual deaf patients of eastern Iran: Insights from exome sequencing analysis. Clin Genet 2024. [PMID: 39107234 DOI: 10.1111/cge.14599] [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: 04/17/2024] [Revised: 07/17/2024] [Accepted: 07/18/2024] [Indexed: 08/09/2024]
Abstract
Hearing loss is one of the most prevalent genetic disorders in humans. Locus and allelic heterogeneity cause fundamental challenges in hearing loss genetic diagnosis and management of patients and their families. This study examined the genetic profile of patients with prelingual hearing loss who were referred to the Genetic Foundation of Khorasan Razavi spanning over a decade. Deleterious variants in GJB2 were evaluated through Sanger sequencing among 745 non-syndromic hearing loss patients. Furthermore, exome sequencing was applied in 250 patients with negative GJB2 sequencing results and 30 patients with syndromic hearing loss. The findings revealed a relatively low frequency of GJB2 variants among the studied patients. Exome sequencing successfully identified the genetic causes of hearing loss in 70% of the patients. Moreover, variants in 10 genes, namely SLC26A4, MYO15A, TMPRSS3, TMC1, OTOF, CDH23, PJVK, MYO7A, TECTA, and PCDH15, accounted for 66% of the positive exome sequencing findings in this study. At least three prevalent founder alleles in the hearing-impaired population of eastern Iran were identified. This study emphasizes the efficiency of exome sequencing as a powerful tool for determining the etiology of prelingual hearing loss in the eastern Iranian population.
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Affiliation(s)
- Masoome Alerasool
- Faculty of Medicine, Department of Medical Genetics, Mashhad University of Medical Sciences, Mashhad, Iran
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Genetic Laboratory, Genetic Foundation of Khorasan Razavi, Mashhad, Iran
| | - Atieh Eslahi
- Faculty of Medicine, Department of Medical Genetics, Mashhad University of Medical Sciences, Mashhad, Iran
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Barbara Vona
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany
- Institute for Auditory Neuroscience and InnerEarLab, University Medical Center Göttingen, Göttingen, Germany
| | - Mir Salar Kahaei
- Faculty of Medicine, Department of Medical Genetics, Mashhad University of Medical Sciences, Mashhad, Iran
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | | | - Mohsen Rajati
- Sinus and Surgical Endoscopic Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Chochlear Implantation Department, Ear Foundation Research Center, Mashhad, Iran
| | - Alireza Pasdar
- Faculty of Medicine, Department of Medical Genetics, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohammad Mehdi Ghasemi
- Sinus and Surgical Endoscopic Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Chochlear Implantation Department, Ear Foundation Research Center, Mashhad, Iran
| | - Ehsan Saburi
- Faculty of Medicine, Department of Medical Genetics, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Reza Mousavi Ardehaie
- Faculty of Medicine, Department of Medical Genetics, Mashhad University of Medical Sciences, Mashhad, Iran
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Majid Hadadi Aval
- Chochlear Implantation Department, Ear Foundation Research Center, Mashhad, Iran
- Paramedical and Rehabilitation Faculty, University of Medical Sciences, Mashhad, Iran
- Chochlear Implantation Division, Khorasan Cochlear Implant Center, Mashhad, Iran
| | - Mohammad Reza Tale
- Chochlear Implantation Department, Ear Foundation Research Center, Mashhad, Iran
- Chochlear Implantation Division, Khorasan Cochlear Implant Center, Mashhad, Iran
| | - Navid Nourizadeh
- Sinus and Surgical Endoscopic Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Chochlear Implantation Department, Ear Foundation Research Center, Mashhad, Iran
| | - Mohammad Reza Afzalzadeh
- Sinus and Surgical Endoscopic Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Chochlear Implantation Department, Ear Foundation Research Center, Mashhad, Iran
| | - Hamid Tayarani Niknezhad
- Chochlear Implantation Department, Ear Foundation Research Center, Mashhad, Iran
- Chochlear Implantation Division, Khorasan Cochlear Implant Center, Mashhad, Iran
| | - Majid Mojarrad
- Faculty of Medicine, Department of Medical Genetics, Mashhad University of Medical Sciences, Mashhad, Iran
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Genetic Laboratory, Genetic Foundation of Khorasan Razavi, Mashhad, Iran
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Zhuri D, Guler HS, Yalcintepe S, Demir S, Atli E, Atli EI, Gurkan H. Investigation of Targeted Genes and Identification of Novel Variants with Next Generation Sequencing Method in Hearing Loss. J Int Adv Otol 2024; 20:312-324. [PMID: 39161163 PMCID: PMC11363168 DOI: 10.5152/iao.2024.22919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Accepted: 03/10/2024] [Indexed: 08/21/2024] Open
Abstract
Hearing loss is a widespread condition throughout the world. It may affect patients from newborns to the elderly. There are too many reasons for hearing loss, including congenital hearing loss, virus infections, age-related situations, and traumatic situations, which may be related to the immune-mediated system. Fifty percent of hearing loss is related to genetic mutations and defects; genetic causes are highly heterogeneous, so the analysis of new variants are important for diagnosis. We aimed to describe the importance of detected gene variations by using targeted gene panels in the Next-Generation-Sequencing (NGS) platform. Eighty-one hearing loss targeted genes were investigated using Illumina NextSeq550 technology in 100 participants with hearing loss between 2017 and 2022 in our Genetic Diseases Evaluation Center. Targeted genes were performed on 100 patients with hearing loss diagnosis. The total number of detected variants was 77. Forty-seven cases have likely pathogenic/pathogenic variants. Thirty of them have uncertain clinical significance variants, and from the detected variants, 8 are novel. In this research, we highlighted that earlier detection of hearing loss using molecular genetic methods may help us understand the etiology and orient for a better prognosis. Results detected by using the NGS platform can assist and improve the diagnosis. In this study, the diagnostic rate with targeted genes was detected as 35.29%. It has an important role in clinical practice as the recommendation of cochlear implants. Clarifying the genotype and phenotype correlation helps us figure out the etiology of hearing loss and also the worth of genetic counseling in hereditary hearing loss.
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Affiliation(s)
- Drenushe Zhuri
- Department of Medical Genetics, Trakya University Faculty of Medicine, Edirne, Türkiye
| | - Hazal Sezginer Guler
- Department of Medical Genetics, Trakya University Faculty of Medicine, Edirne, Türkiye
| | - Sinem Yalcintepe
- Department of Medical Genetics, Trakya University Faculty of Medicine, Edirne, Türkiye
| | - Selma Demir
- Department of Medical Genetics, Trakya University Faculty of Medicine, Edirne, Türkiye
| | - Engin Atli
- Department of Medical Genetics, Trakya University Faculty of Medicine, Edirne, Türkiye
| | - Emine Ikbal Atli
- Department of Medical Genetics, Trakya University Faculty of Medicine, Edirne, Türkiye
| | - Hakan Gurkan
- Department of Medical Genetics, Trakya University Faculty of Medicine, Edirne, Türkiye
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Bertani-Torres W, Lezirovitz K, Alencar-Coutinho D, Pardono E, da Costa SS, Antunes LDN, de Oliveira J, Otto PA, Pingault V, Mingroni-Netto RC. Waardenburg Syndrome: The Contribution of Next-Generation Sequencing to the Identification of Novel Causative Variants. Audiol Res 2023; 14:9-25. [PMID: 38391765 PMCID: PMC10886116 DOI: 10.3390/audiolres14010002] [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: 10/01/2023] [Revised: 12/08/2023] [Accepted: 12/13/2023] [Indexed: 02/24/2024] Open
Abstract
Waardenburg syndrome (WS) is characterized by hearing loss and pigmentary abnormalities of the eyes, hair, and skin. The condition is genetically heterogeneous, and is classified into four clinical types differentiated by the presence of dystopia canthorum in type 1 and its absence in type 2. Additionally, limb musculoskeletal abnormalities and Hirschsprung disease differentiate types 3 and 4, respectively. Genes PAX3, MITF, SOX10, KITLG, EDNRB, and EDN3 are already known to be associated with WS. In WS, a certain degree of molecularly undetected patients remains, especially in type 2. This study aims to pinpoint causative variants using different NGS approaches in a cohort of 26 Brazilian probands with possible/probable diagnosis of WS1 (8) or WS2 (18). DNA from the patients was first analyzed by exome sequencing. Seven of these families were submitted to trio analysis. For inconclusive cases, we applied a targeted NGS panel targeting WS/neurocristopathies genes. Causative variants were detected in 20 of the 26 probands analyzed, these being five in PAX3, eight in MITF, two in SOX10, four in EDNRB, and one in ACTG1 (type 2 Baraitser-Winter syndrome, BWS2). In conclusion, in our cohort of patients, the detection rate of the causative variant was 77%, confirming the superior detection power of NGS in genetically heterogeneous diseases.
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Affiliation(s)
- William Bertani-Torres
- Centro de Estudos sobre o Genoma Humano e Células Tronco, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo 05508-090, Brazil
- Department of Embryology and Genetics of Malformations, INSERM (Institut National de la Santé et de la Recherche Médicale) UMR (Unité Mixte de Recherche) 1163, Université Paris-Cité and Institut Imagine, 75015 Paris, France
| | - Karina Lezirovitz
- Otorhinolaryngology Lab-LIM 32, Hospital das Clínicas, Faculdade de Medicina, Universidade de São Paulo, São Paulo 01246-000, Brazil
| | - Danillo Alencar-Coutinho
- Otorhinolaryngology Lab-LIM 32, Hospital das Clínicas, Faculdade de Medicina, Universidade de São Paulo, São Paulo 01246-000, Brazil
| | - Eliete Pardono
- Instituto de Ciências da Saúde, Universidade Paulista UNIP, São Paulo 04026-002, Brazil
- Colégio Miguel de Cervantes, São Paulo 05618-001, Brazil
| | - Silvia Souza da Costa
- Centro de Estudos sobre o Genoma Humano e Células Tronco, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo 05508-090, Brazil
| | - Larissa do Nascimento Antunes
- Centro de Estudos sobre o Genoma Humano e Células Tronco, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo 05508-090, Brazil
| | - Judite de Oliveira
- Médecine Génomique des Maladies Rares, AP-HP, Hôpital Necker-Enfants Malades, 75015 Paris, France
| | - Paulo Alberto Otto
- Centro de Estudos sobre o Genoma Humano e Células Tronco, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo 05508-090, Brazil
| | - Véronique Pingault
- Department of Embryology and Genetics of Malformations, INSERM (Institut National de la Santé et de la Recherche Médicale) UMR (Unité Mixte de Recherche) 1163, Université Paris-Cité and Institut Imagine, 75015 Paris, France
- Médecine Génomique des Maladies Rares, AP-HP, Hôpital Necker-Enfants Malades, 75015 Paris, France
| | - Regina Célia Mingroni-Netto
- Centro de Estudos sobre o Genoma Humano e Células Tronco, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo 05508-090, Brazil
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Chen W, Zhou Q, Chen H, Li H, Chen J. Novel compound heterozygous variants of SLC12A3 gene in a Chinese patient with Gitelman syndrome: a case report. Front Genet 2023; 14:1067242. [PMID: 37377595 PMCID: PMC10291089 DOI: 10.3389/fgene.2023.1067242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 05/04/2023] [Indexed: 06/29/2023] Open
Abstract
Background: The Gitelman syndrome (GS) is an autosomal recessive disorder of renal tubular salt handling. Gitelman syndrome is characterized by hypokalemia, metabolic alkalosis, hypomagnesemia, hypocalciuria, and renin-angiotensin-aldosterone system (RAAS) activation, and is caused by variants in the SLC12A3 gene. Gitelman syndrome has a heterogeneous phenotype, which may or may not include a range of clinical signs, posing certain difficulties for clinical diagnosis. Case presentation: A 49-year-old man was admitted to our hospital due to muscular weakness. The patient's history revealed previous recurrent muscular weakness events associated with hypokalemia, featured by a minimum serum potassium value of 2.3 mmol/L. The reported male patient had persistent hypokalemia, hypocalciuria and normal blood pressure, without presenting obvious metabolic alkalosis, growth retardation, hypomagnesemia, hypochloremia or RAAS activation. We performed whole-exome sequencing and identified a novel compound heterozygous variant in the SLC12A3 gene, c.965-1_976delGCGGACATTTTTGinsACCGAAAATTTT in exon8 and c.1112T>C in exon9 in the proband. Conclusion: This is a study to report a heterogeneous phenotype Gitelman syndrome with a novel pathogenic compound heterozygous variant in the SLC12A3 gene. This genetic study expands the variants spectrum, and improve the diagnostic accuracy of Gitelman syndrome. Meanwhile, further functional studies are required to investigate the pathophysiological mechanisms of Gitelman syndrome.
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Affiliation(s)
- Wenqing Chen
- Kidney Disease Center, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
- Key Laboratory of Kidney Disease Prevention and Control Technology, Hangzhou, Zhejiang, China
- Institute of Nephropathy, Zhejiang University, Hangzhou, China
- Zhejiang Clinical Research Center of Kidney and Urinary System Disease, Hangzhou, China
| | - Qin Zhou
- Kidney Disease Center, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
- Key Laboratory of Kidney Disease Prevention and Control Technology, Hangzhou, Zhejiang, China
- Institute of Nephropathy, Zhejiang University, Hangzhou, China
- Zhejiang Clinical Research Center of Kidney and Urinary System Disease, Hangzhou, China
| | - Hongjun Chen
- Kidney Disease Center, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
- Key Laboratory of Kidney Disease Prevention and Control Technology, Hangzhou, Zhejiang, China
- Institute of Nephropathy, Zhejiang University, Hangzhou, China
- Zhejiang Clinical Research Center of Kidney and Urinary System Disease, Hangzhou, China
| | - Heng Li
- Kidney Disease Center, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
- Key Laboratory of Kidney Disease Prevention and Control Technology, Hangzhou, Zhejiang, China
- Institute of Nephropathy, Zhejiang University, Hangzhou, China
- Zhejiang Clinical Research Center of Kidney and Urinary System Disease, Hangzhou, China
| | - Jianghua Chen
- Kidney Disease Center, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
- Key Laboratory of Kidney Disease Prevention and Control Technology, Hangzhou, Zhejiang, China
- Institute of Nephropathy, Zhejiang University, Hangzhou, China
- Zhejiang Clinical Research Center of Kidney and Urinary System Disease, Hangzhou, China
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Zeng B, Xu H, Yu Y, Li S, Tian Y, Li T, Yang Z, Wang H, Wang G, Chang M, Tang W. Increased diagnostic yield in a cohort of hearing loss families using a comprehensive stepwise strategy of molecular testing. Front Genet 2022; 13:1057293. [PMID: 36568381 PMCID: PMC9768221 DOI: 10.3389/fgene.2022.1057293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 11/14/2022] [Indexed: 12/12/2022] Open
Abstract
Hearing loss is one of the most common sensory disorders in humans. This study proposes a stepwise strategy of deafness gene detection using multiplex PCR combined with high-throughput sequencing, Sanger sequencing, multiplex ligation-dependent probe amplification (MLPA), and whole-exome sequencing (WES) to explore its application in molecular diagnosis of hearing loss families. A total of 152 families with hearing loss were included in this study, the highest overall diagnosis rate was 73% (111/152). The diagnosis rate of multiplex PCR combined with high-throughput sequencing was 52.6% (80/152). One families was diagnosed by Sanger sequencing of GJB2 exon 1. Two families were diagnosed by MLPA analysis of the STRC gene. The diagnosis rate with additional contribution from WES was 18.4% (28/152). We identified 21 novel variants from 15 deafness genes by WES. Combining WES and deep clinical phenotyping, we diagnosed 11 patients with syndromic hearing loss (SHL). This study demonstrated improved diagnostic yield in a cohort of hearing loss families and confirmed the advantages of a stepwise strategy in the molecular diagnosis of hearing loss.
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Affiliation(s)
- Beiping Zeng
- BGI College and Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China,National Health Commission Key Laboratory of Birth Defects Prevention, Henan Key Laboratory of Population Defects Prevention, Henan Institute of Reproduction Health Science and Technology, Zhengzhou, China
| | - Hongen Xu
- Precision Medicine Center, Academy of Medical Science, Zhengzhou University, Zhengzhou, China,The Research and Application Center of Precision Medicine, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yanan Yu
- Precision Medicine Center, Academy of Medical Science, Zhengzhou University, Zhengzhou, China
| | - Siqi Li
- Department of Physiology and Neurobiology, Academy of Medical Science, Zhengzhou University, Zhengzhou, China
| | - Yongan Tian
- Precision Medicine Center, Academy of Medical Science, Zhengzhou University, Zhengzhou, China
| | - Tiandong Li
- College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Zengguang Yang
- Precision Medicine Center, Academy of Medical Science, Zhengzhou University, Zhengzhou, China
| | - Haili Wang
- National Health Commission Key Laboratory of Birth Defects Prevention, Henan Key Laboratory of Population Defects Prevention, Henan Institute of Reproduction Health Science and Technology, Zhengzhou, China
| | - Guangke Wang
- Department of Otorhinolaryngology Head and Neck Surgery, Henan Provincial People’s Hospital, Zhengzhou, China
| | - Mingxiu Chang
- National Health Commission Key Laboratory of Birth Defects Prevention, Henan Key Laboratory of Population Defects Prevention, Henan Institute of Reproduction Health Science and Technology, Zhengzhou, China,*Correspondence: Mingxiu Chang, ; Wenxue Tang,
| | - Wenxue Tang
- The Research and Application Center of Precision Medicine, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, China,*Correspondence: Mingxiu Chang, ; Wenxue Tang,
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Liao EN, Taketa E, Mohamad NI, Chan DK. Outcomes of Gene Panel Testing for Sensorineural Hearing Loss in a Diverse Patient Cohort. JAMA Netw Open 2022; 5:e2233441. [PMID: 36166228 PMCID: PMC9516276 DOI: 10.1001/jamanetworkopen.2022.33441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
IMPORTANCE A genetic diagnosis can help elucidate the prognosis of hearing loss, thus significantly affecting management. Previous studies on diagnostic yield of hearing loss genetic tests have been based on largely homogenous study populations. OBJECTIVES To examine the diagnostic yield of genetic testing in a diverse population of children, accounting for sociodemographic and patient characteristics, and assess whether these diagnoses are associated with subsequent changes in clinical management. DESIGN, SETTING, AND PARTICIPANTS This retrospective cohort study included 2075 patients seen at the Children's Communications Clinic, of whom 517 completed hearing loss gene panel testing between January 1, 2015, and November 1, 2021, at the University of California, San Francisco Benioff Children's Hospital system. From those 517 patients, 426 children with at least 2 audiograms were identified and analyzed. Data were gathered from November 2021 to January 2022 and analyzed from January to February 2022. MAIN OUTCOMES AND MEASURES The measures of interest were sociodemographic characteristics (age at testing, gender, race and ethnicity, primary language, and insurance type), hearing loss characteristics, and medical variables. The outcome was genetic testing results. Variables were compared with univariate and multivariable logistic regression. RESULTS Of the 2075 patients seen at the Children's Communications Clinic, 517 (median [range] age, 8 [0-31] years; 264 [51.1%] male; 351 [67.9%] from an underrepresented minority [URM] group) underwent a hearing loss panel genetic test between January 1, 2015, and November 1, 2021. Among those 517 patients, 426 children (median [range] age, 8 [0-18] years; 221 [51.9%] male; 304 [71.4%] from an URM group) with 2 or more audiograms were included in a subsequent analysis. On multivariable logistic regression, age at testing (odds ratio [OR], 0.87; 95% CI, 0.78-0.97), URM group status (OR, 0.29; 95% CI, 0.13-0.66), comorbidities (OR, 0.27; 95% CI, 0.14-0.53), late-identified hearing loss (passed newborn hearing screen; OR, 0.27; 95% CI, 0.08-0.86), and unilateral hearing loss (OR, 0.04; 95% CI, 0.005-0.33) were the only factors associated with genetic diagnosis. No association was found between genetic diagnosis yield and other sociodemographic variables or hearing loss characteristics. Patients in URM and non-URM groups had statistically similar clinical features. A total of 32 of 109 children (29.4%) who received a genetic diagnosis received diagnoses that significantly affected prognosis because of identification of syndromic or progressive sensorineural hearing loss or auditory neuropathy spectrum disorder relating to otoferlin. CONCLUSIONS AND RELEVANCE This cohort study's findings suggest that genetic testing may be broadly useful in improving clinical management of children with hearing loss. More research is warranted to discover and characterize diagnostic genes for those who have been historically underrepresented in research and medicine.
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Affiliation(s)
- Elizabeth N. Liao
- Department of Otolaryngology–Head & Neck Surgery, University of California, San Francisco
| | - Emily Taketa
- Department of Otolaryngology–Head & Neck Surgery, University of California, San Francisco
| | - Noura I. Mohamad
- Department of Otolaryngology–Head & Neck Surgery, University of California, San Francisco
| | - Dylan K. Chan
- Department of Otolaryngology–Head & Neck Surgery, University of California, San Francisco
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Xiang J, Jin Y, Song N, Chen S, Shen J, Xie W, Sun X, Peng Z, Sun Y. Comprehensive genetic testing improves the clinical diagnosis and medical management of pediatric patients with isolated hearing loss. BMC Med Genomics 2022; 15:142. [PMID: 35761346 PMCID: PMC9235092 DOI: 10.1186/s12920-022-01293-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 06/17/2022] [Indexed: 11/10/2022] Open
Abstract
Purpose Genetic testing is widely used in diagnosing genetic hearing loss in patients. Other than providing genetic etiology, the benefits of genetic testing in pediatric patients with hearing loss are less investigated. Methods From 2018–2020, pediatric patients who initially presented isolated hearing loss were enrolled. Comprehensive genetic testing, including GJB2/SLC26A4 multiplex amplicon sequencing, STRC/OTOA copy number variation analysis, and exome sequencing, were hierarchically offered. Clinical follow-up and examinations were performed. Results A total of 80 pediatric patients who initially presented isolated hearing loss were considered as nonsyndromic hearing loss and enrolled in this study. The definitive diagnosis yield was 66% (53/80) and the likely diagnosis yield was 8% (6/80) through comprehensive genetic testing. With the aid of genetic testing and further clinical follow-up and examinations, the clinical diagnoses and medical management were altered in eleven patients (19%, 11/59); five were syndromic hearing loss; six were nonsyndromic hearing loss mimics. Conclusion Syndromic hearing loss and nonsyndromic hearing loss mimics are common in pediatric patients who initially present with isolated hearing loss. The comprehensive genetic testing provides not only a high diagnostic yield but also valuable information for clinicians to uncover subclinical or pre-symptomatic phenotypes, which allows early diagnosis of SHL, and leads to precise genetic counseling and changes the medical management. Supplementary Information The online version contains supplementary material available at 10.1186/s12920-022-01293-x.
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Evaluation of copy number variants for genetic hearing loss: a review of current approaches and recent findings. Hum Genet 2021; 141:387-400. [PMID: 34811589 DOI: 10.1007/s00439-021-02365-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 09/02/2021] [Indexed: 01/22/2023]
Abstract
Structural variation includes a change in copy number, orientation, or location of a part of the genome. Copy number variants (CNVs) are a common cause of genetic hearing loss, comprising nearly 20% of diagnosed cases. While large deletions involving the gene STRC are the most common pathogenic CNVs, a significant proportion of known hearing loss genes also contain pathogenic CNVs. In this review, we provide an overview of currently used methods for detection of CNVs in genes known to cause hearing loss including molecular techniques such as multiplex ligation probe amplification (MLPA) and digital droplet polymerase chain reaction (ddPCR), array-CGH and single-nucleotide polymorphism (SNP) arrays, as well as techniques for detection of CNVs using next-generation sequencing data analysis including targeted gene panel, exome, and genome sequencing data. In addition, in this review, we compile published data on pathogenic hearing loss CNVs to provide an up-to-date overview. We show that CNVs have been identified in 29 different non-syndromic hearing loss genes. An understanding of the contribution of CNVs to genetic hearing loss is critical to the current diagnosis of hearing loss and is crucial for future gene therapies. Thus, evaluation for CNVs is required in any modern pipeline for genetic diagnosis of hearing loss.
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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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