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Türkyılmaz A, Cimbek EA, Kardeş H, Çebi AH, Acar Arslan E, Karagüzel G. A triple molecular diagnosis in a Turkish individual with hypotrichosis, deafness, and diabetes. Clin Dysmorphol 2024; 33:118-120. [PMID: 38818819 DOI: 10.1097/mcd.0000000000000499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2024]
Affiliation(s)
| | - Emine Ayça Cimbek
- Pediatric Endocrinology, Faculty of Medicine, Karadeniz Technical University, Trabzon
| | - Hakan Kardeş
- Pediatric Endocrinology, Faculty of Medicine, Karadeniz Technical University, Trabzon
| | | | - Elif Acar Arslan
- Department of Pediatric Neurology, Marmara University, Faculty of Medicine, İstanbul, Türkiye
| | - Gülay Karagüzel
- Pediatric Endocrinology, Faculty of Medicine, Karadeniz Technical University, Trabzon
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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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3
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Franz L, Incognito A, Gallo C, Turolla L, Scquizzato E, Cenedese R, Matarazzo A, Savegnago D, Zanatta P, Genovese E, de Filippis C, Marioni G. Audiological Phenotypes of Connexin Gene Mutation Patterns: A Glance at Different GJB2/GJB6 Gene Mutation Profiles. CHILDREN (BASEL, SWITZERLAND) 2024; 11:194. [PMID: 38397306 PMCID: PMC10887074 DOI: 10.3390/children11020194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 01/28/2024] [Accepted: 02/01/2024] [Indexed: 02/25/2024]
Abstract
GJB2 mutations are the most common cause of autosomal-recessive non-syndromic sensorineural hearing loss (SNHL). The available evidence shows large phenotypic variability across different genotypes and allelic variants. The aim of this study was to investigate the clinical and audiological features of a cohort of subjects with different GJB2/GJB6 gene mutation profiles from a tertiary referral center in Northeastern Italy. We considered 57 patients with GJB2/GJB6 mutations presenting with congenital, non-syndromic SNHL, mainly coming from the Veneto region (Italy). The samples were screened for mutations in exons 1 and 2 of the GJB2 gene and for the GJB6 gene deletion del (GJB6-D13S1830). Free-field and air-conduction frequency-specific thresholds and the pure-tone average (PTA) were considered in the statistical analysis. Five patients (8.87%) had connexin gene mutations in simple heterozygosis, 15 (26.31%) in compound heterozygosis, 34 (59.64%) in homozygosis, and 3 (5.26%) with digenic patterns. The frequency-specific air-conduction thresholds showed significantly different mean values across the different genotypes (Roy's largest-root test, p = 0.0473). Despite the evidence already available on genetic SNHL, many new insights are to be expected. Further large-scale prospective studies including different populations are necessary to confirm these preliminary findings about the clinical and audiological features of patients with different GJB2/GJB6 gene mutation patterns.
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Affiliation(s)
- Leonardo Franz
- Phoniatrics and Audiology Unit, Department of Neuroscience DNS, University of Padova, 35122 Treviso, Italy; (L.F.); (A.I.); (C.G.); (R.C.); (D.S.); (C.d.F.)
| | - Alessandro Incognito
- Phoniatrics and Audiology Unit, Department of Neuroscience DNS, University of Padova, 35122 Treviso, Italy; (L.F.); (A.I.); (C.G.); (R.C.); (D.S.); (C.d.F.)
| | - Chiara Gallo
- Phoniatrics and Audiology Unit, Department of Neuroscience DNS, University of Padova, 35122 Treviso, Italy; (L.F.); (A.I.); (C.G.); (R.C.); (D.S.); (C.d.F.)
| | - Licia Turolla
- Medical Genetics Unit, Treviso Hospital, 31100 Treviso, Italy;
| | - Elisa Scquizzato
- Molecular Pathology Laboratory, Unit of Pathological Anatomy, Treviso Hospital, 31100 Treviso, Italy;
| | - Roberta Cenedese
- Phoniatrics and Audiology Unit, Department of Neuroscience DNS, University of Padova, 35122 Treviso, Italy; (L.F.); (A.I.); (C.G.); (R.C.); (D.S.); (C.d.F.)
| | - Alessandro Matarazzo
- Phoniatrics and Audiology Unit, Department of Neuroscience DNS, University of Padova, 35122 Treviso, Italy; (L.F.); (A.I.); (C.G.); (R.C.); (D.S.); (C.d.F.)
| | - Daniel Savegnago
- Phoniatrics and Audiology Unit, Department of Neuroscience DNS, University of Padova, 35122 Treviso, Italy; (L.F.); (A.I.); (C.G.); (R.C.); (D.S.); (C.d.F.)
| | - Paolo Zanatta
- Department of Anesthesiology and Critical Care, Treviso Hospital, 31100 Treviso, Italy;
| | - Elisabetta Genovese
- Otorhinolaryngology Unit, Department of Medical and Surgical Sciences for Children and Adults, University of Modena and Reggio Emilia, 41121 Modena, Italy;
| | - Cosimo de Filippis
- Phoniatrics and Audiology Unit, Department of Neuroscience DNS, University of Padova, 35122 Treviso, Italy; (L.F.); (A.I.); (C.G.); (R.C.); (D.S.); (C.d.F.)
| | - Gino Marioni
- Phoniatrics and Audiology Unit, Department of Neuroscience DNS, University of Padova, 35122 Treviso, Italy; (L.F.); (A.I.); (C.G.); (R.C.); (D.S.); (C.d.F.)
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Heyward A, Hagerty K, Lichten L, Howell J, Tey CS, Dedhia K, Kavalieratos D, Govil N. The qualitative experiences of otolaryngologists with genetic services in pediatric hearing loss evaluation. J Community Genet 2023; 14:377-385. [PMID: 37156903 PMCID: PMC10444707 DOI: 10.1007/s12687-023-00649-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 04/27/2023] [Indexed: 05/10/2023] Open
Abstract
Genetic testing is one of the most high-yield diagnostic tests in the evaluation of pediatric sensorineural (SNHL) hearing loss, leading to a genetic diagnosis in 40-65% of patients. Previous research has focused on the utility of genetic testing in pediatric SNHL and otolaryngologists' general understanding of genetics. This qualitative study examines otolaryngologists' perceptions about facilitators and barriers when ordering genetic testing in the workup of pediatric hearing loss. Potential solutions for overcoming barriers are also explored. Eleven (N = 11) semi-structured interviews were conducted with otolaryngologists in the USA. Most participants were currently practicing in a southern, academic, urban setting and had completed a pediatric otolaryngology fellowship. Insurance was one of the main barriers to testing, and increased genetics provider accessibility was the most frequently cited solution to increase utilization of genetic services. Difficulty acquiring insurance coverage and unfamiliarity with the genetic testing process were the most common reasons otolaryngologists referred patients to genetics clinics for genetic testing, as opposed to ordering testing themselves. This study suggests that otolaryngologists recognize the importance and utility of genetic testing, but a lack of genetics-specific skills, knowledge, and resources makes it difficult for them to facilitate testing. Multidisciplinary hearing loss clinics that include genetics providers may increase the overall accessibility of genetic services.
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Affiliation(s)
- Aaliyah Heyward
- Genetics Department, Ochsner Health Medical Center, New Orleans, LA, 70121, USA
- Genetic Counseling Training Program, Emory University School of Medicine, 100 Woodruff Circle, Atlanta, GA, 30322, USA
| | - Kelsi Hagerty
- Genetic Counseling Training Program, Emory University School of Medicine, 100 Woodruff Circle, Atlanta, GA, 30322, USA
- Pediatric Hematology/ Oncology, Aflac Cancer and Blood Disorders Center, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Lauren Lichten
- Pediatric Hematology/ Oncology, Aflac Cancer and Blood Disorders Center, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Julie Howell
- Genetics Department, Kaiser Permanente, 20 Glenlake Pkwy NE, Sandy Springs, GA, 30328, USA
| | - Ching Siong Tey
- Department of Otolaryngology-Head and Neck Surgery, Emory University School of Medicine, 1400 Tullie Road, Atlanta, GA, 30323, USA
| | - Kavita Dedhia
- Otolaryngology Head and Neck Surgery, The Children's Hospital of Philadelphia and University of Pennsylvania, 3500 Civic Center Blvd, 5Th Floor, Philadelphia, PA, 19104, USA
| | - Dio Kavalieratos
- Division of Palliative Medicine, Department of Family and Preventive Medicine, Emory University, 100 Woodruff Circle, Atlanta, GA, 30322, USA
| | - Nandini Govil
- Department of Otolaryngology-Head and Neck Surgery, Emory University School of Medicine, 1400 Tullie Road, Atlanta, GA, 30323, USA.
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Moon PK, Qian ZJ, Stevenson DA, Chang KW. Single Versus Multigene Testing for Hereditary Hearing Loss: Use and Costs in a Commercially Insured Cohort. Otolaryngol Head Neck Surg 2023; 168:1472-1476. [PMID: 36939467 DOI: 10.1002/ohn.204] [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: 04/14/2022] [Revised: 10/20/2022] [Accepted: 10/31/2022] [Indexed: 01/23/2023]
Abstract
OBJECTIVE The objectives of this study were to describe trends in single-gene GJB2/6 (connexin 26/30) and multigene hearing loss panel (HLP) testing for hereditary hearing loss using real-world evidence. STUDY DESIGN Retrospective study using insurance claims data. SETTING Optum Data Mart database from 2015 to 2020. METHODS Rates of overall and hearing-specific genetic testing and costs to insurers and patients were reported. Linear regression models were used to assess the proportion of single-gene GJB2/6 testing over time. Additional linear regression models were used to assess changes in costs over time. RESULTS From 2015 to 2020, 91,986 children received genetic testing for any indication, of which 601 (0.65%) received hearing-specific tests. The proportion of single-gene GJB2/6 testing remained similar over time (mean difference [MD]: -1.3% per year; 95% confidence interval [CI]: -4.3%, 1.7%), while multigene HLP use increased over time (MD: 4.0% per year; 95% CI: 0.4%, 7.5%). The median charge for single-gene GJB2/6 testing remained constant during the study period (MD: -$34; 95% CI: -$86, $18), while the median charge for multigene HLP decreased during the study period (MD: -$145 per year; 95% CI: -$278, -$12). CONCLUSION Compared to molecular testing for GJB2/6, HLPs are becoming more common for hereditary hearing loss. The comprehensiveness of HLP and decreasing costs provide justification for its more widespread adoption moving forward.
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Affiliation(s)
- Peter K Moon
- Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Stanford, California, USA
| | - Z Jason Qian
- Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Stanford, California, USA
| | - David A Stevenson
- Department of Pediatrics-Medical Genetics, Stanford University School of Medicine, California, USA
| | - Kay W Chang
- Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Stanford, California, USA
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Full etiologic spectrum of pediatric severe to profound hearing loss of consecutive 119 cases. Sci Rep 2022; 12:12335. [PMID: 35853923 PMCID: PMC9296524 DOI: 10.1038/s41598-022-16421-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 07/11/2022] [Indexed: 12/03/2022] Open
Abstract
Determining the etiology of severe-to-profound sensorineural hearing loss (SP-SNHL) in pediatric subjects is particularly important in aiding the decision for auditory rehabilitation. We aimed to update the etiologic spectrum of pediatric SP-SNHL by combining internal auditory canal (IAC)-MRI with comprehensive and state-of-the-art genetic testings. From May 2013 to September 2020, 119 cochlear implantees under the age of 15 years with SP-SNHL were all prospectively recruited. They were subjected to genetic tests, including exome sequencing, and IAC-MRI for etiologic diagnosis. Strict interpretation of results were made based on ACMG/AMP guidelines and by an experienced neuroradiologist. The etiology was determined in of 65.5% (78/119) of our cohort. If only one of the two tests was done, the etiologic diagnostic rate would be reduced by at least 21.8%. Notably, cochlear nerve deficiency (n = 20) detected by IAC-MRI topped the etiology list of our cohort, followed by DFNB4 (n = 18), DFNB1 (n = 10), DFNB9 (n = 10) and periventricular leukomalacia associated with congenital CMV infection (n = 8). Simultaneous application of state-of-the-art genetic tests and IAC-MRI is essential for etiologic diagnosis, and if lesions of the auditory nerve or central nerve system are carefully examined on an MRI, we can identify the cause of deafness in more than 65% of pediatric SP-SNHL cases.
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Li MM, Tayoun AA, DiStefano M, Pandya A, Rehm HL, Robin NH, Schaefer AM, Yoshinaga-Itano C. Clinical evaluation and etiologic diagnosis of hearing loss: A clinical practice resource of the American College of Medical Genetics and Genomics (ACMG). Genet Med 2022; 24:1392-1406. [PMID: 35802133 DOI: 10.1016/j.gim.2022.03.018] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 03/28/2022] [Indexed: 11/26/2022] Open
Abstract
Hearing loss is a common and complex condition that can occur at any age, can be inherited or acquired, and is associated with a remarkably wide array of etiologies. The diverse causes of hearing loss, combined with the highly variable and often overlapping presentations of different forms of hearing loss, challenge the ability of traditional clinical evaluations to arrive at an etiologic diagnosis for many deaf and hard-of-hearing individuals. However, identifying the etiology of hearing loss may affect clinical management, improve prognostic accuracy, and refine genetic counseling and assessment of the likelihood of recurrence for relatives of deaf and hard-of-hearing individuals. Linguistic and cultural identities associated with being deaf or hard-of-hearing can complicate access to and the effectiveness of clinical care. These concerns can be minimized when genetic and other health care services are provided in a linguistically and culturally sensitive manner. This clinical practice resource offers information about the frequency, causes, and presentations of hearing loss and suggests approaches to the clinical and genetic evaluation of deaf and hard-of-hearing individuals aimed at identifying an etiologic diagnosis and providing informative and effective patient education and genetic counseling.
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Affiliation(s)
- Marilyn M Li
- Department of Pathology and Laboratory Medicine, Department of Pediatrics, Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Ahmad Abou Tayoun
- Al Jalila Genomics Center, Al Jalila Children's Specialty Hospital, Mohammed Bin Rashid University, Dubai, United Arab Emirates
| | | | - Arti Pandya
- Department of Pediatrics, University of North Carolina School of Medicine, Chapel Hill, NC
| | - Heidi L Rehm
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Nathaniel H Robin
- Departments of Genetics and Pediatrics, University of Alabama at Birmingham, Birmingham, AL
| | - Amanda M Schaefer
- Department of Otolaryngology-Head & Neck Surgery, Molecular Otolaryngology and Renal Research Laboratories, University of Iowa, Iowa City, IA
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Morell M, Rojas L, Haulena M, Busse B, Siebert U, Shadwick RE, Raverty SA. Selective Inner Hair Cell Loss in a Neonate Harbor Seal (Phoca vitulina). Animals (Basel) 2022; 12:ani12020180. [PMID: 35049802 PMCID: PMC8772928 DOI: 10.3390/ani12020180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 01/06/2022] [Accepted: 01/07/2022] [Indexed: 01/19/2023] Open
Abstract
Simple Summary Congenital hearing loss (i.e., hearing impairment present at birth) is recognized in humans and other terrestrial species, but there is a lack of information on congenital malformations and associated hearing loss in pinnipeds (seals, sea lions, and walruses). Baseline knowledge on marine mammal inner ear malformations is essential to differentiate between congenital and acquired abnormalities, which may be caused by infectious agents, age, or anthropogenic interactions, such as noise exposure. Analysis of the cochlea of a neonate harbor seal (Phoca vitulina) revealed bilateral loss of inner hair cells (sensory cells responsible for transducing the auditory signal) while the outer hair cells (sensory cells responsible for sound amplification and frequency selectivity and sensitivity) were intact. The selective inner hair cell loss (up to 84.6% of loss) was more severe in the basal turn, where the high frequencies are encoded. Potential causes and consequences are discussed. This is the first report of a case of selective inner hair cell loss in a marine mammal neonate, likely congenital. Abstract Congenital hearing loss is recognized in humans and other terrestrial species. However, there is a lack of information on its prevalence or pathophysiology in pinnipeds. It is important to have baseline knowledge on marine mammal malformations in the inner ear, to differentiate between congenital and acquired abnormalities, which may be caused by infectious pathogens, age, or anthropogenic interactions, such as noise exposure. Ultrastructural evaluation of the cochlea of a neonate harbor seal (Phoca vitulina) by scanning electron microscopy revealed bilateral loss of inner hair cells with intact outer hair cells. The selective inner hair cell loss was more severe in the basal turn, where high-frequency sounds are encoded. The loss of inner hair cells started around 40% away from the apex or tip of the spiral, reaching a maximum loss of 84.6% of hair cells at 80–85% of the length from the apex. Potential etiologies and consequences are discussed. This is believed to be the first case report of selective inner hair cell loss in a marine mammal neonate, likely congenital.
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Affiliation(s)
- Maria Morell
- Institute for Terrestrial and Aquatic Wildlife Research, University of Veterinary Medicine Hannover, Foundation, 25761 Büsum, Germany;
- Zoology Department, The University of British Columbia, Vancouver, BC V6T 1Z4, Canada;
- Correspondence:
| | - Laura Rojas
- Faculty of Veterinary Medicine and Zootechnics, National Autonomous University of Mexico, Av. Universidad 3000, Delegación Coyoacán, Mexico City 04510, Mexico;
| | - Martin Haulena
- Vancouver Aquarium Marine Science Center, Vancouver, BC V6G 3E2, Canada;
| | - Björn Busse
- Department of Osteology and Biomechanics, University Medical Center Hamburg-Eppendorf, 22529 Hamburg, Germany;
| | - Ursula Siebert
- Institute for Terrestrial and Aquatic Wildlife Research, University of Veterinary Medicine Hannover, Foundation, 25761 Büsum, Germany;
| | - Robert E. Shadwick
- Zoology Department, The University of British Columbia, Vancouver, BC V6T 1Z4, Canada;
| | - Stephen A. Raverty
- Zoology Department, The University of British Columbia, Vancouver, BC V6T 1Z4, Canada;
- Animal Health Center, Ministry of Agriculture, Abbotsford, BC V3G 2M3, Canada;
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Lazareva LA, Elizbaryan IS, Azamatova SA, Muzaeva BR, Sushcheva NA. [Triggers and predictors of development and formation of sensorineural hearing loss]. Vestn Otorinolaringol 2022; 87:34-43. [PMID: 35605270 DOI: 10.17116/otorino20228702134] [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: 06/15/2023]
Abstract
The purpose of the study is to review the results of scientific researches in recent years in an expanded interdisciplinary view of the problem of etiopathogenesis of sensorineural hearing loss, as well as the role of comorbidities and triggers in the formation of persistent changes in the audio-receiving part of the auditory analyzer.
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Affiliation(s)
- L A Lazareva
- Kuban State Medical University, Krasnodar, Russia
| | | | - S A Azamatova
- Adygei Republican Center for Rehabilitation of the Adygea Republican Clinical Hospital, Republic of Adygea, Russia
| | - B R Muzaeva
- Kuban State Medical University, Krasnodar, Russia
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Abstract
Compelling evidence indicates that some newborns harboring genetic variants associated with hearing loss might not be identified by current physiologic newborn hearing screening (NBHS) rendering current NBHS protocols suboptimal. Incorporating genomic sequencing into NBHS would improve clinical diagnosis and decrease time to early intervention efforts.
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Affiliation(s)
- Calli Ober Mitchell
- Department of Obstetrics and Gynecology, Brigham and Women's Hospital, NRB 160, 77 Avenue Louis Pasteur, Boston, MA 02115, USA. https://twitter.com/CalliMitchell3
| | - Cynthia Casson Morton
- Department of Obstetrics and Gynecology, Brigham and Women's Hospital, Harvard Medical School, NRB 160, 77 Avenue Louis Pasteur, Boston, MA 02115, USA; Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Manchester Centre for Audiology and Deafness, School of Health Sciences, University of Manchester, UK.
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Machine learning-based genetic diagnosis models for hereditary hearing loss by the GJB2, SLC26A4 and MT-RNR1 variants. EBioMedicine 2021; 69:103322. [PMID: 34161886 PMCID: PMC8237285 DOI: 10.1016/j.ebiom.2021.103322] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 03/18/2021] [Accepted: 03/18/2021] [Indexed: 12/16/2022] Open
Abstract
Background Hereditary hearing loss (HHL) is the most common sensory deficit, which highly afflicts humans. With gene sequencing technology development, more variants will be identified and support genetic diagnoses, which is difficult for human experts to diagnose. This study aims to develop a machine learning-based genetic diagnosis model of HHL-related variants of GJB2, SLC26A4 and MT-RNR1. Methods This case-control study included 1898 subjects, among which 1354 were HHL patients and 544 were carriers. Risk assessment models were established based on variants at 144 sites in three genes related to HHL by building six machine learning (ML) models. We compared the ML models with the genetic risk score (GRS) and expert interpretation (EI) to verify the clinical performance. Findings Among the six ML models, the support vector machine (SVM) showed the best performance. For the prediction of HHL-related gene sites in subjects with variants, the area under the receiver operating characteristic (AUC) of the SVM model was 0.803 (0.680–0.814) in the 10-fold stratified cross-validation and 0.751 (0.635–0.779) in external validation. The predicted results were better than both EI and GRS. Furthermore, 11 sites were identified as the smallest feature set that can be accurately predicted. Interpretation The developed SVM model has great potential to be an efficient and effective tool for HHL prediction when high throughput sequencing data are available.
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Belcher R, Virgin F, Duis J, Wootten C. Genetic and Non-genetic Workup for Pediatric Congenital Hearing Loss. Front Pediatr 2021; 9:536730. [PMID: 33829002 PMCID: PMC8020033 DOI: 10.3389/fped.2021.536730] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 02/25/2021] [Indexed: 01/06/2023] Open
Abstract
Hearing loss is one of the most common concerns for presentation for a geneticist. Presentation prior to the age of one (congenital hearing loss), profound sensorineural hearing loss (SNHL), and bilateral hearing loss are sensitive and should raise concern for genetic causes of hearing loss and prompt referral for genetic testing. Genetic testing particularly in this instance offers the opportunity for anticipatory guidance including possible course of the hearing loss over time and also connection and evaluation for additional congenital anomalies that may be associated with an underlying syndrome vs. isolated genetic hearing loss.
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Affiliation(s)
- Ryan Belcher
- Division of Pediatric Otolaryngology, Vanderbilt Department of Otolaryngology - Head and Neck Surgery, Monroe Carell Jr. Children's Hospital, Nashville, TN, United States
| | - Frank Virgin
- Division of Pediatric Otolaryngology, Vanderbilt Department of Otolaryngology - Head and Neck Surgery, Monroe Carell Jr. Children's Hospital, Nashville, TN, United States
| | - Jessica Duis
- Division of Pediatric Otolaryngology, Vanderbilt Department of Otolaryngology - Head and Neck Surgery, Monroe Carell Jr. Children's Hospital, Nashville, TN, United States
| | - Christopher Wootten
- Division of Pediatric Otolaryngology, Vanderbilt Department of Otolaryngology - Head and Neck Surgery, Monroe Carell Jr. Children's Hospital, Nashville, TN, United States
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Božanić Urbančič N, Battelino S, Tesovnik T, Trebušak Podkrajšek K. The Importance of Early Genetic Diagnostics of Hearing Loss in Children. MEDICINA (KAUNAS, LITHUANIA) 2020; 56:E471. [PMID: 32937936 PMCID: PMC7558651 DOI: 10.3390/medicina56090471] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 08/30/2020] [Accepted: 09/10/2020] [Indexed: 11/28/2022]
Abstract
Hearing loss is one of the most common sensory deficits. It carries severe medical and social consequences, and therefore, universal newborn hearing screening was introduced at the beginning of this century. Affected patients can have hearing loss as a solitary deficit (non-syndromic hearing loss) or have other organs affected as well (syndromic hearing loss). In around 60% of cases, congenital hearing loss has a genetic etiology, where disease-causing variants can change any component of the hearing pathway. Genetic testing is usually performed by sequencing. Sanger sequencing enables analysis of the limited number of genes strictly preselected according to the clinical presentation and the prevalence among the hearing loss patients. In contrast, next-generation sequencing allows broad analysis of the numerous genes related to hearing loss, exome, or the whole genome. Identification of the genetic etiology is possible, and it makes the foundation for the genetic counselling in the family. Furthermore, it enables the identification of the comorbidities that may need a referral for specialty care, allows early treatment, helps with identification of candidates for cochlear implant, appropriate aversive/protective management, and is the foundation for the development of novel therapeutic options.
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Affiliation(s)
- Nina Božanić Urbančič
- Department of Otorhinolaryngology and Cervicofacial Surgery, University Medical Centre Ljubljana, Zaloska 2, 1000 Ljubljana, Slovenia;
- Department of Otorhinolaryngology, Faculty of Medicine, University of Ljubljana, Vrazov trg 2, 1000 Ljubljana, Slovenia
| | - Saba Battelino
- Department of Otorhinolaryngology and Cervicofacial Surgery, University Medical Centre Ljubljana, Zaloska 2, 1000 Ljubljana, Slovenia;
- Department of Otorhinolaryngology, Faculty of Medicine, University of Ljubljana, Vrazov trg 2, 1000 Ljubljana, Slovenia
| | - Tine Tesovnik
- University Children’s Hospital, University Medical Centre Ljubljana, Bohoriceva 20, 1000 Ljubljana, Slovenia; (T.T.); (K.T.P.)
| | - Katarina Trebušak Podkrajšek
- University Children’s Hospital, University Medical Centre Ljubljana, Bohoriceva 20, 1000 Ljubljana, Slovenia; (T.T.); (K.T.P.)
- Faculty of Medicine, Institute of Biochemistry, University of Ljubljana, Vrazov trg 2, 1000 Ljubljana, Slovenia
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14
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May T, Cannon A, Moss IP, Nakano-Okuno M, Hardy S, Miskell EL, Kelley WV, Curry W, East KM, Acemgil A, Schach J, Sodeke SO, Fouad MN, Johnson RD, Richards JL, Knight SJ, Korf B. Recruiting diversity where it exists: The Alabama Genomic Health Initiative. J Genet Couns 2020; 29:471-478. [PMID: 32220047 PMCID: PMC7484696 DOI: 10.1002/jgc4.1258] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 02/16/2020] [Accepted: 02/21/2020] [Indexed: 12/27/2022]
Abstract
Lack of diversity among genomic research participants results in disparities in benefits from genetic testing. To address this, the Alabama Genomic Health Initiative employed community engagement strategies to recruit diverse populations where they lived. In this paper, we describe our engagement techniques and recruitment strategies, which resulted in significant improvement in representation of African American participants. While African American participation has not reached the representation of this community as a percentage of Alabama's overall population (26%-27%), we have achieved an overall representation exceeding 20% for African Americans. We believe this demonstrates the value of engagement and recruitment where diverse populations reside.
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Affiliation(s)
- Thomas May
- Elson S. Floyd College of Medicine, Washington State
University, Vancouver, WA, USA
- HudsonAlpha Institute for Biotechnology, Huntsville, AL,
USA
| | - Ashley Cannon
- University of Alabama at Birmingham, Birmingham, AL,
USA
| | - Irene P. Moss
- University of Alabama at Birmingham, Birmingham, AL,
USA
| | | | - Sharonda Hardy
- University of Alabama at Birmingham, Birmingham, AL,
USA
| | | | | | - William Curry
- University of Alabama at Birmingham, Birmingham, AL,
USA
| | - Kelly M. East
- HudsonAlpha Institute for Biotechnology, Huntsville, AL,
USA
| | - Aras Acemgil
- University of Alabama at Birmingham, Birmingham, AL,
USA
| | - Julie Schach
- University of Alabama at Birmingham, Birmingham, AL,
USA
| | - Stephen O. Sodeke
- National Center for Bioethics, Tuskegee University,
Tuskegee, AL, USA
| | - Mona N. Fouad
- University of Alabama at Birmingham, Birmingham, AL,
USA
| | | | | | - Sara J. Knight
- Division of Epidemiology, Department of Internal Medicine,
University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Bruce Korf
- University of Alabama at Birmingham, Birmingham, AL,
USA
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