1
|
Brotto D, Greggio M, De Filippis C, Trevisi P. Autosomal Recessive Non-Syndromic Deafness: Is AAV Gene Therapy a Real Chance? Audiol Res 2024; 14:239-253. [PMID: 38525683 PMCID: PMC10961695 DOI: 10.3390/audiolres14020022] [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: 11/17/2023] [Revised: 02/01/2024] [Accepted: 02/15/2024] [Indexed: 03/26/2024] Open
Abstract
The etiology of sensorineural hearing loss is heavily influenced by genetic mutations, with approximately 80% of cases attributed to genetic causes and only 20% to environmental factors. Over 100 non-syndromic deafness genes have been identified in humans thus far. In non-syndromic sensorineural hearing impairment, around 75-85% of cases follow an autosomal recessive inheritance pattern. In recent years, groundbreaking advancements in molecular gene therapy for inner-ear disorders have shown promising results. Experimental studies have demonstrated improvements in hearing following a single local injection of adeno-associated virus-derived vectors carrying an additional normal gene or using ribozymes to modify the genome. These pioneering approaches have opened new possibilities for potential therapeutic interventions. Following the PRISMA criteria, we summarized the AAV gene therapy experiments showing hearing improvement in the preclinical phases of development in different animal models of DFNB deafness and the AAV gene therapy programs currently in clinical phases targeting autosomal recessive non syndromic hearing loss. A total of 17 preclinical studies and 3 clinical studies were found and listed. Despite the hurdles, there have been significant breakthroughs in the path of HL gene therapy, holding great potential for providing patients with novel and effective treatment.
Collapse
Affiliation(s)
- Davide Brotto
- Department of Neuroscience DNS, Otolaryngology Section, Padova University, 35128 Padova, Italy; (D.B.); (C.D.F.); (P.T.)
- Otolaryngology Unit, Azienda Ospedale Università Padova, 35128 Padova, Italy
| | - Marco Greggio
- Department of Neuroscience DNS, Otolaryngology Section, Padova University, 35128 Padova, Italy; (D.B.); (C.D.F.); (P.T.)
- Otolaryngology Unit, Azienda Ospedale Università Padova, 35128 Padova, Italy
| | - Cosimo De Filippis
- Department of Neuroscience DNS, Otolaryngology Section, Padova University, 35128 Padova, Italy; (D.B.); (C.D.F.); (P.T.)
| | - Patrizia Trevisi
- Department of Neuroscience DNS, Otolaryngology Section, Padova University, 35128 Padova, Italy; (D.B.); (C.D.F.); (P.T.)
- Otolaryngology Unit, Azienda Ospedale Università Padova, 35128 Padova, Italy
| |
Collapse
|
2
|
Ketterer MC, Birkenhäger R, Beck R, Arndt S, Aschendorff A, Kunze M. Postnatal genetic umbilical cord analysis for earliest possible detection of inherited hearing impairment. Eur Arch Otorhinolaryngol 2023; 280:4811-4817. [PMID: 37093292 PMCID: PMC10562316 DOI: 10.1007/s00405-023-07986-y] [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: 01/15/2023] [Accepted: 04/17/2023] [Indexed: 04/25/2023]
Abstract
INTRODUCTION The most common sensorineural disorder in humans is hearing impairment and approximately 60% of prelingual hearing disorders are genetic. Especially parents with a congenital deaf child want to know as early as possible whether their second born child has the same genetic defect or not. The aim of this study is to demonstrate that postnatal genetic umbilical cord analysis is both the earliest detection possibility and sufficient. METHODS We included first born children with severe hearing impairment that underwent cochlear implantation. All included patients were analyzed genetically and exhibited mutations of either DFNB1 loci or SLC26A4 gene. Additionally, the umbilical cord of the sibling underwent genetic analysis to detect hereditary genetic mutations as early as possible. RESULTS 49 newborn children out of 22 families were included in this study. Genetic analysis revealed clinical relevant mutations in all first born children and in four siblings via umbilical cord analysis. All patients who have been diagnosed with a relevant genetic mutation that caused severe hearing impairment underwent hearing rehabilitation via cochlear implant surgery. CONCLUSION This study demonstrates the sufficient and early as possible detection of known genetically hearing disorders via umbilical cord analysis. In case of a known familial genetic hearing disorder, it is advisable to analyze newborn siblings for the corresponding genetic defect as soon as possible, to be able to plan and initiate clinical care for the patient as early as possible. It is also extremely important for the parents to obtain clear information about the auditory status of the newborn.
Collapse
Affiliation(s)
- Manuel Christoph Ketterer
- Department of Otorhinolaryngology-Head and Neck Surgery, Faculty of Medicine, Medical Center-University of Freiburg, University of Freiburg, Killianstrasse 5, 79106, Freiburg, Germany.
| | - Ralf Birkenhäger
- Department of Otorhinolaryngology-Head and Neck Surgery, Faculty of Medicine, Medical Center-University of Freiburg, University of Freiburg, Killianstrasse 5, 79106, Freiburg, Germany
- Molecular Biological Laboratory, Section for Clinical and Experimental Otology, University Medical Center Freiburg, Freiburg, Germany
| | - Rainer Beck
- Department of Otorhinolaryngology-Head and Neck Surgery, Faculty of Medicine, Medical Center-University of Freiburg, University of Freiburg, Killianstrasse 5, 79106, Freiburg, Germany
| | - Susan Arndt
- Department of Otorhinolaryngology-Head and Neck Surgery, Faculty of Medicine, Medical Center-University of Freiburg, University of Freiburg, Killianstrasse 5, 79106, Freiburg, Germany
| | - Antje Aschendorff
- Department of Otorhinolaryngology-Head and Neck Surgery, Faculty of Medicine, Medical Center-University of Freiburg, University of Freiburg, Killianstrasse 5, 79106, Freiburg, Germany
| | - Mirjam Kunze
- Department of Obstetrics and Gynecology, Medical Center, University of Freiburg, Freiburg, Germany
| |
Collapse
|
3
|
Clabout T, Maes L, Acke F, Wuyts W, Van Schil K, Coucke P, Janssens S, De Leenheer E. Negative Molecular Diagnostics in Non-Syndromic Hearing Loss: What Next? Genes (Basel) 2022; 14:genes14010105. [PMID: 36672845 PMCID: PMC9859074 DOI: 10.3390/genes14010105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/23/2022] [Accepted: 12/26/2022] [Indexed: 12/31/2022] Open
Abstract
Congenital hearing loss has an impact on almost every facet of life. In more than 50% of cases, a genetic cause can be identified. Currently, extensive genetic testing is available, although the etiology of some patients with obvious familial hearing loss remains unknown. We selected a cohort of mutation-negative patients to optimize the diagnostic yield for genetic hearing impairment. In this retrospective study, 21 patients (17 families) with negative molecular diagnostics for non-syndromic hearing loss (gene panel analysis) were included based on a positive family history with a similar type of hearing loss. Additional genetic testing was performed using a whole exome sequencing panel (WESHL panel v2.0) in four families with the strongest likelihood of genetic hearing impairment. In this cohort (n = 21), the severity of hearing loss was most commonly moderate (52%). Additional genetic testing revealed pathogenic copy number variants in the STRC gene in two families. In summary, regular re-evaluation of hearing loss patients with presumably genetic etiology after negative molecular diagnostics is recommended, as we might miss newly discovered deafness genes. The switch from gene panel analysis to whole exome sequencing or whole genome sequencing for the testing of congenital hearing loss seems promising.
Collapse
Affiliation(s)
- Thomas Clabout
- Faculty of Medicine and Health Sciences, Ghent University, Corneel Heymanslaan 10, B-9000 Ghent, Belgium
| | - Laurence Maes
- Faculty of Medicine and Health Sciences, Ghent University, Corneel Heymanslaan 10, B-9000 Ghent, Belgium
| | - Frederic Acke
- Department of Otorhinolaryngology, Ghent University Hospital, Corneel Heymanslaan 10, B-9000 Ghent, Belgium
| | - Wim Wuyts
- Center of Medical Genetics, Antwerp University Hospital and University of Antwerp, Prins Boudewijnlaan 43, B-2650 Edegem, Belgium
| | - Kristof Van Schil
- Center of Medical Genetics, Antwerp University Hospital and University of Antwerp, Prins Boudewijnlaan 43, B-2650 Edegem, Belgium
| | - Paul Coucke
- Center for Medical Genetics, Ghent University, Corneel Heymanslaan 10, B-9000 Ghent, Belgium
| | - Sandra Janssens
- Center for Medical Genetics, Ghent University, Corneel Heymanslaan 10, B-9000 Ghent, Belgium
| | - Els De Leenheer
- Department of Otorhinolaryngology, Ghent University Hospital, Corneel Heymanslaan 10, B-9000 Ghent, Belgium
- Correspondence: ; Tel.: +32-93322332
| |
Collapse
|
4
|
Thorpe RK, Walls WD, Corrigan R, Schaefer A, Wang K, Huygen P, Casavant TL, Smith RJH. AudioGene: refining the natural history of KCNQ4, GSDME, WFS1, and COCH-associated hearing loss. Hum Genet 2022; 141:877-887. [PMID: 35038006 PMCID: PMC9092196 DOI: 10.1007/s00439-021-02424-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 12/20/2021] [Indexed: 12/24/2022]
Abstract
Autosomal dominant non-syndromic hearing loss (ADNSHL) displays gene-specific progression of hearing loss, which is amenable to sequential audioprofiling. We sought to refine the natural history of ADNSHL by examining audiometric data in 5-year increments. 2175 audiograms were included from four genetic causes of ADNSHL-KCNQ4 (DFNA2), GSDME (DFNA5), WFS1 (DFNA6/14/38), and COCH (DFNA9). Annual threshold deterioration (ATD) was calculated for each gene: for the speech-frequency pure tone average, the ATD, respectively, was 0.72 dB/year, 0.94 dB/year, 0.53 dB/year, and 1.41 dB/year, with the largest drops occurring from ages 45-50 (0.89 dB/year; KCNQ4), 5-10 (1.42 dB/year; GSDME), 40-45 (0.83 dB/year; WFS1), and 50-55 (2.09 dB/year; COCH). 5-year interval analysis of audiograms reveals the gene specific natural history of KCNQ4, GSDME, WFS1 and COCH-related progressive hearing loss. Identifying ages at which hearing loss is most rapid informs clinical care and patient expectations. Natural history data are also essential to define outcomes of clinical trials that test novel therapies designed to correct or ameliorate these genetic forms of hearing loss.
Collapse
Affiliation(s)
- Ryan K Thorpe
- Department of Otolaryngology-Head and Neck Surgery, University of Iowa, Iowa City, Iowa, USA
| | - W Daniel Walls
- Department of Otolaryngology-Head and Neck Surgery, University of Iowa, Iowa City, Iowa, USA
| | - Rae Corrigan
- Roy J. Carver Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa, USA
| | - Amanda Schaefer
- Department of Otolaryngology-Head and Neck Surgery, University of Iowa, Iowa City, Iowa, USA
| | - Kai Wang
- Department of Biostatistics, University of Iowa, Iowa City, Iowa, USA
| | - Patrick Huygen
- Department of Otorhinolaryngology, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Thomas L Casavant
- Department of Electrical and Computer Engineering, University of Iowa, Iowa City, Iowa, USA
- Center for Bioinformatics and Computational Biology, University of Iowa, Iowa City, Iowa, USA
- Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, Iowa, USA
| | - Richard J H Smith
- Department of Otolaryngology-Head and Neck Surgery, University of Iowa, Iowa City, Iowa, USA.
- Interdisciplinary Graduate Program in Genetics, University of Iowa, Iowa City, Iowa, USA.
- Department of Electrical and Computer Engineering, University of Iowa, Iowa City, Iowa, USA.
- Molecular Otolaryngology and Renal Research Laboratories and Iowa Institute of Human Genetics, Iowa City, Iowa, USA.
| |
Collapse
|
5
|
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.
Collapse
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
| |
Collapse
|
6
|
Naz S. Molecular genetic landscape of hereditary hearing loss in Pakistan. Hum Genet 2021; 141:633-648. [PMID: 34308486 DOI: 10.1007/s00439-021-02320-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 07/17/2021] [Indexed: 01/13/2023]
Abstract
Approximately 14.5 million Pakistani individuals have a hearing loss and half of these cases may be due to genetic causes. Though significant progress has been made in uncovering genetic variants for recessively inherited nonsyndromic deafness, Pendred syndrome, and Usher syndromes, the same is not true for dominantly inherited hearing loss, most syndromic cases and deafness with complex inheritance patterns. Variants of 57 genes have been reported to cause nonsyndromic recessive deafness in Pakistan, though most are rare. Variants of just five genes GJB2, HGF, MYO7A, SLC26A4, and TMC1 together explain 57% of profound deafness while those of GJB2, MYO15A, OTOF, SLC26A4, TMC1, and TMPRSS3 account for 47% of moderate to severe hearing loss. In contrast, although variants of at least 39 genes have been implicated in different deafness syndromes, their prevalence in the population and the spectrum of mutations have not been explored. Furthermore, research on genetics of deafness has mostly focused on individuals from the Punjab province and needs to be extended to other regions of Pakistan. Identifying the genes and their variants causing deafness in all ethnic groups is important as it will pinpoint rare as well as recurrent mutations. This information may ultimately help in offering genetic counseling and future treatments.
Collapse
Affiliation(s)
- Sadaf Naz
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore, 54590, Pakistan.
| |
Collapse
|
7
|
Sadeghian L, Tabatabaiefar MA, Fattahi N, Pourreza MR, Tahmasebi P, Alavi Z, Hashemzadeh Chaleshtori M. Next-generation sequencing reveals a novel pathological mutation in the TMC1 gene causing autosomal recessive non-syndromic hearing loss in an Iranian kindred. Int J Pediatr Otorhinolaryngol 2019; 124:99-105. [PMID: 31176026 DOI: 10.1016/j.ijporl.2019.05.023] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 05/18/2019] [Accepted: 05/19/2019] [Indexed: 01/08/2023]
Abstract
OBJECTIVES Hearing loss (HL) is the most common sensory-neural disorder with excessive clinical and genetic heterogeneity, which negatively affects life quality. Autosomal recessive non-syndromic hearing loss (ARNSHL) is the most common form of the disease with no specific genotype-phenotype correlation in most of the cases. Whole exome sequencing (WES) is a powerful tool to overcome the problem of finding mutations in heterogeneous disorders. METHODS A comprehensive clinical and pedigree examination was performed on a multiplex family from Khuzestan province suffering from hereditary HL. Direct sequencing of GJB2 and genetic linkage analysis of DFNB1A/B was accomplished. WES was utilized to find possible genetic etiology of the disease. Co-segregation analysis of the candidate variant was done. High resolution melting analysis was applied to detect variant status in 50 healthy matched controls. RESULTS Clinical investigations suggested ARNSHL in the pedigree. The family was negative for DFNB1A/B. WES revealed a novel nonsense mutation, c.256G > T (p.Glu86*), in TMC1 segregating with the phenotype in the pedigree. The variant was absent in the controls. CONCLUSION Here, we report successful application of WES to identify the molecular pathogenesis of ARNSHL in a large family. The novel nonsense TMC1 variant meets the criteria of being pathogenic according to the ACMG-AMP variant interpretation guideline.
Collapse
Affiliation(s)
- Ladan Sadeghian
- Cellular and Molecular Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Mohammad Amin Tabatabaiefar
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran; Pediatric Inherited Diseases Research Center, Research Institute for Primordial Prevention of Non-communicable Disease, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Najmeh Fattahi
- Cilinical Biochemistry Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Mohammad Reza Pourreza
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Parisa Tahmasebi
- Department of Biology, Faculty of Sciences, Ilam University, Ilam, Iran
| | - Zahra Alavi
- Department of Genetics, Islamic Azad University, Shahrekord Branch, Shahrekord, Iran
| | - Morteza Hashemzadeh Chaleshtori
- Cellular and Molecular Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran.
| |
Collapse
|
8
|
Peter B, Dougherty MJ, Reed EK, Edelman E, Hanson K. Perceived Gaps in Genetics Training Among Audiologists and Speech-Language Pathologists: Lessons From a National Survey. AMERICAN JOURNAL OF SPEECH-LANGUAGE PATHOLOGY 2019; 28:408-423. [PMID: 31091132 DOI: 10.1044/2018_ajslp-18-0069] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Purpose The aim of this study was to assess knowledge, self-rated confidence, and perceived relevance of genetics in the clinical practice of audiologists and speech-language pathologists (SLPs) toward a better understanding of the need for genetics education, given that genetics plays a growing role in the diagnosis of hearing impairment and communication disorders. Method A survey consisting of 8 demographic items and 16 content questions was returned by 233 audiologists and 283 SLPs. Knowledge of applied genetics was queried with clinical scenarios in a multiple-choice format. Self-assessment of clinical confidence and perceived relevance of genetics in one's field was queried with questions and statements rated on 5-point Likert scales. The benefit of additional training in genetics was rated with a yes/no question, and if answered with yes, suggested topics were entered. Results A large significant gap between confidence in one's own genetics skills and the perceived relevance of genetics was evident, regardless of professional group. Over one third of the audiologists and over two thirds of the SLPs indicated low or somewhat low confidence in their own ability to implement principles of genetics, whereas over two thirds of both groups agreed that genetics is relevant for their field. Regardless of group, confidence scores were significantly and positively associated with relevance scores. Over 80% of respondents in both groups indicated that they would benefit from additional training in genetics. Most commonly suggested topics included genetic causes, general information about genetics, and making referrals. Conclusion Both audiologists and SLPs felt that genetics is relevant for their fields and that additional training in genetics would be beneficial. Future studies should evaluate the effect of genetics training on patient outcomes and the need for incorporating genetics more extensively into audiology and speech-language pathology training programs.
Collapse
Affiliation(s)
- Beate Peter
- Department of Speech and Hearing Science, Arizona State University, Tempe
- Department of Communication Sciences and Disorders, Saint Louis University, MO
| | - Michael J Dougherty
- American Society of Human Genetics, Bethesda, MD
- Department of Pediatrics, University of Colorado School of Medicine, Aurora
| | | | | | - Karen Hanson
- American Society of Human Genetics, Bethesda, MD
| |
Collapse
|
9
|
Pourreza MR, Mohammadi H, Sadeghian L, Asgharzadeh S, Sehhati M, Tabatabaiefar MA. Applying Two Different Bioinformatic Approaches to Discover Novel Genes Associated with Hereditary Hearing Loss via Whole-Exome Sequencing: ENDEAVOUR and HomozygosityMapper. Adv Biomed Res 2018; 7:141. [PMID: 30505812 PMCID: PMC6233028 DOI: 10.4103/abr.abr_80_18] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Hearing loss (HL) is a highly prevalent heterogeneous deficiency of sensory-neural system with involvement of several dozen genes. Whole-exome sequencing (WES) is capable of discovering known and novel genes involved with HL. MATERIALS AND METHODS Two pedigrees with HL background from Khuzestan province of Iran were selected. Polymerase chain reaction-sequencing of GJB2 and homozygosity mapping of 16 DFNB loci were performed. One patient of the first and two affected individuals from the second pedigree were subjected to WES. The result files were analyzed using tools on Ubuntu 16.04. Short reads were mapped to reference genome (hg19, NCBI Build 37). Sorting and duplication removals were done. Variants were obtained and annotated by an online software tool. Variant filtration was performed. In the first family, ENDEAVOUR was applied to prioritize candidate genes. In the second family, a combination of shared variants, homozygosity mapping, and gene expression were implemented to launch the disease-causing gene. RESULTS GJB2 sequencing and linkage analysis established no homozygosity-by-descent at any DFNB loci. Utilizing ENDEAVOUR, BBX: C.C857G (P.A286G), and MYH15: C.C5557T (P.R1853C) were put forward, but none of the variants co-segregated with the phenotype. Two genes, UNC13B and TRAK1, were prioritized in the homozygous regions detected by HomozygosityMapper. CONCLUSION WES is regarded a powerful approach to discover molecular etiology of Mendelian inherited disorders, but as it fails to enrich GC-rich regions, incapability of capturing noncoding regulatory regions and limited specificity and accuracy of copy number variations detection tools from exome data, it is assumed an insufficient procedure.
Collapse
Affiliation(s)
- Mohammad Reza Pourreza
- From the Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Hannane Mohammadi
- Department of Bioinformatics, School of Advanced Technologies in Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Ladan Sadeghian
- Isfahan Cardiovascular Research Center, Isfahan Cardiovascular Research Institute, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Samira Asgharzadeh
- Cellular and Molecular Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Mohammadreza Sehhati
- Department of Bioinformatics, School of Advanced Technologies in Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mohammad Amin Tabatabaiefar
- From the Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
- Pediatric Inherited Diseases Research Center, Research Institute for Primordial Prevention of Noncommunicable Disease, Isfahan University of Medical Sciences, Isfahan, Iran
| |
Collapse
|
10
|
Wangemann P, Marcus DC. Ion and Fluid Homeostasis in the Cochlea. UNDERSTANDING THE COCHLEA 2017. [DOI: 10.1007/978-3-319-52073-5_9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
|