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Reda Del Barrio S, de Vergas Gutiérrez J, Quesada-Espinosa JF, Sánchez-Calvín MT, Gómez-Manjón I, Sierra-Tomillo O, Juárez-Rufián A, García Fernández A. Diagnostic yield of genetic testing in adults with sensorineural hearing loss. ACTA OTORRINOLARINGOLOGICA ESPANOLA 2024; 75:185-191. [PMID: 38346493 DOI: 10.1016/j.otoeng.2023.10.007] [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: 10/06/2023] [Indexed: 02/19/2024]
Abstract
INTRODUCTION The contribution of genetic causes to sensorineural hearing loss (SNHL) in adults is less clear than in children, and genetic diagnosis is still not standardized in adults. In this study we present the genetic results obtained in a cohort of adult patients with SNHL. MATERIALS AND METHODS We included 63 adults with SNHL that received genetic testing between 2019 and 2022. Whole exome sequencing was performed and variants in genes related to hearing loss (virtual panel with 244 genes) were prioritised and analysed. RESULTS 24% (15/63) of patients were genetically diagnosed: 87% (13/15) of patients had non-syndromic hearing loss and 13% (2/15) had syndromic hearing loss. We identified pathogenic and likely pathogenic variants in 11 different genes. CONCLUSIONS Our results show that a significant proportion of adults with SNHL have a genetic origin, and that implementation of genetic testing improves diagnostic accuracy and allows personalized management of these patients.
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Affiliation(s)
- Sara Reda Del Barrio
- Department of Otolaryngology-Head and Neck Surgery, Hospital Universitario 12 de Octubre, Madrid, Spain.
| | | | | | | | - Irene Gómez-Manjón
- Department of Genetics, Hospital Universitario 12 de Octubre, Madrid, Spain
| | | | | | - Alfredo García Fernández
- Department of Otolaryngology-Head and Neck Surgery, Hospital Universitario 12 de Octubre, Madrid, Spain
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Costales M, Diñeiro M, Cifuentes GÁ, Capín R, Otero A, Viejo-Díaz M, Plasencia A, Núñez F, Gómez JR, Llorente JL, Cadiñanos J, Cabanillas R. Clinical Utility of Next-generation Sequencing in the Aetiological Diagnosis of Sensorineural Hearing Loss in a Childhood Hearing Loss Unit. ACTA OTORRINOLARINGOLOGICA ESPANOLA 2020. [DOI: 10.1016/j.otoeng.2019.05.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Costales M, Diñeiro M, Cifuentes GA, Capín R, Otero A, Viejo-Díaz M, Plasencia A, Núñez F, Gómez JR, Llorente JL, Cadiñanos J, Cabanillas R. Clinical utility of next-generation sequencing in the aetiological diagnosis of sensorineural hearing loss in a Childhood Hearing Loss Unit. ACTA OTORRINOLARINGOLOGICA ESPANOLA 2019; 71:166-174. [PMID: 31706454 DOI: 10.1016/j.otorri.2019.05.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 05/28/2019] [Accepted: 05/30/2019] [Indexed: 10/25/2022]
Abstract
INTRODUCTION Sensorineural hearing loss (SNL) is the most prevalent sensory deficit in our environment. Next generation genomic sequencing (NGS) enables an aetiological diagnosis in a high percentage of patients. Our pilot study shows the results of the systematic application of NGS in a Childhood Hearing Loss Unit, as well as its implications for the clinical management of patients and their families. MATERIAL AND METHOD We included 27 patients diagnosed with SNL between 2014 and 2017, in which an environmental cause was ruled out. The genetic test consisted of a panel of genes analyzed by NGS (OTOgenicsTM panel). This panel has been designed to include genes associated with sensorineural or mixed hearing loss, early onset or late, syndromic and non-syndromic, regardless of their inheritance pattern. RESULTS A genetic diagnosis was obtained in 56% (15/27) of the patients (62% in the case of bilateral SNL). Of the patients, 5/27 (19%) presented pathogenic variants in the GJB2 gene and the rest pathogenic and / or probably pathogenic variants in other genes associated with isolated SNL (PR2X2, TECTA and STRC), with syndromic SNL (CHD7, GATA3, COL4A5, MITF and SOX10) or with syndromic and non-syndromic SNL (BSND, ACTG1 and CDH23). DISCUSSION The aetiological diagnosis of SNL is a challenge in clinical practice. Our series demonstrates that it is possible to implement genetic diagnosis in the care routine and that this information has prognostic and therapeutic implications.
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Affiliation(s)
- María Costales
- Servicio de Otorrinolaringología, Hospital Universitario Central de Asturias, Oviedo, España.
| | - Marta Diñeiro
- Instituto Medicina Oncológica Molecular de Asturias (IMOMA), Oviedo, España
| | | | - Raquel Capín
- Instituto Medicina Oncológica Molecular de Asturias (IMOMA), Oviedo, España
| | - Andrea Otero
- Instituto Medicina Oncológica Molecular de Asturias (IMOMA), Oviedo, España
| | - Mónica Viejo-Díaz
- Servicio de Genética, Hospital Universitario Central de Asturias, Oviedo, España
| | - Ana Plasencia
- Servicio de Genética, Hospital Universitario Central de Asturias, Oviedo, España
| | - Faustino Núñez
- Servicio de Otorrinolaringología, Hospital Universitario Central de Asturias, Oviedo, España
| | - Justo Ramón Gómez
- Servicio de Otorrinolaringología, Hospital Universitario Central de Asturias, Oviedo, España
| | - José Luis Llorente
- Servicio de Otorrinolaringología, Hospital Universitario Central de Asturias, Oviedo, España
| | - Juan Cadiñanos
- Instituto Medicina Oncológica Molecular de Asturias (IMOMA), Oviedo, España
| | - Rubén Cabanillas
- Instituto Medicina Oncológica Molecular de Asturias (IMOMA), Oviedo, España
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Cabanillas R, Diñeiro M, Cifuentes GA, Castillo D, Pruneda PC, Álvarez R, Sánchez-Durán N, Capín R, Plasencia A, Viejo-Díaz M, García-González N, Hernando I, Llorente JL, Repáraz-Andrade A, Torreira-Banzas C, Rosell J, Govea N, Gómez-Martínez JR, Núñez-Batalla F, Garrote JA, Mazón-Gutiérrez Á, Costales M, Isidoro-García M, García-Berrocal B, Ordóñez GR, Cadiñanos J. Comprehensive genomic diagnosis of non-syndromic and syndromic hereditary hearing loss in Spanish patients. BMC Med Genomics 2018; 11:58. [PMID: 29986705 PMCID: PMC6038346 DOI: 10.1186/s12920-018-0375-5] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 06/14/2018] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Sensorineural hearing loss (SNHL) is the most common sensory impairment. Comprehensive next-generation sequencing (NGS) has become the standard for the etiological diagnosis of early-onset SNHL. However, accurate selection of target genomic regions (gene panel/exome/genome), analytical performance and variant interpretation remain relevant difficulties for its clinical implementation. METHODS We developed a novel NGS panel with 199 genes associated with non-syndromic and/or syndromic SNHL. We evaluated the analytical sensitivity and specificity of the panel on 1624 known single nucleotide variants (SNVs) and indels on a mixture of genomic DNA from 10 previously characterized lymphoblastoid cell lines, and analyzed 50 Spanish patients with presumed hereditary SNHL not caused by GJB2/GJB6, OTOF nor MT-RNR1 mutations. RESULTS The analytical sensitivity of the test to detect SNVs and indels on the DNA mixture from the cell lines was > 99.5%, with a specificity > 99.9%. The diagnostic yield on the SNHL patients was 42% (21/50): 47.6% (10/21) with autosomal recessive inheritance pattern (BSND, CDH23, MYO15A, STRC [n = 2], USH2A [n = 3], RDX, SLC26A4); 38.1% (8/21) autosomal dominant (ACTG1 [n = 3; 2 de novo], CHD7, GATA3 [de novo], MITF, P2RX2, SOX10), and 14.3% (3/21) X-linked (COL4A5 [de novo], POU3F4, PRPS1). 46.9% of causative variants (15/32) were not in the databases. 28.6% of genetically diagnosed cases (6/21) had previously undetected syndromes (Barakat, Usher type 2A [n = 3] and Waardenburg [n = 2]). 19% of genetic diagnoses (4/21) were attributable to large deletions/duplications (STRC deletion [n = 2]; partial CDH23 duplication; RDX exon 2 deletion). CONCLUSIONS In the era of precision medicine, obtaining an etiologic diagnosis of SNHL is imperative. Here, we contribute to show that, with the right methodology, NGS can be transferred to the clinical practice, boosting the yield of SNHL genetic diagnosis to 50-60% (including GJB2/GJB6 alterations), improving diagnostic/prognostic accuracy, refining genetic and reproductive counseling and revealing clinically relevant undiagnosed syndromes.
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Affiliation(s)
- Rubén Cabanillas
- Instituto de Medicina Oncológica y Molecular de Asturias (IMOMA) S. A, Avda. Richard Grandío s/n, 33193, Oviedo, Spain.
| | - Marta Diñeiro
- Instituto de Medicina Oncológica y Molecular de Asturias (IMOMA) S. A, Avda. Richard Grandío s/n, 33193, Oviedo, Spain
| | - Guadalupe A Cifuentes
- Instituto de Medicina Oncológica y Molecular de Asturias (IMOMA) S. A, Avda. Richard Grandío s/n, 33193, Oviedo, Spain
| | - David Castillo
- Disease Research And Medicine (DREAMgenics) S. L., Oviedo, Spain
| | | | - Rebeca Álvarez
- Instituto de Medicina Oncológica y Molecular de Asturias (IMOMA) S. A, Avda. Richard Grandío s/n, 33193, Oviedo, Spain
| | - Noelia Sánchez-Durán
- Instituto de Medicina Oncológica y Molecular de Asturias (IMOMA) S. A, Avda. Richard Grandío s/n, 33193, Oviedo, Spain
| | - Raquel Capín
- Instituto de Medicina Oncológica y Molecular de Asturias (IMOMA) S. A, Avda. Richard Grandío s/n, 33193, Oviedo, Spain
| | - Ana Plasencia
- Hospital Universitario Central de Asturias, Oviedo, Spain
| | | | | | - Inés Hernando
- Hospital Universitario Central de Asturias, Oviedo, Spain
| | | | | | | | - Jordi Rosell
- Hospital Universitario Son Espases, Palma de Mallorca, Spain
| | - Nancy Govea
- Hospital Universitario Son Espases, Palma de Mallorca, Spain
| | | | | | | | | | - María Costales
- Hospital Universitario Central de Asturias, Oviedo, Spain.,Hospital Universitario Marqués de Valdecilla, Santander, Spain
| | | | | | | | - Juan Cadiñanos
- Instituto de Medicina Oncológica y Molecular de Asturias (IMOMA) S. A, Avda. Richard Grandío s/n, 33193, Oviedo, Spain.
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Shaikh H, Waryah AM, Narsani AK, Iqbal M, Shahzad M, Waryah YM, Shaikh N, Mahmood A. Genetic Testing of Non-familial Deaf Patients for CIB2 and GJB2 Mutations: Phenotype and Genetic Counselling. Biochem Genet 2017; 55:410-420. [PMID: 29086887 DOI: 10.1007/s10528-017-9828-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 09/19/2017] [Indexed: 02/02/2023]
Abstract
CIB2 and GJB2 genes variants contribute significantly in familial cases of prelingual recessive hearing loss (HL). This study was aimed to determine the CIB2 and GJB2 variants and associated phenotype in 150 non-familial individuals with HL. After getting informed consent, 150 non-familial deaf patients were enrolled and blood samples were obtained for DNA extraction. Pure tone air conduction audiometry was performed. Coding exons of CIB2 and GJB2 genes were Sanger sequenced. A tetra primer ARMS assay was developed for recurrent CIB2 variant. Four bi-allelic GJB2 variants, c.71G>A p.(Trp24*), c.231G>A p.(Trp77*), c.235delC p.(Leu79Cysfs3*) and c.35delG p.(Gly11Leufs24*), were found in nine hearing impaired individuals. We also found four homozygotes and five carriers of c.380G>A p. (Arg127His) variant of controversial clinical significance. CIB2 sequencing revealed single recurrent variant c.272T>C p. (Phe91Ser) segregating with HL in ten individuals. Among our patients, c.71G>A (p.Trp24*) was the most common variant, accounted for 45% of GJB2 variants. Two known GJB2 variants, c.235delC p. (Leu79Cysfs3*) and c.310del14 p. (Lys105Argfs2*), are reported here for the first time in Pakistani population. Our data further support the benign nature of c.380G>A p. (Arg127His) variant. For CIB2, c.272T>C p. (Phe91Ser) is the second common cause of HL among our sporadic cases. Phenotypically, in our patients, individuals homozygous for GJB2 variants had profound HL, whereas CIB2 homozygotes had severe to profound prelingual HL. Our results suggest that GJB2 and CIB2 are common cause of HL in different Pakistani ethnicities.
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Affiliation(s)
- Hina Shaikh
- Molecular Biology and Genetics Department, Medical Research Center, Liaquat University of Medical and Health Sciences, Jamshoro, Pakistan
| | - Ali M Waryah
- Molecular Biology and Genetics Department, Medical Research Center, Liaquat University of Medical and Health Sciences, Jamshoro, Pakistan.
| | - Ashok K Narsani
- Institute of Ophthalmology, Liaquat University of Medical and Health Sciences, Jamshoro, Pakistan
| | - Muhammad Iqbal
- Department of Biochemistry and Biotechnology, Islamia University, Bahawalpur, Pakistan
| | - Mohsin Shahzad
- Department of Molecular Biology, Shaheed Zulfiqar Ali Bhutto Medical University, Islamabad, Pakistan
| | - Yar M Waryah
- Molecular Biology and Genetics Department, Medical Research Center, Liaquat University of Medical and Health Sciences, Jamshoro, Pakistan
| | - Naila Shaikh
- Molecular Biology and Genetics Department, Medical Research Center, Liaquat University of Medical and Health Sciences, Jamshoro, Pakistan
| | - Amber Mahmood
- Molecular Biology and Genetics Department, Medical Research Center, Liaquat University of Medical and Health Sciences, Jamshoro, Pakistan
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Núñez-Batalla F, Jáudenes-Casaubón C, Sequí-Canet JM, Vivanco-Allende A, Zubicaray-Ugarteche J, Cabanillas-Farpón R. Aetiological Diagnosis of Child Deafness: CODEPEH Recommendations. ACTA OTORRINOLARINGOLOGICA ESPANOLA 2017. [DOI: 10.1016/j.otoeng.2016.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Aetiological diagnosis of child deafness: CODEPEH recommendations. ACTA OTORRINOLARINGOLOGICA ESPANOLA 2016; 68:43-55. [PMID: 27644946 DOI: 10.1016/j.otorri.2016.05.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 05/19/2016] [Indexed: 12/18/2022]
Abstract
Important progress in the fields of molecular genetics (principally) and diagnostic imaging, together with the lack of a consensus protocol for guiding the diagnostic process after confirming deafness by neonatal screening, have led to this new work document drafted by the Spanish Commission for the Early Detection of Child Deafness (Spanish acronym: CODEPEH). This 2015 Recommendations Document, which is based on the most recent scientific evidence, provides guidance to professionals to support them in making decisions regarding aetiological diagnosis. Such diagnosis should be performed without delay and without impeding early intervention. Early identification of the causes of deafness offers many advantages: it prevents unnecessary trouble for the families, reduces health system expenses caused by performing different tests, and provides prognostic information that may guide therapeutic actions.
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Frequency of GJB2 and del(GJB6-D13S1830) mutations among an Ecuadorian mestizo population. Int J Pediatr Otorhinolaryngol 2014; 78:1648-54. [PMID: 25085072 DOI: 10.1016/j.ijporl.2014.07.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Revised: 07/08/2014] [Accepted: 07/12/2014] [Indexed: 12/11/2022]
Abstract
OBJECTIVE The frequency of GJB2 mutations and of the del(GJB6-D13S1830) mutation has not been established among the Ecuadorian mestizo population diagnosed with autosomal recessive non-syndromic hearing loss. A genetic analysis was therefore designed in order to do so. METHODS The sample population included 111 subjects of which 26 were autosomal recessive non-syndromic hearing loss probands. Posterior to PCR amplification, sequencing analysis of exon 2 was used for mutational detection of the GJB2 gene; a multiplex PCR method was used for detection of the del(GJB6-D13S1830) mutation. The ratio of subjects with a certain state of the mutation (heterozygous/homozygous) is expressed as a percentage and significant differences between probands and controls were calculated using Fisher's exact test; P<0.05 was considered significant. RESULTS A total of 104 mutations belonging to 8 allelic variations were identified. The most common being the V27I (58.9%); however, as this variation is a non-pathogenic polymorphism, Q7X, with a total of 19 mutated alleles, was the most frequent mutation (18.3%). The V27I polymorphism was the only variation distributed homogenously among probands and controls (P=0.351). Based on physical analyses of multiple patients we confirm that Q7X causes a non-syndromic form of hearing loss and propose that it is a possible predominant mutation in the Ecuadorian population. CONCLUSIONS This is the first study of its kind among the Ecuadorian population and a preliminary step in establishing GJB2 and del(GJB6-D13S1830) mutational frequencies in this population; it is also the first to report of such a high frequency of the Q7X mutation. The data presented here brings Ecuador a step closer to providing more efficient treatment for a broader number of patients; additionally, it contributes to a better understanding of the relationship between autosomal recessive non-syndromic hearing loss and mutations on the GJB2 gene.
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