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Raghuvanshi R, Panda KC, Ray CS, Ramchander PV. Targeted Next-Generation Sequencing Analysis Reveals a Novel Genetic Variant in MYO6 Gene in an Indian Family with Postlingual Nonsyndromic Hearing Loss. Genet Test Mol Biomarkers 2024. [PMID: 39019031 DOI: 10.1089/gtmb.2023.0747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/19/2024] Open
Abstract
Background: Hereditary nonsyndromic hearing loss (NSHL) is an extremely heterogeneous disorder, both genetically and clinically. Myosin VI (MYO6) pathogenic variations have been reported to cause both prelingual and postlingual forms of NSHL. Postlingual autosomal dominant cases are often overlooked for genetic etiology in clinical setups. In this study, we used next-generation sequencing (NGS)-based targeted deafness gene panel assay to identify the cause of postlingual hearing loss in an Indian family. Methods: The proband and his father from a multigenerational Indian family affected by postlingual hearing loss were examined via targeted capture of 129 deafness genes, after excluding gap junction protein beta 2 (GJB2) pathogenic variants by Sanger sequencing. NGS data analysis and co-segregation of the candidate variants in the family were carried out. The variant effect was predicted by in silico tools and interpreted following American College of Medical Genetics and Genomics-Association for Molecular Pathology guidelines. Results: A novel heterozygous transversion c.3225T>G, p.(Tyr1075*) in MYO6 gene was identified as the disease-causing variant in this family. This stop-gained variant is predicted to form a truncated myosin VI protein, which is devoid of crucial cargo-binding domain. PCR-RFLP screening in 200 NSHL cases and 200 normal-hearing controls showed the absence of this variant indicating its de novo nature in the population. Furthermore, we reviewed MYO6 variants reported from various populations to date. Conclusions: To the best of our knowledge, this is the first family with MYO6-associated hearing loss from an Indian population. The study also highlights the importance of deafness gene panels in molecular diagnosis of GJB2-negative pedigrees, contributing to genetic counseling in the affected families.
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Affiliation(s)
- Ruchika Raghuvanshi
- Institute of Life Sciences, Nalco Square, Bhubaneswar, India
- Regional Centre for Biotechnology, Faridabad, India
| | - Khirod Chandra Panda
- Ear, Nose, and Throat (ENT) Unit, Capital Hospital, Unit VI, Bhubaneswar, India
- Department of Ear, Nose, and Throat (ENT), Shrirama Chandra Bhanja (SCB) Medical College and Hospital, Cuttack, India
| | - Chinmay Sundar Ray
- Department of Ear, Nose, and Throat (ENT), Shrirama Chandra Bhanja (SCB) Medical College and Hospital, Cuttack, India
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Ji H, Shu Y, Li H. Unveiling a novel GJB2 dominant K22T mutation in a Chinese family with hearing loss. Acta Biochim Biophys Sin (Shanghai) 2024; 56:945-951. [PMID: 38733163 PMCID: PMC11292126 DOI: 10.3724/abbs.2024064] [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: 11/17/2023] [Accepted: 01/16/2024] [Indexed: 05/13/2024] Open
Abstract
Hearing loss constitutes one of the most prevalent conditions within the field of otolaryngology. Recent investigations have revealed that mutations in deafness-associated genes, including point mutations and variations in DNA sequences, can cause hearing impairments. With the ethology of deafness remaining unclear for a substantial portion of the affected population, further screenings for pathogenic mutations are imperative to unveil the underlying mechanisms. On this study, by using next-generation sequencing, we examine 129 commonly implicated deafness-related genes in a Chinese family with hearing loss, revealing a novel heterozygous dominant mutation in the GJB2 gene (GJB2: c.65T>G: p. Lys22Thr). This mutation consistently occurs in affected family members but is not detected in unaffected individuals, strongly suggesting its causative role in hearing loss. Structural analysis indicates potential disruption to the Cx26 gap junction channel's hydrogen bond and electrostatic interactions, aligning with predictions from the PolyPhen and SIFT algorithms. In conclusion, our study provides conclusive evidence that the identified heterozygous GJB2 mutation (GJB2: c.65T>G: p. Lys22Thr), specifically the K22T alteration, is the primary determinant of the family's deafness. This contribution enhances our understanding of the interplay between common deafness-associated genes and hearing loss, offering valuable insights for diagnostic guidance and the formulation of therapeutic strategies for this condition.
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Affiliation(s)
- Haiting Ji
- Department of the Affiliated Eye and ENT HospitalState Key Laboratory of Medical NeurobiologyENT Institute and OtorhinolaryngologyFudan UniversityShanghai200031China
- NHC Key Laboratory of Hearing MedicineFudan UniversityShanghai200031China
- Shanghai Engineering Research Centre of Cochlear ImplantShanghai200031China
- ENT Institute and Otorhinolaryngology Department of Eye & ENT HospitalState Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain ScienceFudan UniversityShanghai200031China
| | - Yilai Shu
- Department of the Affiliated Eye and ENT HospitalState Key Laboratory of Medical NeurobiologyENT Institute and OtorhinolaryngologyFudan UniversityShanghai200031China
- NHC Key Laboratory of Hearing MedicineFudan UniversityShanghai200031China
- Shanghai Engineering Research Centre of Cochlear ImplantShanghai200031China
- ENT Institute and Otorhinolaryngology Department of Eye & ENT HospitalState Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain ScienceFudan UniversityShanghai200031China
- Institutes of Biomedical SciencesFudan UniversityShanghai200032China
| | - Huawei Li
- Department of the Affiliated Eye and ENT HospitalState Key Laboratory of Medical NeurobiologyENT Institute and OtorhinolaryngologyFudan UniversityShanghai200031China
- NHC Key Laboratory of Hearing MedicineFudan UniversityShanghai200031China
- Shanghai Engineering Research Centre of Cochlear ImplantShanghai200031China
- ENT Institute and Otorhinolaryngology Department of Eye & ENT HospitalState Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain ScienceFudan UniversityShanghai200031China
- Institutes of Biomedical SciencesFudan UniversityShanghai200032China
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Ji H, Zhang L, Hussain HMJ, Aftab A, Yu H, Xiao M. Novel cis compound heterozygous variants in MYO6 causes early onset of non-syndromic hearing loss in a Chinese family. Front Genet 2024; 14:1275633. [PMID: 38274113 PMCID: PMC10808792 DOI: 10.3389/fgene.2023.1275633] [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: 08/11/2023] [Accepted: 12/26/2023] [Indexed: 01/27/2024] Open
Abstract
Background: Mutations in the MYO6 gene have been associated with both autosomal dominant non-syndromic hearing loss (ADNSHL) and autosomal recessive non-syndromic hearing loss (ARNSHL), with a cumulative identification of 125 pathogenic variants. To investigate the underlying genetic factor within a Chinese family affected with heriditary hearing loss, prompted the utilization of high-throughput sequencing. Method: A detailed clinical investigation was performed. Genetic testing was performed by using target panel sequencing, and Sanger sequencing. Targeted sequencing identified the variants and Sanger sequencing was employed to validate segregation of the identified variants within family. Additionally, bioinformatics analysis was performed to strengthen our findings. Results: Clinical investigation revealed the family members were affected by progressive and sensorineural hearing loss with an onset around 8-10 years old. Furthermore, genetic testing identified novel MYO6 variants, c.[2377T>G; 2382G>T] p.[Trp793Gly; Lys794Asn], positioned in a cis pattern, as plausible pathogenic contributors to early-onset hearing loss characterized by a severe and progressive course. Moreover, bioinformatics analysis showd disruptin in hydrogen bonding of mutant amino acids with interactive amino acids. Conclusion: Our research uncovered a relationship between mutations in the MYO6 gene and non-syndromic hearing loss. We identified two variants, c.[2377T>G; 2382G>T] p.[Trp793Gly; Lys794Asn] in MYO6 as strong candidates responsible for the observed progressive hereditary hearing loss. This study not only adds to our knowledge about hearing problems related to MYO6 but also reveals the presence of monogenic compound heterozygosity. Our study will provide a new sight for genetic diagnosis in such patients and their management for future use.
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Affiliation(s)
- Haiting Ji
- Department of Otorhinolaryngology, Affiliated Eye and ENT Hospital of Fudan University, Shanghai, China
- ENT Institute and Otorhinolaryngology, Department of Eye and ENT Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China
- NHC Key Laboratory of Hearing Medicine, Fudan University, Shanghai, China
| | - Lichun Zhang
- Department of Otorhinolaryngology, Head and Neck Surgery, Otto Körner, Rostock University Medical Center, Rostock, Germany
| | | | - Ayesha Aftab
- Department of Biological Sciences, International Islamic University, Islamabad, Pakistan
| | - Huiqian Yu
- Department of Otorhinolaryngology, Affiliated Eye and ENT Hospital of Fudan University, Shanghai, China
- ENT Institute and Otorhinolaryngology, Department of Eye and ENT Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China
- NHC Key Laboratory of Hearing Medicine, Fudan University, Shanghai, China
| | - Min Xiao
- Shanghai Ji Ai Genetics and IVF Institute, The Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
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Forrester-Gauntlett B, Peters L, Oback B. Grainyhead-like 2 is required for morphological integrity of mouse embryonic stem cells and orderly formation of inner ear-like organoids. Front Cell Dev Biol 2023; 11:1112069. [PMID: 37745294 PMCID: PMC10513505 DOI: 10.3389/fcell.2023.1112069] [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: 11/30/2022] [Accepted: 08/21/2023] [Indexed: 09/26/2023] Open
Abstract
Mutations in the transcription factor gene grainyhead-like 2 (GRHL2) are associated with progressive non-syndromic sensorineural deafness autosomal dominant type 28 (DFNA28) in humans. Since complete loss of Grhl2 is lethal in mouse embryos, we studied its role during inner ear pathology and hearing loss in vitro. To this end, we generated different homozygous deletions to knockout Grhl2 in mouse embryonic stem cells (Grhl2-KO ESCs), including some mimicking naturally occurring truncations in the dimerisation domain related to human DFNA28. Under naïve culture conditions, Grhl2-KO cells in suspension were more heterogenous in size and larger than wild-type controls. Adherent Grhl2-KO cells were also larger, with a less uniform shape, flattened, less circular morphology, forming loose monolayer colonies with poorly defined edges. These changes correlated with lower expression of epithelial cadherin Cdh1 but no changes in tight junction markers (Ocln, Tjp2) or other Grhl isoforms (Grhl1, Grhl3). Clonogenicity from single cells, proliferation rates of cell populations and proliferation markers were reduced in Grhl2-KO ESCs. We next induced stepwise directed differentiation of Grhl2-KO ESCs along an otic pathway, giving rise to three-dimensional inner ear-like organoids (IELOs). Quantitative morphometry revealed that Grhl2-KO cells initially formed larger IELOs with a less compacted structure, more eccentric shape and increased surface area. These morphological changes persisted for up to one week. They were partially rescued by forced cell aggregation and fully restored by stably overexpressing exogenous Grhl2 in Grhl2-KO ESCs, indicating that Grhl2 alters cell-cell interactions. On day 8, aggregates were transferred into minimal maturation medium to allow self-guided organogenesis for another two weeks. During this period, Grhl2-KO cells and wild-type controls developed similarly, expressing neural, neuronal and sensory hair cell markers, while maintaining their initial differences in size and shape. In summary, Grhl2 is required for morphological maintenance of ESCs and orderly formation of IELOs, consistent with an essential role in organising epithelial integrity during inner ear development. Our findings validate quantitative morphometry as a useful, non-invasive screening method for molecular phenotyping of candidate mutations during organoid development.
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Affiliation(s)
- Blaise Forrester-Gauntlett
- Animal Biotech, AgResearch, Hamilton, New Zealand
- School of Science, University of Waikato, Hamilton, New Zealand
| | - Linda Peters
- School of Science, University of Waikato, Hamilton, New Zealand
| | - Björn Oback
- Animal Biotech, AgResearch, Hamilton, New Zealand
- School of Science, University of Waikato, Hamilton, New Zealand
- School of Medical Sciences, University of Auckland, Auckland, New Zealand
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Li Q, Wang S, Liang P, Li W, Wang J, Fan B, Yang Y, An X, Chen J, Zha D. A novel splice site variant c.1183 + 1 G > C in DFNA5 causing autosomal dominant nonsyndromic hearing loss in a Chinese family. BMC Med Genomics 2022; 15:163. [PMID: 35864542 PMCID: PMC9306051 DOI: 10.1186/s12920-022-01315-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 07/11/2022] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND The most frequent clinical presentation of autosomal dominant nonsyndromic hearing loss (ADNSHL) is bilateral, symmetrical, postlingual progressive sensorineural hearing loss, which begins with impairment at high frequencies and eventually progresses to hearing loss at all frequencies. Autosomal dominant deafness-5 (DFNA5) is a subtype of ADNSHL caused by heterozygous variants in the gasdermin E (GSDME, also known as DFNA5) gene. METHODS Deafness gene NGS panel analysis were performed on the proband of a six-generation Chinese family with hearing loss. The co-segregation analysis between the hearing loss and the novel variant was analyzed by Sanger sequencing and pure-tone audiometry. The minigene splicing assay was performed to evaluate the potential effect of the variant on messenger RNA splicing in vitro. RESULTS The family exhibited autosomal dominant, progressive, postlingual, nonsyndromic sensorineural hearing loss, which was similar to that of the previously reported DFNA5 families. A novel heterozygous splice site variant in GSDME gene intron 8 was identified, which co-segregated with the hearing loss phenotype of the family. The variant caused skipping of exon 8 in the mutant transcript, leading to the direct linking of exons 7 and 9. CONCLUSIONS We identified a novel GSDME splice site variant c.1183 + 1 G > C in an extended Chinese family, which led to the skipping of exon 8. The results extended the pathogenic variants spectrum of the GSDME gene, provided further support for the 'gain-of-function' mechanism of DFNA5, and afforded a molecular interpretation for these patients with ADNSHL.
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Affiliation(s)
- Qiong Li
- Department of Otolaryngology-Head and Neck Surgery, Xijing Hospital, Air Force Medical University, 127 Changle West Road, Xi'an, 710032, Shaanxi, People's Republic of China
| | - Shujuan Wang
- Department of Otolaryngology-Head and Neck Surgery, Xijing Hospital, Air Force Medical University, 127 Changle West Road, Xi'an, 710032, Shaanxi, People's Republic of China
| | - Pengfei Liang
- Department of Otolaryngology-Head and Neck Surgery, Xijing Hospital, Air Force Medical University, 127 Changle West Road, Xi'an, 710032, Shaanxi, People's Republic of China
| | - Wei Li
- Department of Otolaryngology-Head and Neck Surgery, Xijing Hospital, Air Force Medical University, 127 Changle West Road, Xi'an, 710032, Shaanxi, People's Republic of China
| | - Jian Wang
- Department of Otolaryngology-Head and Neck Surgery, Xijing Hospital, Air Force Medical University, 127 Changle West Road, Xi'an, 710032, Shaanxi, People's Republic of China
| | - Bei Fan
- Department of Otolaryngology-Head and Neck Surgery, Xijing Hospital, Air Force Medical University, 127 Changle West Road, Xi'an, 710032, Shaanxi, People's Republic of China
| | - Yang Yang
- Department of Otolaryngology-Head and Neck Surgery, Xijing Hospital, Air Force Medical University, 127 Changle West Road, Xi'an, 710032, Shaanxi, People's Republic of China
| | - Xiaogang An
- Department of Otolaryngology-Head and Neck Surgery, Xijing Hospital, Air Force Medical University, 127 Changle West Road, Xi'an, 710032, Shaanxi, People's Republic of China
| | - Jun Chen
- Department of Otolaryngology-Head and Neck Surgery, Xijing Hospital, Air Force Medical University, 127 Changle West Road, Xi'an, 710032, Shaanxi, People's Republic of China.
| | - Dingjun Zha
- Department of Otolaryngology-Head and Neck Surgery, Xijing Hospital, Air Force Medical University, 127 Changle West Road, Xi'an, 710032, Shaanxi, People's Republic of China.
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Chiereghin C, Robusto M, Massa V, Castorina P, Ambrosetti U, Asselta R, Soldà G. Role of Cytoskeletal Diaphanous-Related Formins in Hearing Loss. Cells 2022; 11:cells11111726. [PMID: 35681420 PMCID: PMC9179844 DOI: 10.3390/cells11111726] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 05/16/2022] [Accepted: 05/18/2022] [Indexed: 02/04/2023] Open
Abstract
Hearing relies on the proper functioning of auditory hair cells and on actin-based cytoskeletal structures. Diaphanous-related formins (DRFs) are evolutionarily conserved cytoskeletal proteins that regulate the nucleation of linear unbranched actin filaments. They play key roles during metazoan development, and they seem particularly pivotal for the correct physiology of the reproductive and auditory systems. Indeed, in Drosophila melanogaster, a single diaphanous (dia) gene is present, and mutants show sterility and impaired response to sound. Vertebrates, instead, have three orthologs of the diaphanous gene: DIAPH1, DIAPH2, and DIAPH3. In humans, defects in DIAPH1 and DIAPH3 have been associated with different types of hearing loss. In particular, heterozygous mutations in DIAPH1 are responsible for autosomal dominant deafness with or without thrombocytopenia (DFNA1, MIM #124900), whereas regulatory mutations inducing the overexpression of DIAPH3 cause autosomal dominant auditory neuropathy 1 (AUNA1, MIM #609129). Here, we provide an overview of the expression and function of DRFs in normal hearing and deafness.
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Affiliation(s)
- Chiara Chiereghin
- IRCCS Humanitas Research Hospital, Via Manzoni 56, 20089 Milan, Italy; (C.C.); (R.A.)
| | - Michela Robusto
- Experimental Therapeutics Program, IFOM ETS—The AIRC Institute of Molecular Oncology, Via Adamello 16, 20139 Milan, Italy;
| | - Valentina Massa
- Dipartimento di Scienze della Salute, Università degli Studi di Milano, Via Di Rudinì 8, 20146 Milan, Italy;
| | | | - Umberto Ambrosetti
- Dipartimento di Scienze Cliniche e di Comunità, Università degli Studi di Milano and Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, UO Audiologia, Via F. Sforza 35, 20122 Milan, Italy;
| | - Rosanna Asselta
- IRCCS Humanitas Research Hospital, Via Manzoni 56, 20089 Milan, Italy; (C.C.); (R.A.)
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Milan, Italy
| | - Giulia Soldà
- IRCCS Humanitas Research Hospital, Via Manzoni 56, 20089 Milan, Italy; (C.C.); (R.A.)
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Milan, Italy
- Correspondence:
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Han S, Zhang D, Guo Y, Fu Z, Guan G. Prevalence and Characteristics of STRC Gene Mutations (DFNB16): A Systematic Review and Meta-Analysis. Front Genet 2021; 12:707845. [PMID: 34621290 PMCID: PMC8491653 DOI: 10.3389/fgene.2021.707845] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 08/13/2021] [Indexed: 11/13/2022] Open
Abstract
Background: Mutations in the STRC (MIM 606440) gene, inducing DFNB16, are considered a major cause of mild–moderate autosomal recessive non-syndromic hearing loss (ARNSHL). We conducted a systematic review and meta-analysis to determine the global prevalence and characteristics of STRC variations, important information required for genetic counseling. Methods: PubMed, Google Scholar, Medline, Embase, and Web of Science were searched for relevant articles published before January 2021. Results: The pooled prevalence of DFNB16 in GJB2-negative patients with hearing loss was 4.08% (95% CI: 0.0289–0.0573), and the proportion of STRC variants in the mild–moderate hearing loss group was 14.36%. Monoallelic mutations of STRC were 4.84% (95% CI: 0.0343–0.0680) in patients with deafness (non-GJB2) and 1.36% (95% CI: 0.0025–0.0696) in people with normal hearing. The DFNB16 prevalence in genetically confirmed patients (non-GJB2) was 11.10% (95% CI: 0.0716–0.1682). Overall pooled prevalence of deafness–infertility syndrome (DIS) was 36.75% (95% CI: 0.2122–0.5563) in DFNB16. The prevalence of biallelic deletions in STRC gene mutations was 70.85% (95% CI: 0.5824–0.8213). Conclusion: Variants in the STRC gene significantly contribute to mild–moderate hearing impairment. Moreover, biallelic deletions are a main feature of STRC mutations. Copy number variations associated with infertility should be seriously considered when investigating DFNB16.
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Affiliation(s)
- Shuang Han
- Department of Otolaryngology Head and Neck Surgery, The Second Hospital of Jilin University, Changchun, China
| | - Dejun Zhang
- Department of Otolaryngology Head and Neck Surgery, The Second Hospital of Jilin University, Changchun, China
| | - Yingyuan Guo
- Department of Otolaryngology Head and Neck Surgery, The Second Hospital of Jilin University, Changchun, China
| | - Zeming Fu
- Department of Otolaryngology Head and Neck Surgery, The Second Hospital of Jilin University, Changchun, China
| | - Guofang Guan
- Department of Otolaryngology Head and Neck Surgery, The Second Hospital of Jilin University, Changchun, China
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Abstract
Almost 25 years have passed since a mutation of a formin gene, DIAPH1, was identified as being responsible for a human inherited disorder: a form of sensorineural hearing loss. Since then, our knowledge of the links between formins and disease has deepened considerably. Mutations of DIAPH1 and six other formin genes (DAAM2, DIAPH2, DIAPH3, FMN2, INF2 and FHOD3) have been identified as the genetic cause of a variety of inherited human disorders, including intellectual disability, renal disease, peripheral neuropathy, thrombocytopenia, primary ovarian insufficiency, hearing loss and cardiomyopathy. In addition, alterations in formin genes have been associated with a variety of pathological conditions, including developmental defects affecting the heart, nervous system and kidney, aging-related diseases, and cancer. This review summarizes the most recent discoveries about the involvement of formin alterations in monogenic disorders and other human pathological conditions, especially cancer, with which they have been associated. In vitro results and experiments in modified animal models are discussed. Finally, we outline the directions for future research in this field.
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Affiliation(s)
| | - Miguel A. Alonso
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, 28049 Madrid, Spain;
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Liang P, Chen F, Wang S, Li Q, Li W, Wang J, Chen J, Zha D. Whole exome sequencing of six Chinese families with hereditary non-syndromic hearing loss. Int J Pediatr Otorhinolaryngol 2021; 148:110817. [PMID: 34265623 DOI: 10.1016/j.ijporl.2021.110817] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 06/03/2021] [Accepted: 06/24/2021] [Indexed: 11/29/2022]
Abstract
OBJECTIVES Hereditary non-syndromic hearing loss (NSHL) has a high genetic heterogeneity with about 152 genes identified as associated molecular causes. The present study aimed to detect the possible damaging variants of the deaf probands from six unrelated Chinese families. METHODS After excluding the pathogenic/likely pathogenic variants in the most common genes, GJB2 and SLC26A4, 12 probands with prelingual deafness and autosomal recessive inheritance were evaluated by whole-exome sequencing (WES). All the candidate variants were verified by Sanger sequencing in all patients and their parents. RESULTS Biallelic variants were identified in all deaf patients. Among these six families, 10 potentially causative variants, including 3 reported and 7 novel variants, in 3 different deafness-associated autosomal recessive (DFNB) genes (MYO15A, COL11A2, and CDH23) were identified. These novel variants are thought to be pathogenic or likely pathogenic for theirs predicted damage function upon the protein as while as cosegregated with the deafness phenotype. The variants in MYO15A were frequent with 7/10 candidate ones. CONCLUSION Next-generation sequencing (NGS) approach becomes more cost-effective and efficient when analyzing large-scale genes compared to the conventional polymerase chain reaction-based Sanger sequencing, which is often used to screen common deafness-related genes. The current findings further extend the pathogenic/likely pathogenic variants spectrum of hearing loss in the Chinese population, which has a positive significance for genetic counseling.
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Affiliation(s)
- Pengfei Liang
- Department of Otolaryngology-Head and Neck Surgery, Xijing Hospital, Air Force Medical University, Xi'an, China
| | - Fengping Chen
- Department of Otolaryngology-Head and Neck Surgery, Xijing Hospital, Air Force Medical University, Xi'an, China
| | - Shujuan Wang
- Department of Otolaryngology-Head and Neck Surgery, Xijing Hospital, Air Force Medical University, Xi'an, China
| | - Qiong Li
- Department of Otolaryngology-Head and Neck Surgery, Xijing Hospital, Air Force Medical University, Xi'an, China
| | - Wei Li
- Department of Otolaryngology-Head and Neck Surgery, Xijing Hospital, Air Force Medical University, Xi'an, China
| | - Jian Wang
- Department of Otolaryngology-Head and Neck Surgery, Xijing Hospital, Air Force Medical University, Xi'an, China
| | - Jun Chen
- Department of Otolaryngology-Head and Neck Surgery, Xijing Hospital, Air Force Medical University, Xi'an, China
| | - Dingjun Zha
- Department of Otolaryngology-Head and Neck Surgery, Xijing Hospital, Air Force Medical University, Xi'an, China.
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10
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Lakha R, Montero AM, Jabeen T, Costeas CC, Ma J, Vizcarra CL. Variable Autoinhibition among Deafness-Associated Variants of Diaphanous 1 (DIAPH1). Biochemistry 2021; 60:2320-2329. [PMID: 34279089 DOI: 10.1021/acs.biochem.1c00170] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
One of the earliest mapped human deafness genes, DIAPH1, encodes the formin DIAPH1. To date, at least three distinct mutations in the C-terminal domains and two additional mutations in the N-terminal region are associated with autosomal dominant hearing loss. The underlying molecular mechanisms are not known, and the role of formins in the inner ear is not well understood. In this study, we use biochemical assays to test the hypotheses that autoinhibition and/or actin assembly activities are disrupted by DFNA1 mutations. Our results indicate that C-terminal mutant forms of DIAPH1 are functional in vitro and promote actin filament assembly. Similarly, N-terminal mutants are well-folded and have quaternary structures and thermal stabilities similar to those of the wild-type (WT) protein. The strength of the autoinhibitory interactions varies widely among mutants, with the ttaa, A265S, and I530S mutations having an affinity similar to that of WT and the 1213x and Δag mutations completely abolishing autoinhibition. These data indicate that, in some cases, hearing loss may be linked to weakened inhibition of actin assembly.
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Affiliation(s)
- Rabina Lakha
- Department of Chemistry, Barnard College, New York, New York 10027, United States
| | - Angela M Montero
- Department of Chemistry, Barnard College, New York, New York 10027, United States
| | - Tayyaba Jabeen
- Department of Chemistry, Barnard College, New York, New York 10027, United States
| | - Christina C Costeas
- Department of Chemistry, Barnard College, New York, New York 10027, United States
| | - Jia Ma
- Department of Chemistry, Columbia University, New York, New York 10027, United States
| | - Christina L Vizcarra
- Department of Chemistry, Barnard College, New York, New York 10027, United States
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11
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Novel GRHL2 Gene Variant Associated with Hearing Loss: A Case Report and Review of the Literature. Genes (Basel) 2021; 12:genes12040484. [PMID: 33810548 PMCID: PMC8066333 DOI: 10.3390/genes12040484] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 03/16/2021] [Accepted: 03/23/2021] [Indexed: 11/17/2022] Open
Abstract
In contrast to the recessive form, hearing loss inherited in a dominant manner is more often post-lingual and typically results in a progressive sensorineural hearing loss with variable severity and late onset. Variants in the GRHL2 gene are an extremely rare cause of dominantly inherited hearing loss. Genetic testing is a crucial part of the identification of the etiology of hearing loss in individual patients, especially when performed with next-generation sequencing, enabling simultaneous analysis of numerous genes, including those rarely associated with hearing loss. We aimed to evaluate the genetic etiology of hearing loss in a family with moderate late-onset hearing loss using next-generation sequencing and to conduct a review of reported variants in the GRHL2 gene. We identified a novel disease-causing variant in the GRHL2 gene (NM_024915: c.1510C>T; p.Arg504Ter) in both affected members of the family. They both presented with moderate late-onset hearing loss with no additional clinical characteristics. Reviewing known GRHL2 variants associated with hearing loss, we can conclude that they are more likely to be truncating variants, while the associated onset of hearing loss is variable.
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Wu K, Wang H, Guan J, Lan L, Zhao C, Zhang M, Wang D, Wang Q. A novel variant in diaphanous homolog 1 (DIAPH1) as the cause of auditory neuropathy in a Chinese family. Int J Pediatr Otorhinolaryngol 2020; 133:109947. [PMID: 32087478 DOI: 10.1016/j.ijporl.2020.109947] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 02/11/2020] [Accepted: 02/11/2020] [Indexed: 11/30/2022]
Abstract
OBJECTIVES To determine the genetic cause of non-syndromic autosomal dominant deafness segregating in a Chinese Auditory neuropathy (AN) family. INTRODUCTION AN is a genetically related rare disease characterized by sensorineural hearing loss and retention of hair cell function. Diaphanous Homolog 1 (DIAPH1) is the causative gene of DFNA1. To date, no evidence has been detected to reveal the connection between gene DIAPH1 and AN. MATERIAL AND METHODS Audiological and imageological examinations, genome-wide linkage analysis, and whole exome sequencing (WES) were carried out on the family members. RESULTS In the 13-member branch of the family, 4 patients with preserved otoacoustic emission or cochlear microphonic and abnormal auditory brainstem responses were diagnosed with AN. Linkage analysis detected an interval with a LOD (log odds) score >4 on chr5:138.845-149.509 cM. Using WES we identified a novel frameshift variant c.3551_3552del (p.Glu1184AlafsTer11) in exon 26 of DIAPH1 located in the linkage region. The variant was co-segregated with hearing impairment phenotype in the family except 4 members below the average age of onset. We have found sufficient evidence conforming with the American College of Medical Genetics and Genomics Guideline to consider c.3551_3552del as the genetic cause of the family patients. CONCLUSION It is the first report to expand DIAPH1-related phenotypic spectrum to include AN. Our findings could facilitate the clinical diagnosis and genetic counselling for AN, especially for those with DIAPH1 variants.
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Affiliation(s)
- Kan Wu
- Department of Otolaryngology-Head and Neck Surgery, Chinese PLA Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, 100853, China
| | - Hongyang Wang
- Department of Otolaryngology-Head and Neck Surgery, Chinese PLA Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, 100853, China
| | - Jing Guan
- Department of Otolaryngology-Head and Neck Surgery, Chinese PLA Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, 100853, China
| | - Lan Lan
- Department of Otolaryngology-Head and Neck Surgery, Chinese PLA Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, 100853, China
| | - Cui Zhao
- Department of Otolaryngology-Head and Neck Surgery, Chinese PLA Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, 100853, China
| | - Mengqian Zhang
- Department of Otolaryngology-Head and Neck Surgery, Chinese PLA Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, 100853, China
| | - Dayong Wang
- Department of Otolaryngology-Head and Neck Surgery, Chinese PLA Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, 100853, China.
| | - Qiuju Wang
- Department of Otolaryngology-Head and Neck Surgery, Chinese PLA Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, 100853, China
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Abstract
OBJECTIVE To describe the genetic and phenotypic spectrum of Usher syndrome after 6 years of studies by next-generation sequencing, and propose an up-to-date classification of Usher genes in patients with both visual and hearing impairments suggesting Usher syndrome, and in patients with seemingly isolated deafness. STUDY DESIGN The systematic review and meta-analysis protocol was based on Cochrane and Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. We performed 1) a meta-analysis of data from 11 next-generation sequencing studies in 684 patients with Usher syndrome; 2) a meta-analysis of data from 21 next-generation studies in 2,476 patients with seemingly isolated deafness, to assess the involvement of Usher genes in seemingly nonsyndromic hearing loss, and thus the proportion of patients at high risk of subsequent retinitis pigmentosa (RP); 3) a statistical analysis of differences between parts 1) and 2). RESULTS In patients with both visual and hearing impairments, the biallelic disease-causing mutation rate was assessed for each Usher gene to propose a classification by frequency: USH2A: 50% (341/684) of patients, MYO7A: 21% (144/684), CDH23: 6% (39/684), ADGRV1: 5% (35/684), PCDH15: 3% (21/684), USH1C: 2% (17/684), CLRN1: 2% (14/684), USH1G: 1% (9/684), WHRN: 0.4% (3/684), PDZD7 0.1% (1/684), CIB2 (0/684). In patients with seemingly isolated sensorineural deafness, 7.5% had disease-causing mutations in Usher genes, and are therefore at high risk of developing RP. These new findings provide evidence that usherome dysfunction is the second cause of genetic sensorineural hearing loss after connexin dysfunction. CONCLUSION These results promote generalization of early molecular screening for Usher syndrome in deaf children.
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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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Md Bakri N, Ramachandran V, Hoo FK, Subrayan V, Isa H, Ngah NF, Mohamad NA, Ching SM, Chan YM, Ismail P, Ismail F, Sukiman ES, Wan Sulaiman WA. Copy number variation in VEGF gene as a biomarker of susceptibility to age-related macular degeneration. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2018. [DOI: 10.1016/j.ejmhg.2017.09.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
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Sampaio‐Silva J, Batissoco AC, Jesus‐Santos R, Abath‐Neto O, Scarpelli LC, Nishimura PY, Galindo LT, Bento RF, Oiticica J, Lezirovitz K. Exome Sequencing Identifies a Novel Nonsense Mutation of
MYO6
as the Cause of Deafness in a Brazilian Family. Ann Hum Genet 2017; 82:23-34. [DOI: 10.1111/ahg.12213] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 08/16/2017] [Indexed: 02/04/2023]
Affiliation(s)
- Juliana Sampaio‐Silva
- Laboratório de Otorrinolaringologia/LIM32 Hospital das Clinicas HCFMUSP Faculdade de Medicina Universidade de Sao Paulo Sao Paulo SP Brasil
| | - Ana Carla Batissoco
- Laboratório de Otorrinolaringologia/LIM32 Hospital das Clinicas HCFMUSP Faculdade de Medicina Universidade de Sao Paulo Sao Paulo SP Brasil
| | - Rafaela Jesus‐Santos
- Laboratório de Otorrinolaringologia/LIM32 Hospital das Clinicas HCFMUSP Faculdade de Medicina Universidade de Sao Paulo Sao Paulo SP Brasil
| | - Osório Abath‐Neto
- Departamento de Neurologia Faculdade de Medicina FMUSP Universidade de Sao Paulo Sao Paulo SP Brasil
| | | | | | - Layla Testa Galindo
- Setor de Biologia Molecular Grupo DASA – Diagnósticos da América Barueri SP Brasil
| | - Ricardo Ferreira Bento
- Laboratório de Otorrinolaringologia/LIM32 Hospital das Clinicas HCFMUSP Faculdade de Medicina Universidade de Sao Paulo Sao Paulo SP Brasil
| | - Jeanne Oiticica
- Laboratório de Otorrinolaringologia/LIM32 Hospital das Clinicas HCFMUSP Faculdade de Medicina Universidade de Sao Paulo Sao Paulo SP Brasil
| | - Karina Lezirovitz
- Laboratório de Otorrinolaringologia/LIM32 Hospital das Clinicas HCFMUSP Faculdade de Medicina Universidade de Sao Paulo Sao Paulo SP Brasil
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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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The diagnostic yield of whole-exome sequencing targeting a gene panel for hearing impairment in The Netherlands. Eur J Hum Genet 2016; 25:308-314. [PMID: 28000701 DOI: 10.1038/ejhg.2016.182] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Revised: 10/19/2016] [Accepted: 11/22/2016] [Indexed: 12/12/2022] Open
Abstract
Hearing impairment (HI) is genetically heterogeneous which hampers genetic counseling and molecular diagnosis. Testing of several single HI-related genes is laborious and expensive. In this study, we evaluate the diagnostic utility of whole-exome sequencing (WES) targeting a panel of HI-related genes. Two hundred index patients, mostly of Dutch origin, with presumed hereditary HI underwent WES followed by targeted analysis of an HI gene panel of 120 genes. We found causative variants underlying the HI in 67 of 200 patients (33.5%). Eight of these patients have a large homozygous deletion involving STRC, OTOA or USH2A, which could only be identified by copy number variation detection. Variants of uncertain significance were found in 10 patients (5.0%). In the remaining 123 cases, no potentially causative variants were detected (61.5%). In our patient cohort, causative variants in GJB2, USH2A, MYO15A and STRC, and in MYO6 were the leading causes for autosomal recessive and dominant HI, respectively. Segregation analysis and functional analyses of variants of uncertain significance will probably further increase the diagnostic yield of WES.
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Neuhaus C, Lang-Roth R, Zimmermann U, Heller R, Eisenberger T, Weikert M, Markus S, Knipper M, Bolz H. Extension of the clinical and molecular phenotype of DIAPH1
-associated autosomal dominant hearing loss (DFNA1
). Clin Genet 2016; 91:892-901. [DOI: 10.1111/cge.12915] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 10/27/2016] [Indexed: 12/11/2022]
Affiliation(s)
- C. Neuhaus
- Bioscientia Center for Human Genetics; Ingelheim Germany
| | - R. Lang-Roth
- Department of Otorhinolaryngology, Head and Neck Surgery; University of Cologne; Cologne Germany
| | - U. Zimmermann
- Molecular Physiology of Hearing, Hearing Research Centre Tübingen (THRC), Department of Otolaryngology; University of Tübingen; Tübingen Germany
| | - R. Heller
- Institute of Human Genetics; University Hospital of Cologne; Cologne Germany
| | - T. Eisenberger
- Bioscientia Center for Human Genetics; Ingelheim Germany
| | - M. Weikert
- Gemeinschaftspraxis für Phoniatrie; Pädaudiologie und Hals-Nasen-Ohrenheilkunde; Regensburg Germany
| | - S. Markus
- Kompetenzzentrum für Humangenetik; Gynäkologie und Laboratoriumsmedizin; Regensburg Germany
| | - M. Knipper
- Department of Otorhinolaryngology, Head and Neck Surgery; University of Cologne; Cologne Germany
| | - H.J. Bolz
- Bioscientia Center for Human Genetics; Ingelheim Germany
- Institute of Human Genetics; University Hospital of Cologne; Cologne Germany
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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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Comprehensive genetic testing in the clinical evaluation of 1119 patients with hearing loss. Hum Genet 2016; 135:441-450. [PMID: 26969326 PMCID: PMC4796320 DOI: 10.1007/s00439-016-1648-8] [Citation(s) in RCA: 355] [Impact Index Per Article: 44.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 02/14/2016] [Indexed: 12/11/2022]
Abstract
Hearing loss is the most common sensory deficit in humans, affecting 1 in 500 newborns. Due to its genetic heterogeneity, comprehensive diagnostic testing has not previously been completed in a large multiethnic cohort. To determine the aggregate contribution inheritance makes to non-syndromic hearing loss, we performed comprehensive clinical genetic testing with targeted genomic enrichment and massively parallel sequencing on 1119 sequentially accrued patients. No patient was excluded based on phenotype, inheritance or previous testing. Testing resulted in identification of the underlying genetic cause for hearing loss in 440 patients (39 %). Pathogenic variants were found in 49 genes and included missense variants (49 %), large copy number changes (18 %), small insertions and deletions (18 %), nonsense variants (8 %), splice-site alterations (6 %), and promoter variants (<1 %). The diagnostic rate varied considerably based on phenotype and was highest for patients with a positive family history of hearing loss or when the loss was congenital and symmetric. The spectrum of implicated genes showed wide ethnic variability. These findings support the more efficient utilization of medical resources through the development of evidence-based algorithms for the diagnosis of hearing loss.
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Rosenberg C, Freitas ÉL, Uehara DT, Auricchio MTBM, Costa SS, Oiticica J, Silva AG, Krepischi AC, Mingroni-Netto RC. Genomic copy number alterations in non-syndromic hearing loss. Clin Genet 2015; 89:473-477. [DOI: 10.1111/cge.12683] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2015] [Revised: 10/06/2015] [Accepted: 10/06/2015] [Indexed: 11/30/2022]
Affiliation(s)
- C. Rosenberg
- Department of Genetics and Evolutionary Biology, Institute of Bioscience; University of São Paulo; São Paulo Brazil
| | - É. L. Freitas
- Department of Genetics and Evolutionary Biology, Institute of Bioscience; University of São Paulo; São Paulo Brazil
| | - D. T. Uehara
- Department of Genetics and Evolutionary Biology, Institute of Bioscience; University of São Paulo; São Paulo Brazil
| | - M. T. B. M. Auricchio
- Department of Genetics and Evolutionary Biology, Institute of Bioscience; University of São Paulo; São Paulo Brazil
| | - S. S. Costa
- Department of Genetics and Evolutionary Biology, Institute of Bioscience; University of São Paulo; São Paulo Brazil
| | - J. Oiticica
- Department of Otorhinolaryngology, Medical School; University of São Paulo; São Paulo Brazil
| | - A. G. Silva
- Department of Genetics and Evolutionary Biology, Institute of Bioscience; University of São Paulo; São Paulo Brazil
| | - A. C. Krepischi
- Department of Genetics and Evolutionary Biology, Institute of Bioscience; University of São Paulo; São Paulo Brazil
| | - R. C. Mingroni-Netto
- Department of Genetics and Evolutionary Biology, Institute of Bioscience; University of São Paulo; São Paulo Brazil
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Gee JA, Frausto RF, Chung DWD, Tangmonkongvoragul C, Le DJ, Wang C, Han J, Aldave AJ. Identification of novel PIKFYVE gene mutations associated with Fleck corneal dystrophy. Mol Vis 2015; 21:1093-100. [PMID: 26396486 PMCID: PMC4575904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2015] [Accepted: 09/15/2015] [Indexed: 10/27/2022] Open
Abstract
PURPOSE To report the identification of a novel frameshift mutation and copy number variation (CNV) in PIKFYVE in two probands with fleck corneal dystrophy (FCD). METHODS Slit-lamp examination was performed to identify characteristic features of FCD. After genomic DNA was collected, PCR amplification and automated sequencing of all 41 exons of PIKFYVE was performed. Using genomic DNA, quantitative PCR (qPCR) was performed to detect CNVs within PIKFYVE. RESULTS In the first FCD proband, numerous panstromal punctate opacities were observed in each of the proband's corneas, consistent with the diagnosis of FCD. Screening of PIKFYVE demonstrated a novel heterozygous frameshift mutation in exon 19, c.3151dupA, which is predicted to encode for a truncated PIKFYVE protein, p.(Asp1052Argfs*18). This variant was identified in an affected sister but not in the proband's unaffected mother or brother or 200 control chromosomes. The second FCD proband presented with bilateral, discrete, punctate, grayish-white stromal opacities. Exonic screening of PIKFYVE revealed no causative variant. However, CNV analysis demonstrated the hemizygous deletion of exons 15 and 16. CONCLUSIONS We report a novel heterozygous frameshift mutation (c.3151dupA) and a CNV in PIKFYVE, representing the first CNV and the fifth frameshift mutation associated with FCD.
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Shearer AE, Smith RJH. Massively Parallel Sequencing for Genetic Diagnosis of Hearing Loss: The New Standard of Care. Otolaryngol Head Neck Surg 2015; 153:175-82. [PMID: 26084827 PMCID: PMC4743024 DOI: 10.1177/0194599815591156] [Citation(s) in RCA: 97] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Accepted: 05/22/2015] [Indexed: 01/23/2023]
Abstract
OBJECTIVE To evaluate the use of new genetic sequencing techniques for comprehensive genetic testing for hearing loss. DATA SOURCES Articles were identified from PubMed and Google Scholar databases using pertinent search terms. REVIEW METHODS Literature search identified 30 studies as candidates that met search criteria. Three studies were excluded, and 8 studies were found to be case reports. Twenty studies were included for review analysis, including 7 studies that evaluated controls and 16 studies that evaluated patients with unknown causes of hearing loss; 3 studies evaluated both controls and patients. CONCLUSIONS In the 20 studies included in the review analysis, 426 control samples and 603 patients with unknown causes of hearing loss underwent comprehensive genetic diagnosis for hearing loss using massively parallel sequencing. Control analysis showed a sensitivity and specificity >99%, sufficient for clinical use of these tests. The overall diagnostic rate was 41% (range, 10%-83%) and varied based on several factors, including inheritance and prescreening prior to comprehensive testing. There were significant differences in platforms available with regard to the number and type of genes included and whether copy number variations were examined. Based on these results, comprehensive genetic testing should form the cornerstone of a tiered approach to clinical evaluation of patients with hearing loss along with history, physical examination, and audiometry and can determine further testing that may be required, if any. IMPLICATIONS FOR PRACTICE Comprehensive genetic testing has become the new standard of care for genetic testing for patients with sensorineural hearing loss.
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Affiliation(s)
- A Eliot Shearer
- Department of Otolaryngology-Head and Neck Surgery, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Richard J H Smith
- Department of Otolaryngology-Head and Neck Surgery, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA Interdepartmental PhD Program in Genetics, University of Iowa, Iowa City, Iowa, USA Department of Molecular Physiology & Biophysics, University of Iowa College of Medicine, Iowa City, Iowa, USA
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