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Domínguez-Ruiz M, Ruiz-Palmero L, Buonfiglio PI, García-Vaquero I, Gómez-Rosas E, Goñi M, Villamar M, Morín M, Moreno-Pelayo MA, Elgoyhen AB, del Castillo FJ, Dalamón V, del Castillo I. Novel Pathogenic Variants in the Gene Encoding Stereocilin ( STRC) Causing Non-Syndromic Moderate Hearing Loss in Spanish and Argentinean Subjects. Biomedicines 2023; 11:2943. [PMID: 38001944 PMCID: PMC10668944 DOI: 10.3390/biomedicines11112943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 10/24/2023] [Accepted: 10/27/2023] [Indexed: 11/26/2023] Open
Abstract
Non-syndromic hearing impairment (NSHI) is a very heterogeneous genetic condition, involving over 130 genes. Mutations in GJB2, encoding connexin-26, are a major cause of NSHI (the DFNB1 type), but few other genes have significant epidemiological contributions. Mutations in the STRC gene result in the DFNB16 type of autosomal recessive NSHI, a common cause of moderate hearing loss. STRC is located in a tandem duplicated region that includes the STRCP1 pseudogene, and so it is prone to rearrangements causing structural variations. Firstly, we screened a cohort of 122 Spanish familial cases of non-DFNB1 NSHI with at least two affected siblings and unaffected parents, and with different degrees of hearing loss (mild to profound). Secondly, we screened a cohort of 64 Spanish sporadic non-DFNB1 cases, and a cohort of 35 Argentinean non-DFNB1 cases, all of them with moderate hearing loss. Amplification of marker D15S784, massively parallel DNA sequencing, multiplex ligation-dependent probe amplification and long-range gene-specific PCR followed by Sanger sequencing were used to search and confirm single-nucleotide variants (SNVs) and deletions involving STRC. Causative variants were found in 13 Spanish familial cases (10.7%), 5 Spanish simplex cases (7.8%) and 2 Argentinean cases (5.7%). In all, 34 deleted alleles and 6 SNVs, 5 of which are novel. All affected subjects had moderate hearing impairment. Our results further support this strong genotype-phenotype correlation and highlight the significant contribution of STRC mutations to moderate NSHI in the Spanish population.
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Affiliation(s)
- María Domínguez-Ruiz
- Servicio de Genética, Hospital Universitario Ramón y Cajal, 28034 Madrid, Spain; (M.D.-R.); (L.R.-P.); (I.G.-V.); (E.G.-R.); (M.G.); (M.V.); (M.M.); (M.A.M.-P.); (F.J.d.C.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 28034 Madrid, Spain
| | - Laura Ruiz-Palmero
- Servicio de Genética, Hospital Universitario Ramón y Cajal, 28034 Madrid, Spain; (M.D.-R.); (L.R.-P.); (I.G.-V.); (E.G.-R.); (M.G.); (M.V.); (M.M.); (M.A.M.-P.); (F.J.d.C.)
| | - Paula I. Buonfiglio
- Laboratory of Physiology and Genetics of Hearing, Instituto de Investigaciones en Ingeniería Genética y Biología Molecular “Dr. Héctor N. Torres”, Consejo Nacional de Investigaciones Científicas y Técnicas, Vuelta de Obligado 2490, Ciudad Autónoma de Buenos Aires C1428ADN, Argentina; (P.I.B.); (A.B.E.)
| | - Irene García-Vaquero
- Servicio de Genética, Hospital Universitario Ramón y Cajal, 28034 Madrid, Spain; (M.D.-R.); (L.R.-P.); (I.G.-V.); (E.G.-R.); (M.G.); (M.V.); (M.M.); (M.A.M.-P.); (F.J.d.C.)
| | - Elena Gómez-Rosas
- Servicio de Genética, Hospital Universitario Ramón y Cajal, 28034 Madrid, Spain; (M.D.-R.); (L.R.-P.); (I.G.-V.); (E.G.-R.); (M.G.); (M.V.); (M.M.); (M.A.M.-P.); (F.J.d.C.)
| | - Marina Goñi
- Servicio de Genética, Hospital Universitario Ramón y Cajal, 28034 Madrid, Spain; (M.D.-R.); (L.R.-P.); (I.G.-V.); (E.G.-R.); (M.G.); (M.V.); (M.M.); (M.A.M.-P.); (F.J.d.C.)
| | - Manuela Villamar
- Servicio de Genética, Hospital Universitario Ramón y Cajal, 28034 Madrid, Spain; (M.D.-R.); (L.R.-P.); (I.G.-V.); (E.G.-R.); (M.G.); (M.V.); (M.M.); (M.A.M.-P.); (F.J.d.C.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 28034 Madrid, Spain
| | - Matías Morín
- Servicio de Genética, Hospital Universitario Ramón y Cajal, 28034 Madrid, Spain; (M.D.-R.); (L.R.-P.); (I.G.-V.); (E.G.-R.); (M.G.); (M.V.); (M.M.); (M.A.M.-P.); (F.J.d.C.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 28034 Madrid, Spain
| | - Miguel A. Moreno-Pelayo
- Servicio de Genética, Hospital Universitario Ramón y Cajal, 28034 Madrid, Spain; (M.D.-R.); (L.R.-P.); (I.G.-V.); (E.G.-R.); (M.G.); (M.V.); (M.M.); (M.A.M.-P.); (F.J.d.C.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 28034 Madrid, Spain
| | - Ana B. Elgoyhen
- Laboratory of Physiology and Genetics of Hearing, Instituto de Investigaciones en Ingeniería Genética y Biología Molecular “Dr. Héctor N. Torres”, Consejo Nacional de Investigaciones Científicas y Técnicas, Vuelta de Obligado 2490, Ciudad Autónoma de Buenos Aires C1428ADN, Argentina; (P.I.B.); (A.B.E.)
- Instituto de Farmacología, Facultad de Medicina, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires C1121ABG, Argentina
| | - Francisco J. del Castillo
- Servicio de Genética, Hospital Universitario Ramón y Cajal, 28034 Madrid, Spain; (M.D.-R.); (L.R.-P.); (I.G.-V.); (E.G.-R.); (M.G.); (M.V.); (M.M.); (M.A.M.-P.); (F.J.d.C.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 28034 Madrid, Spain
| | - Viviana Dalamón
- Laboratory of Physiology and Genetics of Hearing, Instituto de Investigaciones en Ingeniería Genética y Biología Molecular “Dr. Héctor N. Torres”, Consejo Nacional de Investigaciones Científicas y Técnicas, Vuelta de Obligado 2490, Ciudad Autónoma de Buenos Aires C1428ADN, Argentina; (P.I.B.); (A.B.E.)
| | - Ignacio del Castillo
- Servicio de Genética, Hospital Universitario Ramón y Cajal, 28034 Madrid, Spain; (M.D.-R.); (L.R.-P.); (I.G.-V.); (E.G.-R.); (M.G.); (M.V.); (M.M.); (M.A.M.-P.); (F.J.d.C.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 28034 Madrid, Spain
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Functional consequences of Genetics variant in TMC1 and TMC2 within a United Arab Emirates family with Pre-lingual hearing loss. Saudi J Biol Sci 2023; 30:103520. [PMID: 36568409 PMCID: PMC9772550 DOI: 10.1016/j.sjbs.2022.103520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 10/30/2022] [Accepted: 11/25/2022] [Indexed: 12/03/2022] Open
Abstract
Hearing loss (HL) is the most prevalent sensory disorder whose etiology comes from environmental and/or genetic factors. Approximately 60 % of HL cases are due to mutations in genes responsible for maintaining a normal hearing function. Despite the monogenic inheritance of hereditary hearing loss (HHL), its diagnosis is challenging as both clinical and genetic heterogeneity characterizes it. Through the development of next-generation sequencing (NGS) techniques, the number of identified mutations responsible for HHL has increased exponentially during the last decade. Mutations in the TMC1 have been reported in several patients with nonsyndromic hereditary hearing loss (NSHHL), more precisely in cases with an autosomal recessive inheritance pattern. In this study, we conducted whole-exome sequencing (WES) analysis of a United Arabs Emirates (UAE) family with autosomal recessive nonsyndromic hearing loss (ARNSHL). This analysis revealed segregation of the TMC1 missense mutation c.596A > T (p.Asn199Ile) with the disease. Bioinformatics analysis supported the pathogenic effect of this mutation and predicted its impact at the proteomics level. Molecular docking analysis of TMC2WT, TMC2R123K, TMC2Q205R, and TMC2R123K + Q205R. Finally, protein docking results suggest a role for TMC2 variants in the phenotypic variability observed within the investigated family.
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Key Words
- ARNSHL, Autosomal Recessive Nonsyndromic Hearing Loss
- GATK, Genome Analysis Toolkit
- GnomAD, Genome Aggregation Database
- HHL, Hereditary Hearing Loss
- HL, Hearing Loss
- NGS, Next Generation Sequencing
- NSHHL, Nonsyndromic Hereditary Hearing Loss
- Non-syndromic Hearing Loss
- PCR, Polymerase Chain Reaction
- Phenotypic variability
- Protein docking
- TMC1
- UAE, United Arabs Emirates
- WES, Whole-Exome Sequencing
- Whole-exome sequencing
- c.596A > T mutation
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Yang JY, Wang WQ, Han MY, Huang SS, Wang GJ, Su Y, Xu JC, Fu Y, Kang DY, Yang K, Zhang X, Liu X, Gao X, Yuan YY, Dai P. Addition of an affected family member to a previously ascertained autosomal recessive nonsyndromic hearing loss pedigree and systematic phenotype-genotype analysis of splice-site variants in MYO15A. BMC Med Genomics 2022; 15:241. [PMCID: PMC9673454 DOI: 10.1186/s12920-022-01368-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 09/29/2022] [Indexed: 11/19/2022] Open
Abstract
Pathogenic variants in MYO15A are known to cause autosomal recessive nonsyndromic hearing loss (ARNSHL), DFNB3. We have previously reported on one ARNSHL family including two affected siblings and identified MYO15A c.5964+3G > A and c.8375 T > C (p.Val2792Ala) as the possible deafness-causing variants. Eight year follow up identified one new affected individual in this family, who also showed congenital, severe to profound sensorineural hearing loss. By whole exome sequencing, we identified a new splice-site variant c.5531+1G > C (maternal allele), in a compound heterozygote with previously identified missense variant c.8375 T > C (p.Val2792Ala) (paternal allele) in MYO15A as the disease-causing variants. The new affected individual underwent unilateral cochlear implantation at the age of 1 year, and 5 year follow-up showed satisfactory speech and language outcomes. Our results further indicate that MYO15A-associated hearing loss is good candidates for cochlear implantation, which is in accordance with previous report. In light of our findings and review of the literatures, 58 splice-site variants in MYO15A are correlated with a severe deafness phenotype, composed of 46 canonical splice-site variants and 12 non-canonical splice-site variants.
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Affiliation(s)
- Jin-Yuan Yang
- grid.488137.10000 0001 2267 2324College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, 28 Fuxing Road, Beijing, 100853 People’s Republic of China ,grid.419897.a0000 0004 0369 313XNational Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, People’s Republic of China ,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, People’s Republic of China
| | - Wei-Qian Wang
- grid.488137.10000 0001 2267 2324College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, 28 Fuxing Road, Beijing, 100853 People’s Republic of China ,grid.419897.a0000 0004 0369 313XNational Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, People’s Republic of China ,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, People’s Republic of China ,grid.488137.10000 0001 2267 2324Department of Otolaryngology, PLA Rocket Force Characteristic Medical Center, 16# XinWai Da Jie, Beijing, 100088 People’s Republic of China
| | - Ming-Yu Han
- grid.488137.10000 0001 2267 2324College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, 28 Fuxing Road, Beijing, 100853 People’s Republic of China ,grid.419897.a0000 0004 0369 313XNational Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, People’s Republic of China ,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, People’s Republic of China
| | - Sha-Sha Huang
- grid.488137.10000 0001 2267 2324College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, 28 Fuxing Road, Beijing, 100853 People’s Republic of China ,grid.419897.a0000 0004 0369 313XNational Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, People’s Republic of China ,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, People’s Republic of China
| | - Guo-Jian Wang
- grid.488137.10000 0001 2267 2324College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, 28 Fuxing Road, Beijing, 100853 People’s Republic of China ,grid.419897.a0000 0004 0369 313XNational Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, People’s Republic of China ,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, People’s Republic of China
| | - Yu Su
- Department of Otolaryngology, Head and Neck Surgery, Chinese PLA General Hospital Affiliated Hainan Hospital, Jianglin Road, Sanya, 572013 People’s Republic of China ,Hainan Province Clinical Research Center for Otolaryngologic and Head and Neck Diseases, Jianglin Road, Sanya, 572013 People’s Republic of China
| | - Jin-Cao Xu
- grid.488137.10000 0001 2267 2324Department of Otolaryngology, PLA Rocket Force Characteristic Medical Center, 16# XinWai Da Jie, Beijing, 100088 People’s Republic of China
| | - Ying Fu
- grid.27255.370000 0004 1761 1174Department of Otorhinolaryngology, Qilu Hospital (Qingdao), Cheeloo College of Medicine, Shandong University, 758 Hefei Road, Qingdao, 266035 Shandong People’s Republic of China
| | - Dong-Yang Kang
- grid.488137.10000 0001 2267 2324College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, 28 Fuxing Road, Beijing, 100853 People’s Republic of China ,grid.419897.a0000 0004 0369 313XNational Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, People’s Republic of China ,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, People’s Republic of China
| | - Kun Yang
- grid.488137.10000 0001 2267 2324Postgraduate Training Base of Jinzhou Medical University, The PLA Rocket Force Characteristic Medical Center, 16# XinWai Da Jie, Beijing, 100088 People’s Republic of China
| | - Xin Zhang
- grid.488137.10000 0001 2267 2324College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, 28 Fuxing Road, Beijing, 100853 People’s Republic of China ,grid.419897.a0000 0004 0369 313XNational Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, People’s Republic of China ,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, People’s Republic of China
| | - Xing Liu
- grid.488137.10000 0001 2267 2324Department of Otolaryngology, PLA Rocket Force Characteristic Medical Center, 16# XinWai Da Jie, Beijing, 100088 People’s Republic of China
| | - Xue Gao
- grid.488137.10000 0001 2267 2324College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, 28 Fuxing Road, Beijing, 100853 People’s Republic of China ,grid.419897.a0000 0004 0369 313XNational Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, People’s Republic of China ,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, People’s Republic of China ,grid.488137.10000 0001 2267 2324Department of Otolaryngology, PLA Rocket Force Characteristic Medical Center, 16# XinWai Da Jie, Beijing, 100088 People’s Republic of China
| | - Yong-Yi Yuan
- grid.488137.10000 0001 2267 2324College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, 28 Fuxing Road, Beijing, 100853 People’s Republic of China ,grid.419897.a0000 0004 0369 313XNational Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, People’s Republic of China ,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, People’s Republic of China
| | - Pu Dai
- grid.488137.10000 0001 2267 2324College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, 28 Fuxing Road, Beijing, 100853 People’s Republic of China ,grid.419897.a0000 0004 0369 313XNational Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, People’s Republic of China ,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, People’s Republic of China
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Kraatari-Tiri M, Haanpää MK, Willberg T, Pohjola P, Keski-Filppula R, Kuismin O, Moilanen JS, Häkli S, Rahikkala E. Clinical and Genetic Characteristics of Finnish Patients with Autosomal Recessive and Dominant Non-Syndromic Hearing Loss Due to Pathogenic TMC1 Variants. J Clin Med 2022; 11:jcm11071837. [PMID: 35407445 PMCID: PMC9000065 DOI: 10.3390/jcm11071837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 03/20/2022] [Accepted: 03/24/2022] [Indexed: 11/16/2022] Open
Abstract
Sensorineural hearing loss (SNHL) is one of the most common sensory deficits worldwide, and genetic factors contribute to at least 50−60% of the congenital hearing loss cases. The transmembrane channel-like protein 1 (TMC1) gene has been linked to autosomal recessive (DFNB7/11) and autosomal dominant (DFNA36) non-syndromic hearing loss, and it is a relatively common genetic cause of SNHL. Here, we report eight Finnish families with 11 affected family members with either recessively inherited homozygous or compound heterozygous TMC1 variants associated with congenital moderate-to-profound hearing loss, or a dominantly inherited heterozygous TMC1 variant associated with postlingual progressive hearing loss. We show that the TMC1 c.1534C>T, p.(Arg512*) variant is likely a founder variant that is enriched in the Finnish population. We describe a novel recessive disease-causing TMC1 c.968A>G, p.(Tyr323Cys) variant. We also show that individuals in this cohort who were diagnosed early and received timely hearing rehabilitation with hearing aids and cochlear implants (CI) have reached good speech perception in noise. Comparison of the genetic data with the outcome of CI rehabilitation increases our understanding of the extent to which underlying pathogenic gene variants explain the differences in CI rehabilitation outcomes.
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Affiliation(s)
- Minna Kraatari-Tiri
- Department of Clinical Genetics, Oulu University Hospital, 90029 Oulu, Finland
- PEDEGO Research Unit, Medical Research Center Oulu, Oulu University Hospital, and University of Oulu, 90014 Oulu, Finland
| | - Maria K Haanpää
- Department of Clinical Genetics, Turku University Hospital, 20521 Turku, Finland
- Department of Genomics, Turku University Hospital, 20521 Turku, Finland
| | - Tytti Willberg
- Department of Otorhinolaryngology, Turku University Hospital, 20521 Turku, Finland
| | - Pia Pohjola
- Department of Genomics, Turku University Hospital, 20521 Turku, Finland
| | - Riikka Keski-Filppula
- Department of Clinical Genetics, Oulu University Hospital, 90029 Oulu, Finland
- PEDEGO Research Unit, Medical Research Center Oulu, Oulu University Hospital, and University of Oulu, 90014 Oulu, Finland
| | - Outi Kuismin
- Department of Clinical Genetics, Oulu University Hospital, 90029 Oulu, Finland
- PEDEGO Research Unit, Medical Research Center Oulu, Oulu University Hospital, and University of Oulu, 90014 Oulu, Finland
| | - Jukka S Moilanen
- Department of Clinical Genetics, Oulu University Hospital, 90029 Oulu, Finland
- PEDEGO Research Unit, Medical Research Center Oulu, Oulu University Hospital, and University of Oulu, 90014 Oulu, Finland
| | - Sanna Häkli
- PEDEGO Research Unit, Medical Research Center Oulu, Oulu University Hospital, and University of Oulu, 90014 Oulu, Finland
- Department of Otorhinolaryngology, Oulu University Hospital, 90029 Oulu, Finland
| | - Elisa Rahikkala
- Department of Clinical Genetics, Oulu University Hospital, 90029 Oulu, Finland
- PEDEGO Research Unit, Medical Research Center Oulu, Oulu University Hospital, and University of Oulu, 90014 Oulu, Finland
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Genetic etiology of non-syndromic hearing loss in Europe. Hum Genet 2022; 141:683-696. [PMID: 35044523 DOI: 10.1007/s00439-021-02425-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Accepted: 12/20/2021] [Indexed: 12/17/2022]
Abstract
Hearing impairment not etiologically associated with clinical signs in other organs (non-syndromic) is genetically heterogeneous, so that over 120 genes are currently known to be involved. The frequency of mutations in each gene and the most frequent mutations vary throughout populations. Here we review the genetic etiology of non-syndromic hearing impairment (NSHI) in Europe. Over the years, epidemiological data were scarce because of the large number of involved genes, whose screening was not cost-effective until implementation of massively parallel DNA sequencing. In Europe, the most common form of autosomal recessive NSHI is DFNB1, which accounts for 11-57% of the cases. Mutations in STRC account for 16% of the recessive cases, and only a few more (MYO15A, MYO7A, LOXHD1, USH2A, TMPRSS3, CDH23, TMC1, OTOF, OTOA, SLC26A4, ADGRV1 and TECTA) have contributions higher than 2%. As regards autosomal-dominant NSHI, DFNA22 (MYO6) and DFNA8/12 (TECTA) represent the most common forms, accounting for 21% and 18% of elucidated cases, respectively. The contribution of ACTG1 and WFS1 drops to 9% in both cases, followed by POU4F3 (6.5%), MYO7A (5%), MYH14 and COL11A2 (4% each). Four additional genes contribute 2.5% each one (MITF, KCNQ4, EYA4, SOX10) and the remaining are residually represented. X-linked hearing loss and maternally-inherited NSHI have minor contributions in most countries. Further knowledge on the genetic epidemiology of NSHI in Europe needs a standardization of the experimental approaches and a stratification of the results according to clinical features, familial history and patterns of inheritance, to facilitate comparison between studies.
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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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7
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Dong X, Cong S. The emerging roles of long non-coding RNAs in polyglutamine diseases. J Cell Mol Med 2021; 25:8095-8102. [PMID: 34318578 PMCID: PMC8419158 DOI: 10.1111/jcmm.16808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 07/02/2021] [Accepted: 07/08/2021] [Indexed: 11/30/2022] Open
Abstract
Polyglutamine (polyQ) diseases are characterized by trinucleotide repeat amplifications within genes, thus resulting in the formation of polyQ peptides, selective neuronal degeneration and possibly death due to neurodegenerative diseases (NDDs). Long non-coding RNAs (lncRNAs), which exceed 200 nucleotides in length, have been shown to play important roles in several pathological processes of NDDs, including polyQ diseases. Some lncRNAs have been consistently identified to be specific to polyQ diseases, and circulating lncRNAs are among the most promising novel candidates in the search for non-invasive biomarkers for the diagnosis and prognosis of polyQ diseases. In this review, we describe the emerging roles of lncRNAs in polyQ diseases and provide an overview of the general biology of lncRNAs, their implications in pathophysiology and their potential roles as future biomarkers and applications for therapy.
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Affiliation(s)
- Xiaoyu Dong
- Department of Neurology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Shuyan Cong
- Department of Neurology, Shengjing Hospital of China Medical University, Shenyang, China
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Hirsch Y, Tangshewinsirikul C, Booth KT, Azaiez H, Yefet D, Quint A, Weiden T, Brownstein Z, Macarov M, Davidov B, Pappas J, Rabin R, Kenna MA, Oza AM, Lafferty K, Amr SS, Rehm HL, Kolbe DL, Frees K, Nishimura C, Luo M, Farra C, Morton CC, Scher SY, Ekstein J, Avraham KB, Smith RJH, Shen J. A synonymous variant in MYO15A enriched in the Ashkenazi Jewish population causes autosomal recessive hearing loss due to abnormal splicing. Eur J Hum Genet 2021; 29:988-997. [PMID: 33398081 PMCID: PMC8187401 DOI: 10.1038/s41431-020-00790-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 11/04/2020] [Accepted: 11/25/2020] [Indexed: 11/09/2022] Open
Abstract
Nonsyndromic hearing loss is genetically heterogeneous. Despite comprehensive genetic testing, many cases remain unsolved because the clinical significance of identified variants is uncertain or because biallelic pathogenic variants are not identified for presumed autosomal recessive cases. Common synonymous variants are often disregarded. Determining the pathogenicity of synonymous variants may improve genetic diagnosis. We report a synonymous variant c.9861 C > T/p.(Gly3287=) in MYO15A in homozygosity or compound heterozygosity with another pathogenic or likely pathogenic MYO15A variant in 10 unrelated families with nonsyndromic sensorineural hearing loss. Biallelic variants in MYO15A were identified in 21 affected and were absent in 22 unaffected siblings. A mini-gene assay confirms that the synonymous variant leads to abnormal splicing. The variant is enriched in the Ashkenazi Jewish population. Individuals carrying biallelic variants involving c.9861 C > T often exhibit progressive post-lingual hearing loss distinct from the congenital profound deafness typically associated with biallelic loss-of-function MYO15A variants. This study establishes the pathogenicity of the c.9861 C > T variant in MYO15A and expands the phenotypic spectrum of MYO15A-related hearing loss. Our work also highlights the importance of multicenter collaboration and data sharing to establish the pathogenicity of a relatively common synonymous variant for improved diagnosis and management of hearing loss.
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Affiliation(s)
- Yoel Hirsch
- Dor Yeshorim, Committee for Prevention of Jewish Genetic Diseases, Brooklyn, NY, 11211, USA
| | - Chayada Tangshewinsirikul
- Division of Maternal Fetal Medicine, Department of Obstetrics and Gynecology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, 10400, Thailand
- Department of Obstetrics and Gynecology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Kevin T Booth
- Molecular Otolaryngology and Renal Research Laboratories, The University of Iowa, Iowa City, IA, 52242, USA
- Department of Neurobiology, Harvard Medical School, Boston, MA, 02215, USA
| | - Hela Azaiez
- Molecular Otolaryngology and Renal Research Laboratories, The University of Iowa, Iowa City, IA, 52242, USA
| | - Devorah Yefet
- Dor Yeshorim, Committee for Prevention of Jewish Genetic Diseases, Jerusalem, 91506, Israel
| | - Adina Quint
- Dor Yeshorim, Committee for Prevention of Jewish Genetic Diseases, Jerusalem, 91506, Israel
| | - Tzvi Weiden
- Dor Yeshorim, Committee for Prevention of Jewish Genetic Diseases, Jerusalem, 91506, Israel
| | - Zippora Brownstein
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Michal Macarov
- Department of Genetics and Metabolic Diseases, Hadassah Medical Center, Jerusalem, 91120, Israel
| | - Bella Davidov
- Department of Medical Genetics, Rabin Medical Center, Petah Tikva, 49100, Israel
| | - John Pappas
- Department of Pediatrics, New York University School of Medicine, New York, NY, 10016, USA
| | - Rachel Rabin
- Department of Pediatrics, New York University School of Medicine, New York, NY, 10016, USA
| | - Margaret A Kenna
- Department of Otolaryngology and Communication Enhancement, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Harvard Medical School Center for Hereditary Deafness, Boston, MA, 02115, USA
| | - Andrea M Oza
- Department of Otolaryngology and Communication Enhancement, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, Cambridge, MA, 02139, USA
| | - Katherine Lafferty
- Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, Cambridge, MA, 02139, USA
- Maine Medical Center, Scarborough, ME, 04074, USA
| | - Sami S Amr
- Harvard Medical School Center for Hereditary Deafness, Boston, MA, 02115, USA
- Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, Cambridge, MA, 02139, USA
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Heidi L Rehm
- Harvard Medical School Center for Hereditary Deafness, Boston, MA, 02115, USA
- Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, Cambridge, MA, 02139, USA
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Diana L Kolbe
- Molecular Otolaryngology and Renal Research Laboratories, The University of Iowa, Iowa City, IA, 52242, USA
| | - Kathy Frees
- Molecular Otolaryngology and Renal Research Laboratories, The University of Iowa, Iowa City, IA, 52242, USA
| | - Carla Nishimura
- Molecular Otolaryngology and Renal Research Laboratories, The University of Iowa, Iowa City, IA, 52242, USA
| | - Minjie Luo
- The Children's Hospital of Philadelphia, The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Chantal Farra
- Medical Genetics Unit, American University of Beirut Medical Center, AUBMC, 1107 2020, Beirut, Lebanon
| | - Cynthia C Morton
- Department of Obstetrics and Gynecology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Harvard Medical School Center for Hereditary Deafness, Boston, MA, 02115, USA
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Manchester Centre for Audiology and Deafness, School of Health Sciences, The University of Manchester, Manchester, M13 9PL, UK
| | - Sholem Y Scher
- Dor Yeshorim, Committee for Prevention of Jewish Genetic Diseases, Brooklyn, NY, 11211, USA
| | - Josef Ekstein
- Dor Yeshorim, Committee for Prevention of Jewish Genetic Diseases, Brooklyn, NY, 11211, USA
| | - Karen B Avraham
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, 6997801, Israel.
| | - Richard J H Smith
- Molecular Otolaryngology and Renal Research Laboratories, The University of Iowa, Iowa City, IA, 52242, USA.
| | - Jun Shen
- Harvard Medical School Center for Hereditary Deafness, Boston, MA, 02115, USA.
- Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, Cambridge, MA, 02139, USA.
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA.
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Gallo S, Trevisi P, Rigon C, Caserta E, Seif Ali D, Bovo R, Martini A, Cassina M. Auditory Outcome after Cochlear Implantation in Children with DFNB7/11 Caused by Pathogenic Variants in TMC1 Gene. Audiol Neurootol 2020; 26:157-163. [PMID: 33352559 DOI: 10.1159/000510156] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 07/14/2020] [Indexed: 11/19/2022] Open
Abstract
INTRODUCTION Non-syndromic hereditary hearing loss is characterized by extreme genetic heterogeneity. So far, more than 100 pathogenic or likely pathogenic variants in TMC1 gene have been reported in patients with autosomal recessive hearing loss (HL) DFNB7/11. The prevailing auditory phenotype of individuals with DFNB7/11 is congenital, profound, bilateral HL, but the functional outcome after cochlear implantation (CI) described in the literature is variable. The objective of this work is to evaluate the auditory outcome after CI in pediatric patients with DFNB7/11, born to non-consanguineous parents. METHODS A retrospective analysis of genetic and audiological data of DFNB7/11 patients followed up in a single Italian otolaryngology clinic was performed. Cases with biallelic pathogenic variants in TMC1 were selected from the cohort of children with non-syndromic hearing loss who had undergone CI and had been molecularly characterized by multigene panel testing. All patients underwent extensive audiological assessment, and the auditory outcome after CI was evaluated. RESULTS DFNB7/11 was diagnosed in a total of 3 patients from 2 non-consanguineous families; a novel disease-causing variant in TMC1 was detected [c.962G>A p.(Trp321*)]. All the affected children showed the typical DFNB7/11 phenotype characterized by prelingual, severe-to-profound HL. The patients showed an excellent functional outcome after CI; speech perception, nonverbal cognition, and speech performance were comparable to those of patients with DFNB1 deafness. DISCUSSION/CONCLUSION Our results do not support the variable auditory outcome reported in the literature, which may be affected by several social and environmental factors and by the genetic background.
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Affiliation(s)
- Samanta Gallo
- Otolaryngology Unit, Department of Neurosciences, University of Padova, Padova, Italy
| | - Patrizia Trevisi
- Otolaryngology Unit, Department of Neurosciences, University of Padova, Padova, Italy
| | - Chiara Rigon
- Clinical Genetics Unit, Department of Women's and Children's Health, University of Padova, Padova, Italy
| | - Ezio Caserta
- Otolaryngology Unit, Department of Neurosciences, University of Padova, Padova, Italy
| | - Dario Seif Ali
- Clinical Genetics Unit, Department of Women's and Children's Health, University of Padova, Padova, Italy
| | - Roberto Bovo
- Otolaryngology Unit, Department of Neurosciences, University of Padova, Padova, Italy
| | - Alessandro Martini
- Otolaryngology Unit, Department of Neurosciences, University of Padova, Padova, Italy
| | - Matteo Cassina
- Clinical Genetics Unit, Department of Women's and Children's Health, University of Padova, Padova, Italy,
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Adadey SM, Quaye O, Amedofu GK, Awandare GA, Wonkam A. Screening for GJB2-R143W-Associated Hearing Impairment: Implications for Health Policy and Practice in Ghana. Public Health Genomics 2020; 23:184-189. [PMID: 33302283 DOI: 10.1159/000512121] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 09/23/2020] [Indexed: 11/19/2022] Open
Abstract
Genetic factors significantly contribute to the burden of hearing impairment (HI) in Ghana as there is a high carrier frequency (1.5%) of the connexin 26 gene founder variant GJB2-R143W in the healthy Ghanaian population. GJB2-R143W mutation accounts for nearly 26% of causes in families segregating congenital non-syndromic HI. With HI associated with high genetic fitness, this indicates that Ghana will likely sustain an increase in the number of individuals living with inheritable HI. There is a universal newborn hearing screening (UNHS) program in Ghana. However, this program does not include genetic testing. Adding genetic testing of GJB2-R143W mutation for the population, prenatal and neonatal stages may lead to guiding genetic counseling for individual and couples, early detection of HI for at-risk infants, and improvement of medical management, including speech therapy and audiologic intervention, as well as provision of the needed social service to enhance parenting and education for children with HI. Based on published research on the genetics of HI in Ghana, we recommend that the UNHS program should include genetic screening for the GJB2-R143W gene variant for newborns who did not pass the initial UNHS tests. This will require an upgrade and resourcing of public health infrastructures to implement the rapid and cost-effective GJB2-R143W testing, followed by appropriate genetic and anticipatory guidance for medical care.
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Affiliation(s)
- Samuel M Adadey
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana.,Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Osbourne Quaye
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana
| | - Geoffrey K Amedofu
- Department of Eye Ear Nose & Throat, School of Medical Sciences, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Gordon A Awandare
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana
| | - Ambroise Wonkam
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa,
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11
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Xiang YB, Xu CY, Xu YZ, Li HZ, Zhou LL, Xu XQ, Chen ZH, Tang SH. Next-generation sequencing identifies rare pathogenic and novel candidate variants in a cohort of Chinese patients with syndromic or nonsyndromic hearing loss. Mol Genet Genomic Med 2020; 8:e1539. [PMID: 33095980 PMCID: PMC7767562 DOI: 10.1002/mgg3.1539] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 09/27/2020] [Accepted: 10/02/2020] [Indexed: 11/15/2022] Open
Abstract
Background Hearing loss (HL) is a common sensory disorder in humans characterized by extreme clinical and genetic heterogeneity. In recent years, next‐generation sequencing (NGS) technologies have proven to be highly effective and powerful tools for population genetic studies of HL. Here, we analyzed clinical and molecular data from 21 Chinese deaf families who did not have hotspot mutations in the common deafness genes GJB2, SLC26A4, GJB3, and MT‐RNR1. Method Targeted next‐generation sequencing (TGS) of 127 known deafness genes was performed in probands of 12 families, while whole‐exome sequencing (WES) or trio‐WES was used for the remaining nine families. Results Potential pathogenic mutations in a total of 12 deafness genes were identified in 13 probands; the mutations were observed in GJB2, CDH23, EDNRB, MYO15A, OTOA, OTOF, TBC1D24, SALL1, TMC1, TWNK, USH1C, and USH1G, with eight of the identified mutations being novel. Further, a copy number variant (CNV) was detected in one proband with heterozygous deletion of chromosome 4p16.3‐4p15.32. Thus, the total diagnostic rate using NGS in our deafness patients reached 66.67% (14/21). Conclusions These results expand the mutation spectrum of deafness‐causing genes and provide support for the use of NGS detection technologies for routine molecular diagnosis in Chinese deaf populations.
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Affiliation(s)
- Yan-Bao Xiang
- Key Laboratory of Birth Defects, Department of Genetics, Wenzhou Central Hospital, Wenzhou, China
| | - Chen-Yang Xu
- Key Laboratory of Birth Defects, Department of Genetics, Wenzhou Central Hospital, Wenzhou, China
| | - Yun-Zhi Xu
- Key Laboratory of Birth Defects, Department of Genetics, Wenzhou Central Hospital, Wenzhou, China
| | - Huan-Zheng Li
- Key Laboratory of Birth Defects, Department of Genetics, Wenzhou Central Hospital, Wenzhou, China
| | - Li-Li Zhou
- Key Laboratory of Birth Defects, Department of Genetics, Wenzhou Central Hospital, Wenzhou, China
| | - Xue-Qin Xu
- Key Laboratory of Birth Defects, Department of Genetics, Wenzhou Central Hospital, Wenzhou, China
| | - Zi-Hui Chen
- Key laboratory of Medical Genetic, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, China
| | - Shao-Hua Tang
- Key Laboratory of Birth Defects, Department of Genetics, Wenzhou Central Hospital, Wenzhou, China.,Key laboratory of Medical Genetic, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, China
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12
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Xu P, Jiang F, Zhang H, Yin R, Cen L, Zhang W. Calcium Carbonate/Gelatin Methacrylate Microspheres for 3D Cell Culture in Bone Tissue Engineering. Tissue Eng Part C Methods 2020; 26:418-432. [DOI: 10.1089/ten.tec.2020.0064] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Affiliation(s)
- Pengwei Xu
- School of Mechanical and Power Engineering, East China University of Science and Technology, Shanghai, China
| | - Fuliang Jiang
- School of Mechanical and Power Engineering, East China University of Science and Technology, Shanghai, China
| | - Hongbo Zhang
- School of Mechanical and Power Engineering, East China University of Science and Technology, Shanghai, China
| | - Ruixue Yin
- School of Mechanical and Power Engineering, East China University of Science and Technology, Shanghai, China
| | - Lian Cen
- School of Chemical Engineering, East China University of Science and Technology, Shanghai, China
| | - Wenjun Zhang
- School of Mechatronics and Automation, Shanghai University, Shanghai, China
- Division of Biomedical Engineering, University of Saskatchewan, Saskatoon, Canada
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Whole exome sequencing identifies novel compound heterozygous pathogenic variants in the MYO15A gene leading to autosomal recessive non-syndromic hearing loss. Mol Biol Rep 2020; 47:5355-5364. [DOI: 10.1007/s11033-020-05618-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 06/22/2020] [Indexed: 12/22/2022]
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14
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M. Adadey S, Tingang Wonkam E, Twumasi Aboagye E, Quansah D, Asante-Poku A, Quaye O, K. Amedofu G, A. Awandare G, Wonkam A. Enhancing Genetic Medicine: Rapid and Cost-Effective Molecular Diagnosis for a GJB2 Founder Mutation for Hearing Impairment in Ghana. Genes (Basel) 2020; 11:genes11020132. [PMID: 32012697 PMCID: PMC7074138 DOI: 10.3390/genes11020132] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 01/21/2020] [Accepted: 01/22/2020] [Indexed: 12/17/2022] Open
Abstract
In Ghana, gap-junction protein β 2 (GJB2) variants account for about 25.9% of familial hearing impairment (HI) cases. The GJB2-p.Arg143Trp (NM_004004.6:c.427C>T/OMIM: 121011.0009/rs80338948) variant remains the most frequent variant associated with congenital HI in Ghana, but has not yet been investigated in clinical practice. We therefore sought to design a rapid and cost-effective test to detect this variant. We sampled 20 hearing-impaired and 10 normal hearing family members from 8 families segregating autosomal recessive non syndromic HI. In addition, a total of 111 unrelated isolated individuals with HI were selected, as well as 50 normal hearing control participants. A restriction fragment length polymorphism (RFLP) test was designed, using the restriction enzyme NciI optimized and validated with Sanger sequencing, for rapid genotyping of the common GJB2-p.Arg143Trp variant. All hearing-impaired participants from 7/8 families were homozygous positive for the GJB2-p.Arg143Trp mutation using the NciI-RFLP test, which was confirmed with Sanger sequencing. The investigation of 111 individuals with isolated non-syndromic HI that were previously Sanger sequenced found that the sensitivity of the GJB2-p.Arg143Trp NciI-RFLP testing was 100%. All the 50 control subjects with normal hearing were found to be negative for the variant. Although the test is extremely valuable, it is not 100% specific because it cannot differentiate between other mutations at the recognition site of the restriction enzyme. The GJB2-p.Arg143Trp NciI-RFLP-based diagnostic test had a high sensitivity for genotyping the most common GJB2 pathogenic and founder variant (p.Arg143Trp) within the Ghanaian populations. We recommend the adoption and implementation of this test for hearing impairment genetic clinical investigations to complement the newborn hearing screening program in Ghana. The present study is a practical case scenario of enhancing genetic medicine in Africa.
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Affiliation(s)
- Samuel M. Adadey
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra P. O. Box LG 54, Ghana; (S.M.A.); (E.T.A.); (D.Q.); (A.A.-P.); (O.Q.); (G.A.A.)
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa;
| | - Edmond Tingang Wonkam
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa;
| | - Elvis Twumasi Aboagye
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra P. O. Box LG 54, Ghana; (S.M.A.); (E.T.A.); (D.Q.); (A.A.-P.); (O.Q.); (G.A.A.)
| | - Darius Quansah
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra P. O. Box LG 54, Ghana; (S.M.A.); (E.T.A.); (D.Q.); (A.A.-P.); (O.Q.); (G.A.A.)
| | - Adwoa Asante-Poku
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra P. O. Box LG 54, Ghana; (S.M.A.); (E.T.A.); (D.Q.); (A.A.-P.); (O.Q.); (G.A.A.)
- Bacteriology Department, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra P.O. Box LG 581, Ghana
| | - Osbourne Quaye
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra P. O. Box LG 54, Ghana; (S.M.A.); (E.T.A.); (D.Q.); (A.A.-P.); (O.Q.); (G.A.A.)
| | - Geoffrey K. Amedofu
- Department of Eye Ear Nose & Throat, School of Medical Sciences, Kwame Nkrumah University of Science and Technology, Kumasi AK-039-5028, Ghana;
| | - Gordon A. Awandare
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra P. O. Box LG 54, Ghana; (S.M.A.); (E.T.A.); (D.Q.); (A.A.-P.); (O.Q.); (G.A.A.)
| | - Ambroise Wonkam
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa;
- Correspondence: ; Tel.: +27-21-4066-307
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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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16
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Yue X, Sheng Y, Kang L, Xiao R. Distinct functions of TMC channels: a comparative overview. Cell Mol Life Sci 2019; 76:4221-4232. [PMID: 31584127 PMCID: PMC11105308 DOI: 10.1007/s00018-019-03214-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 06/25/2019] [Accepted: 06/28/2019] [Indexed: 12/18/2022]
Abstract
In the past two decades, transmembrane channel-like (TMC) proteins have attracted a significant amount of research interest, because mutations of Tmc1 lead to hereditary deafness. As evolutionarily conserved membrane proteins, TMC proteins are widely involved in diverse sensorimotor functions of many species, such as hearing, chemosensation, egg laying, and food texture detection. Interestingly, recent structural and physiological studies suggest that TMC channels may share a similar membrane topology with the Ca2+-activated Cl- channel TMEM16 and the mechanically activated OSCA1.2/TMEM63 channel. Namely, these channels form dimers and each subunit consists of ten transmembrane segments. Despite this important structural insight, a key question remains: what is the gating mechanism of TMC channels? The major technical hurdle to answer this question is that the reconstitution of TMC proteins as functional ion channels has been challenging in mammalian heterologous systems. Since TMC channels are conserved across taxa, genetic studies of TMC channels in model organisms such as C. elegans, Drosophila, and zebrafish may provide us critical information on the physiological function and regulation of TMCs. Here, we present a comparative overview on the diverse functions of TMC channels in different species.
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Affiliation(s)
- Xiaomin Yue
- Department of Neurosurgery of the First Affiliated Hospital, Institute of Neuroscience, NHC and CAMS Key Laboratory of Medical Neurobiology, Zhejiang University School of Medicine, Hangzhou, China
| | - Yi Sheng
- Department of Aging and Geriatric Research, Institute on Aging, University of Florida, Gainesville, FL, USA
| | - Lijun Kang
- Department of Neurosurgery of the First Affiliated Hospital, Institute of Neuroscience, NHC and CAMS Key Laboratory of Medical Neurobiology, Zhejiang University School of Medicine, Hangzhou, China.
| | - Rui Xiao
- Department of Aging and Geriatric Research, Institute on Aging, University of Florida, Gainesville, FL, USA.
- Department of Pharmacology and Therapeutics, College of Medicine, University of Florida, Gainesville, FL, USA.
- Center for Smell and Taste, University of Florida, Gainesville, FL, USA.
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17
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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.
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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.
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18
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Zhang J, Guan J, Wang H, Yin L, Wang D, Zhao L, Zhou H, Wang Q. Genotype-phenotype correlation analysis of MYO15A variants in autosomal recessive non-syndromic hearing loss. BMC MEDICAL GENETICS 2019; 20:60. [PMID: 30953472 PMCID: PMC6451310 DOI: 10.1186/s12881-019-0790-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Accepted: 03/20/2019] [Indexed: 12/13/2022]
Abstract
Background MYO15A variants are responsible for human non-syndromic autosomal recessive deafness (DFNB3). The majority of MYO15A variants are associated with a congenital severe-to-profound hearing loss phenotype, except for MYO15A variants in exon 2, which cause a milder auditory phenotype, suggesting a genotype-phenotype correlation of MYO15A. However, MYO15A variants not in exon 2 related to a milder phenotype have also been reported, indicating that the genotype-phenotype correlation of MYO15A is complicated. This study aimed to provide more cases of MYO15A variation with diverse phenotypes to analyse this complex correlation. Methods Fifteen Chinese autosomal recessive non-syndromic hearing loss (ARNSHL) individuals with MYO15A variants (8 males and 7 females) from 14 unrelated families, identified by targeted gene capture of 127 known candidate deafness genes, were recruited. Additionally, we conducted a review of the literature to further analyses all reported MYO15A genotype-phenotype relationships worldwide. Results We identified 16 novel variants and 12 reported pathogenic MYO15A variants in 15 patients, two of which presented with a milder phenotype. Interestingly, one of these cases carried two reported pathogenic variants in exon 2, while the other carried two novel variants not in exon 2. Based on our literature review, MYO15A genotype-phenotype correlation analysis showed that almost all domains were reported to be correlated with a milder phenotype. However, variants in the N-terminal domain were more likely to cause a milder phenotype. Using next-generation sequencing (NGS), we also found that the number of known MYO15A variants with milder phenotypes in Southeast Asia has increased in recent years. Conclusion Our work extended the MYO15A variant spectrum, enriched our knowledge of auditory phenotypes, and tried to explore the genotype-phenotype correlation in different populations in order to investigate the cause of the complex MYO15A genotype-phenotype correlation. Electronic supplementary material The online version of this article (10.1186/s12881-019-0790-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jing Zhang
- Chinese PLA Institute of Otolaryngology, Chinese PLA General Hospital, Medical School of Chinese PLA, 28 Fuxing Road, Beijing, 100853, China.,Department of Otolaryngology of Tianjin Medical University General Hospital, Tianjin, 300052, China
| | - Jing Guan
- Chinese PLA Institute of Otolaryngology, Chinese PLA General Hospital, Medical School of Chinese PLA, 28 Fuxing Road, Beijing, 100853, China.
| | - Hongyang Wang
- Chinese PLA Institute of Otolaryngology, Chinese PLA General Hospital, Medical School of Chinese PLA, 28 Fuxing Road, Beijing, 100853, China
| | | | - Dayong Wang
- Chinese PLA Institute of Otolaryngology, Chinese PLA General Hospital, Medical School of Chinese PLA, 28 Fuxing Road, Beijing, 100853, China
| | - Lidong Zhao
- Chinese PLA Institute of Otolaryngology, Chinese PLA General Hospital, Medical School of Chinese PLA, 28 Fuxing Road, Beijing, 100853, China
| | - Huifang Zhou
- Department of Otolaryngology of Tianjin Medical University General Hospital, Tianjin, 300052, China
| | - Qiuju Wang
- Chinese PLA Institute of Otolaryngology, Chinese PLA General Hospital, Medical School of Chinese PLA, 28 Fuxing Road, Beijing, 100853, China.
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19
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Morgan A, Lenarduzzi S, Cappellani S, Pecile V, Morgutti M, Orzan E, Ghiselli S, Ambrosetti U, Brumat M, Gajendrarao P, La Bianca M, Faletra F, Grosso E, Sirchia F, Sensi A, Graziano C, Seri M, Gasparini P, Girotto G. Genomic Studies in a Large Cohort of Hearing Impaired Italian Patients Revealed Several New Alleles, a Rare Case of Uniparental Disomy (UPD) and the Importance to Search for Copy Number Variations. Front Genet 2018; 9:681. [PMID: 30622556 PMCID: PMC6309105 DOI: 10.3389/fgene.2018.00681] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 12/07/2018] [Indexed: 11/13/2022] Open
Abstract
Hereditary hearing loss (HHL) is a common disorder characterized by a huge genetic heterogeneity. The definition of a correct molecular diagnosis is essential for proper genetic counseling, recurrence risk estimation, and therapeutic options. From 20 to 40% of patients carry mutations in GJB2 gene, thus, in more than half of cases it is necessary to look for causative variants in the other genes so far identified (~100). In this light, the use of next-generation sequencing technologies has proved to be the best solution for mutational screening, even though it is not always conclusive. Here we describe a combined approach, based on targeted re-sequencing (TRS) of 96 HHL genes followed by high-density SNP arrays, aimed at the identification of the molecular causes of non-syndromic HHL (NSHL). This strategy has been applied to study 103 Italian unrelated cases, negative for mutations in GJB2, and led to the characterization of 31% of them (i.e., 37% of familial and 26.3% of sporadic cases). In particular, TRS revealed TECTA and ACTG1 genes as major players in the Italian population. Furthermore, two de novo missense variants in ACTG1 have been identified and investigated through protein modeling and molecular dynamics simulations, confirming their likely pathogenic effect. Among the selected patients analyzed by SNP arrays (negative to TRS, or with a single variant in a recessive gene) a molecular diagnosis was reached in ~36% of cases, highlighting the importance to look for large insertions/deletions. Moreover, copy number variants analysis led to the identification of the first case of uniparental disomy involving LOXHD1 gene. Overall, taking into account the contribution of GJB2, plus the results from TRS and SNP arrays, it was possible to reach a molecular diagnosis in ~51% of NSHL cases. These data proved the usefulness of a combined approach for the analysis of NSHL and for the definition of the epidemiological picture of HHL in the Italian population.
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Affiliation(s)
- Anna Morgan
- Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy
| | | | | | - Vanna Pecile
- IRCCS Materno Infantile Burlo Garofolo, Trieste, Italy
| | | | - Eva Orzan
- IRCCS Materno Infantile Burlo Garofolo, Trieste, Italy
| | - Sara Ghiselli
- IRCCS Materno Infantile Burlo Garofolo, Trieste, Italy
| | - Umberto Ambrosetti
- Audiologia, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, University of Milan, Milan, Italy
| | - Marco Brumat
- Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy
| | | | | | | | - Enrico Grosso
- Medical Genetics Unit, Azienda Ospedaliero-Universitaria Città della Salute e della Scienza di Torino, Turin, Italy
| | - Fabio Sirchia
- IRCCS Materno Infantile Burlo Garofolo, Trieste, Italy
| | - Alberto Sensi
- Medical Genetics Unit, Department of Clinical Pathology, Azienda Unità Sanitaria Locale (AUSL) della Romagna, Cesena, Italy
| | - Claudio Graziano
- Unit of Medical Genetics, S. Orsola-Malpighi Hospital, Bologna, Italy
| | - Marco Seri
- Unit of Medical Genetics, S. Orsola-Malpighi Hospital, Bologna, Italy
| | - Paolo Gasparini
- Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy.,IRCCS Materno Infantile Burlo Garofolo, Trieste, Italy
| | - Giorgia Girotto
- Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy.,IRCCS Materno Infantile Burlo Garofolo, Trieste, Italy
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20
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Wang H, Wu K, Guan J, Yang J, Xie L, Xiong F, Lan L, Wang D, Wang Q. Identification of four TMC1 variations in different Chinese families with hereditary hearing loss. Mol Genet Genomic Med 2018; 6:504-513. [PMID: 29654653 PMCID: PMC6081220 DOI: 10.1002/mgg3.394] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 03/07/2018] [Accepted: 03/09/2018] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Variants in TMC1 (transmembrane channel-like 1) can cause both autosomal dominant and recessive hearing loss in human population. Mice with Tmc1 variants have been shown to be ideal animal models for gene therapy. In this article, we report four TMC1 variants in four different Chinese families and the follow-up auditory phenotype of a previously reported family. METHODS Four families with TMC1 variants, as well as a previously described family with TMC1 variant orthologous to the Beethoven mouse, were recruited in this study. A comprehensive auditory evaluation was performed on all ascertained family members. High-throughput sequencing was conducted using genomic DNA from the probands and other family members to identify probable deafness genes. RESULTS We identified four TMC1 (NM_138691.2) variations, including two pathogenic variants, c.1714G>A, and c.1253T>A, one likely pathogenic variant, c.[797T>C];[797T>C], and one single nucleotide polymorphism (SNP), c.2276G>A. Among these variants, c.[797T>C];[797T>C] is a novel likely pathogenic variant, and c.1714G>A and c.1253T>A are known pathogenic variants at the DFNB7/11 (DFNA36) locus. Phenotype-genotype correlation analysis of TMC1 variants showed that the TMC1 dominant variation-related phenotype was late-onset, progressive, high frequency to all frequency sensorineural hearing loss, while the TMC1 recessive variant was related to congenital all frequency sensorineural hearing impairment. CONCLUSIONS Two pathogenic, one likely pathogenic variants and one SNP of TMC1 were identified in four Chinese families with hereditary hearing loss, indicating that TMC1 may be a more frequent cause of hearing loss than expected. TMC1 variants related to hearing loss result in specific phenotypes. The TMC1 c.1253T>A (p.M418K) variation, homologous to the Tmc1 c. 1235 T> A (p.M412K) variant in Beethoven mice, was the second report of this variant in human patients with hearing loss, suggesting the possibility to translational gene therapy from Beethoven mice to human patients.
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Affiliation(s)
- Hongyang Wang
- Institute of OtolaryngologyChinese PLA General HospitalMedical School of Chinese PLABeijingChina
| | - Kaiwen Wu
- Institute of OtolaryngologyChinese PLA General HospitalMedical School of Chinese PLABeijingChina
| | - Jing Guan
- Institute of OtolaryngologyChinese PLA General HospitalMedical School of Chinese PLABeijingChina
| | - Ju Yang
- Institute of OtolaryngologyChinese PLA General HospitalMedical School of Chinese PLABeijingChina
| | - Linyi Xie
- Institute of OtolaryngologyChinese PLA General HospitalMedical School of Chinese PLABeijingChina
| | - Fen Xiong
- Institute of OtolaryngologyChinese PLA General HospitalMedical School of Chinese PLABeijingChina
| | - Lan Lan
- Institute of OtolaryngologyChinese PLA General HospitalMedical School of Chinese PLABeijingChina
| | - Dayong Wang
- Institute of OtolaryngologyChinese PLA General HospitalMedical School of Chinese PLABeijingChina
| | - Qiuju Wang
- Institute of OtolaryngologyChinese PLA General HospitalMedical School of Chinese PLABeijingChina
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21
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Li X, Zhang D, Zhang H, Guan Z, Song Y, Liu R, Zhu Z, Yang C. Microwell Array Method for Rapid Generation of Uniform Agarose Droplets and Beads for Single Molecule Analysis. Anal Chem 2018; 90:2570-2577. [PMID: 29350029 DOI: 10.1021/acs.analchem.7b04040] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Compartmentalization of aqueous samples in uniform emulsion droplets has proven to be a useful tool for many chemical, biological, and biomedical applications. Herein, we introduce an array-based emulsification method for rapid and easy generation of monodisperse agarose-in-oil droplets in a PDMS microwell array. The microwells are filled with agarose solution, and subsequent addition of hot oil results in immediate formation of agarose droplets due to the surface-tension of the liquid solution. Because droplet size is determined solely by the array unit dimensions, uniform droplets with preselectable diameters ranging from 20 to 100 μm can be produced with relative standard deviations less than 3.5%. The array-based droplet generation method was used to perform digital PCR for absolute DNA quantitation. The array-based droplet isolation and sol-gel switching property of agarose enable formation of stable beads by chilling the droplet array at -20 °C, thus, maintaining the monoclonality of each droplet and facilitating the selective retrieval of desired droplets. The monoclonality of droplets was demonstrated by DNA sequencing and FACS analysis, suggesting the robustness and flexibility of the approach for single molecule amplification and analysis. We believe our approach will lead to new possibilities for a great variety of applications, such as single-cell gene expression studies, aptamer selection, and oligonucleotide analysis.
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Affiliation(s)
- Xingrui Li
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University , Xiamen 361005, People's Republic of China
| | - Dongfeng Zhang
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University , Xiamen 361005, People's Republic of China
| | - Huimin Zhang
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University , Xiamen 361005, People's Republic of China
| | - Zhichao Guan
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University , Xiamen 361005, People's Republic of China
| | - Yanling Song
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University , Xiamen 361005, People's Republic of China.,The MOE Key Laboratory of Analysis and Detection Technology for Food Safety, State Key Laboratory of Photocatalysis on Energy and Environment, College of Biological Science and Engineering, Fuzhou University , Fuzhou 350116, People's Republic of China
| | - Ruochen Liu
- Department of Chemistry and Chemical Biology, Rutgers University , Piscataway, New Jersey United States
| | - Zhi Zhu
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University , Xiamen 361005, People's Republic of China
| | - Chaoyong Yang
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University , Xiamen 361005, People's Republic of China
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22
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Targeted Next-Generation Sequencing of a Deafness Gene Panel (MiamiOtoGenes) Analysis in Families Unsuitable for Linkage Analysis. BIOMED RESEARCH INTERNATIONAL 2018; 2018:3103986. [PMID: 29568747 PMCID: PMC5820677 DOI: 10.1155/2018/3103986] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 09/28/2017] [Accepted: 11/01/2017] [Indexed: 11/18/2022]
Abstract
Hearing loss (HL) is a common sensory disorder in humans with high genetic heterogeneity. To date, over 145 loci have been identified to cause nonsyndromic deafness. Furthermore, there are countless families unsuitable for the conventional linkage analysis. In the present study, we used a custom capture panel (MiamiOtoGenes) to target sequence 180 deafness-associated genes in 5 GJB2 negative deaf probands with autosomal recessive nonsyndromic HL from Iran. In these 5 families, we detected one reported and six novel mutations in 5 different deafness autosomal recessive (DFNB) genes (TRIOBP, LHFPL5, CDH23, PCDH15, and MYO7A). The custom capture panel in our study provided an efficient and comprehensive diagnosis for known deafness genes in small families.
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23
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Ellis–van Creveld syndrome and profound deafness resulted by sequence variants in the EVC / EVC2 and TMC1 genes. J Genet 2017; 96:1005-1014. [DOI: 10.1007/s12041-017-0868-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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24
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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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25
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Sommen M, Wuyts W, Van Camp G. Molecular diagnostics for hereditary hearing loss in children. Expert Rev Mol Diagn 2017; 17:751-760. [PMID: 28593790 DOI: 10.1080/14737159.2017.1340834] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
INTRODUCTION Hearing loss (HL) is the most common birth defect in industrialized countries with far-reaching social, psychological and cognitive implications. It is an extremely heterogeneous disease, complicating molecular testing. The introduction of next-generation sequencing (NGS) has resulted in great progress in diagnostics allowing to study all known HL genes in a single assay. The diagnostic yield is currently still limited, but has the potential to increase substantially. Areas covered: In this review the utility of NGS and the problems for comprehensive molecular testing for HL are evaluated and discussed. Expert commentary: Different publications have proven the appropriateness of NGS for molecular testing of heterogeneous diseases such as HL. However, several problems still exist, such as pseudogenic background of some genes and problematic copy number variant analysis on targeted NGS data. Another main challenge for the future will be the establishment of population specific mutation-spectra to achieve accurate personalized comprehensive molecular testing for HL.
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Affiliation(s)
- Manou Sommen
- a Center of Medical Genetics , University of Antwerp & Antwerp University Hospital , Antwerp , Belgium
| | - Wim Wuyts
- a Center of Medical Genetics , University of Antwerp & Antwerp University Hospital , Antwerp , Belgium
| | - Guy Van Camp
- a Center of Medical Genetics , University of Antwerp & Antwerp University Hospital , Antwerp , Belgium
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26
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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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27
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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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28
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Pediatric otolaryngology, molecular diagnosis of hereditary hearing loss: next-generation sequencing approach. Curr Opin Otolaryngol Head Neck Surg 2016; 23:480-4. [PMID: 26488533 DOI: 10.1097/moo.0000000000000208] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
PURPOSE OF REVIEW Sensorineural hearing loss (SNHL) is the most common sensory birth defect. The purpose of this article is to review the advances in next-generation sequencing (NGS) and molecular diagnosis of hereditary hearing loss. RECENT FINDINGS Early diagnosis and detection of SNHL is critical for the development of appropriate speech and language, as neuroplasticity peaks in the first few years of life. There has been increased accuracy of NGS genetic testing, which has helped created a paradigm shift in the diagnosis of hearing loss. The diagnostic yield of genetic testing now approaches that of radiographic imaging; however, there remains a difference in cost and time delay. With the introduction of comprehensive genetic panels, 23-129 genes can be sequenced from the same blood sample. SUMMARY Diagnostic genetic testing of SNHL in the past has been confined to a few genes through Sanger sequencing. The advent of NGS allows for development of comprehensive genetic panels, which test for up to 129 genes while improving the accuracy and efficiency of testing. This type of testing may become more common as the costs decrease and more genes are discovered.
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29
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Rehman AU, Bird JE, Faridi R, Shahzad M, Shah S, Lee K, Khan SN, Imtiaz A, Ahmed ZM, Riazuddin S, Santos-Cortez RLP, Ahmad W, Leal SM, Riazuddin S, Friedman TB. Mutational Spectrum of MYO15A and the Molecular Mechanisms of DFNB3 Human Deafness. Hum Mutat 2016; 37:991-1003. [PMID: 27375115 DOI: 10.1002/humu.23042] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 06/26/2016] [Indexed: 12/17/2022]
Abstract
Deafness in humans is a common neurosensory disorder and is genetically heterogeneous. Across diverse ethnic groups, mutations of MYO15A at the DFNB3 locus appear to be the third or fourth most common cause of autosomal-recessive, nonsyndromic deafness. In 49 of the 67 exons of MYO15A, there are currently 192 recessive mutations identified, including 14 novel mutations reported here. These mutations are distributed uniformly across MYO15A with one enigmatic exception; the alternatively spliced giant exon 2, encoding 1,233 residues, has 17 truncating mutations but no convincing deafness-causing missense mutations. MYO15A encodes three distinct isoform classes, one of which is 395 kDa (3,530 residues), the largest member of the myosin superfamily of molecular motors. Studies of Myo15 mouse models that recapitulate DFNB3 revealed two different pathogenic mechanisms of hearing loss. In the inner ear, myosin 15 is necessary both for the development and the long-term maintenance of stereocilia, mechanosensory sound-transducing organelles that extend from the apical surface of hair cells. The goal of this Mutation Update is to provide a comprehensive review of mutations and functions of MYO15A.
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Affiliation(s)
- Atteeq U Rehman
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, Maryland, 20892
| | - Jonathan E Bird
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, Maryland, 20892
| | - Rabia Faridi
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, Maryland, 20892.,Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, 54550, Pakistan
| | - Mohsin Shahzad
- Department of Otorhinolaryngology Head & Neck Surgery, School of Medicine, University of Maryland, Baltimore, Maryland, 21201
| | - Sujay Shah
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, Maryland, 20892
| | - Kwanghyuk Lee
- Center for Statistical Genetics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030
| | - Shaheen N Khan
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, 54550, Pakistan
| | - Ayesha Imtiaz
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, Maryland, 20892
| | - Zubair M Ahmed
- Department of Otorhinolaryngology Head & Neck Surgery, School of Medicine, University of Maryland, Baltimore, Maryland, 21201
| | - Saima Riazuddin
- Department of Otorhinolaryngology Head & Neck Surgery, School of Medicine, University of Maryland, Baltimore, Maryland, 21201
| | - Regie Lyn P Santos-Cortez
- Center for Statistical Genetics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030
| | - Wasim Ahmad
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Suzanne M Leal
- Center for Statistical Genetics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030
| | - Sheikh Riazuddin
- Allama Iqbal Medical Research Centre, Jinnah Hospital Complex, University of Health Sciences, Lahore, 54550, Pakistan
| | - Thomas B Friedman
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, Maryland, 20892.
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Advances in Molecular Genetics and the Molecular Biology of Deafness. BIOMED RESEARCH INTERNATIONAL 2016; 2016:5629093. [PMID: 27525271 PMCID: PMC4971315 DOI: 10.1155/2016/5629093] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 06/13/2016] [Indexed: 11/17/2022]
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Yan D, Tekin D, Bademci G, Foster J, Cengiz FB, Kannan-Sundhari A, Guo S, Mittal R, Zou B, Grati M, Kabahuma RI, Kameswaran M, Lasisi TJ, Adedeji WA, Lasisi AO, Menendez I, Herrera M, Carranza C, Maroofian R, Crosby AH, Bensaid M, Masmoudi S, Behnam M, Mojarrad M, Feng Y, Duman D, Mawla AM, Nord AS, Blanton SH, Liu XZ, Tekin M. Spectrum of DNA variants for non-syndromic deafness in a large cohort from multiple continents. Hum Genet 2016; 135:953-61. [PMID: 27344577 PMCID: PMC5497215 DOI: 10.1007/s00439-016-1697-z] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 06/11/2016] [Indexed: 12/21/2022]
Abstract
Hearing loss is the most common sensory deficit in humans with causative variants in over 140 genes. With few exceptions, however, the population-specific distribution for many of the identified variants/genes is unclear. Until recently, the extensive genetic and clinical heterogeneity of deafness precluded comprehensive genetic analysis. Here, using a custom capture panel (MiamiOtoGenes), we undertook a targeted sequencing of 180 genes in a multi-ethnic cohort of 342 GJB2 mutation-negative deaf probands from South Africa, Nigeria, Tunisia, Turkey, Iran, India, Guatemala, and the United States (South Florida). We detected causative DNA variants in 25 % of multiplex and 7 % of simplex families. The detection rate varied between 0 and 57 % based on ethnicity, with Guatemala and Iran at the lower and higher end of the spectrum, respectively. We detected causative variants within 27 genes without predominant recurring pathogenic variants. The most commonly implicated genes include MYO15A, SLC26A4, USH2A, MYO7A, MYO6, and TRIOBP. Overall, our study highlights the importance of family history and generation of databases for multiple ethnically discrete populations to improve our ability to detect and accurately interpret genetic variants for pathogenicity.
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Affiliation(s)
- Denise Yan
- Department of Otolaryngology (D-48), University of Miami Miller School of Medicine, 1666 NW 12th Avenue, Miami, FL, 33136, USA
| | - Demet Tekin
- Department of Otolaryngology (D-48), University of Miami Miller School of Medicine, 1666 NW 12th Avenue, Miami, FL, 33136, USA
| | - Guney Bademci
- Department of Human Genetics, John P. Hussman Institute for Human Genomics, University of Miami, 1501 NW 10th Avenue, BRB-610 (M-860), Miami, FL, 33136, USA
| | - Joseph Foster
- Department of Otolaryngology (D-48), University of Miami Miller School of Medicine, 1666 NW 12th Avenue, Miami, FL, 33136, USA.,Department of Human Genetics, John P. Hussman Institute for Human Genomics, University of Miami, 1501 NW 10th Avenue, BRB-610 (M-860), Miami, FL, 33136, USA
| | - F Basak Cengiz
- Department of Human Genetics, John P. Hussman Institute for Human Genomics, University of Miami, 1501 NW 10th Avenue, BRB-610 (M-860), Miami, FL, 33136, USA
| | - Abhiraami Kannan-Sundhari
- Department of Otolaryngology (D-48), University of Miami Miller School of Medicine, 1666 NW 12th Avenue, Miami, FL, 33136, USA
| | - Shengru Guo
- Department of Human Genetics, John P. Hussman Institute for Human Genomics, University of Miami, 1501 NW 10th Avenue, BRB-610 (M-860), Miami, FL, 33136, USA
| | - Rahul Mittal
- Department of Otolaryngology (D-48), University of Miami Miller School of Medicine, 1666 NW 12th Avenue, Miami, FL, 33136, USA
| | - Bing Zou
- Department of Otolaryngology (D-48), University of Miami Miller School of Medicine, 1666 NW 12th Avenue, Miami, FL, 33136, USA
| | - Mhamed Grati
- Department of Otolaryngology (D-48), University of Miami Miller School of Medicine, 1666 NW 12th Avenue, Miami, FL, 33136, USA
| | - Rosemary I Kabahuma
- Department of Otorhinolaryngology, Steve Biko Academic Hospital, University of Pretoria, Cnr Malan and Steve Biko Road, Gezina, Pretoria, South Africa
| | - Mohan Kameswaran
- Madras ENT Research Foundation (MERF), No-1, 1st Cross Street, Off. II Main Road, Raja Annamalai Puram, Chennai, 600028, Tamil Nadu, India
| | - Taye J Lasisi
- Department of Otorhinolaryngology, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Waheed A Adedeji
- Department of Otorhinolaryngology, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Akeem O Lasisi
- Department of Otorhinolaryngology, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Ibis Menendez
- Department of Human Genetics, John P. Hussman Institute for Human Genomics, University of Miami, 1501 NW 10th Avenue, BRB-610 (M-860), Miami, FL, 33136, USA
| | - Marianna Herrera
- Institute for Research on Genetic and Metabolic Diseases, INVEGEM, Guatemala City, Guatemala
| | - Claudia Carranza
- Institute for Research on Genetic and Metabolic Diseases, INVEGEM, Guatemala City, Guatemala
| | - Reza Maroofian
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, RILD Wellcome Wolfson Centre, Exeter, UK
| | - Andrew H Crosby
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, RILD Wellcome Wolfson Centre, Exeter, UK
| | - Mariem Bensaid
- Laboratoire Procédés de Criblage Moléculaire et Cellulaire, Centre de Biotechnologie de Sfax, Université de Sfax, Sfax, Tunisia
| | - Saber Masmoudi
- Laboratoire Procédés de Criblage Moléculaire et Cellulaire, Centre de Biotechnologie de Sfax, Université de Sfax, Sfax, Tunisia
| | | | - Majid Mojarrad
- Department of Medical Genetics, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Yong Feng
- Department of Otolaryngology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Duygu Duman
- Division of Genetics, Department of Pediatrics, Ankara University School of Medicine, Ankara, Turkey
| | - Alex M Mawla
- Department of Neurobiology, Physiology, and Behavior, Center for Neuroscience, UC Davis, Davis, CA, 95616, USA.,Department of Psychiatry and Behavioral Sciences, Center for Neuroscience, UC Davis, Davis, CA, 95616, USA
| | - Alex S Nord
- Department of Neurobiology, Physiology, and Behavior, Center for Neuroscience, UC Davis, Davis, CA, 95616, USA.,Department of Psychiatry and Behavioral Sciences, Center for Neuroscience, UC Davis, Davis, CA, 95616, USA
| | - Susan H Blanton
- Department of Otolaryngology (D-48), University of Miami Miller School of Medicine, 1666 NW 12th Avenue, Miami, FL, 33136, USA.,Department of Human Genetics, John P. Hussman Institute for Human Genomics, University of Miami, 1501 NW 10th Avenue, BRB-610 (M-860), Miami, FL, 33136, USA.,Dr. John T. Macdonald Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Xue Z Liu
- Department of Otolaryngology (D-48), University of Miami Miller School of Medicine, 1666 NW 12th Avenue, Miami, FL, 33136, USA. .,Department of Human Genetics, John P. Hussman Institute for Human Genomics, University of Miami, 1501 NW 10th Avenue, BRB-610 (M-860), Miami, FL, 33136, USA. .,Department of Otolaryngology, Xiangya Hospital, Central South University, Changsha, Hunan, China.
| | - Mustafa Tekin
- Department of Otolaryngology (D-48), University of Miami Miller School of Medicine, 1666 NW 12th Avenue, Miami, FL, 33136, USA. .,Department of Human Genetics, John P. Hussman Institute for Human Genomics, University of Miami, 1501 NW 10th Avenue, BRB-610 (M-860), Miami, FL, 33136, USA. .,Dr. John T. Macdonald Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, 33136, USA.
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Sommen M, Schrauwen I, Vandeweyer G, Boeckx N, Corneveaux JJ, van den Ende J, Boudewyns A, De Leenheer E, Janssens S, Claes K, Verstreken M, Strenzke N, Predöhl F, Wuyts W, Mortier G, Bitner-Glindzicz M, Moser T, Coucke P, Huentelman MJ, Van Camp G. DNA Diagnostics of Hereditary Hearing Loss: A Targeted Resequencing Approach Combined with a Mutation Classification System. Hum Mutat 2016; 37:812-9. [PMID: 27068579 DOI: 10.1002/humu.22999] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 03/29/2016] [Indexed: 12/12/2022]
Abstract
Although there are nearly 100 different causative genes identified for nonsyndromic hearing loss (NSHL), Sanger sequencing-based DNA diagnostics usually only analyses three, namely, GJB2, SLC26A4, and OTOF. As this is seen as inadequate, there is a need for high-throughput diagnostic methods to detect disease-causing variations, including single-nucleotide variations (SNVs), insertions/deletions (Indels), and copy-number variations (CNVs). In this study, a targeted resequencing panel for hearing loss was developed including 79 genes for NSHL and selected forms of syndromic hearing loss. One-hundred thirty one presumed autosomal-recessive NSHL (arNSHL) patients of Western-European ethnicity were analyzed for SNVs, Indels, and CNVs. In addition, we established a straightforward variant classification system to deal with the large number of variants encountered. We estimate that combining prescreening of GJB2 with our panel leads to a diagnosis in 25%-30% of patients. Our data show that after GJB2, the most commonly mutated genes in a Western-European population are TMC1, MYO15A, and MYO7A (3.1%). CNV analysis resulted in the identification of causative variants in two patients in OTOA and STRC. One of the major challenges for diagnostic gene panels is assigning pathogenicity for variants. A collaborative database collecting all identified variants from multiple centers could be a valuable resource for hearing loss diagnostics.
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Affiliation(s)
- Manou Sommen
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - Isabelle Schrauwen
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium.,Neurogenomics Division, Translational Genomics Research Institute, Phoenix, Arizona
| | - Geert Vandeweyer
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - Nele Boeckx
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - Jason J Corneveaux
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, Arizona
| | - Jenneke van den Ende
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium.,Antwerp University Hospital, Antwerp, Belgium
| | - An Boudewyns
- Department of Otorhinolaryngology, Head & Neck Surgery, Antwerp University Hospital, Antwerp, Belgium
| | - Els De Leenheer
- Center of Medical Genetics, Ghent University, Ghent, Belgium
| | - Sandra Janssens
- Center of Medical Genetics, Ghent University, Ghent, Belgium
| | - Kathleen Claes
- Center of Medical Genetics, Ghent University, Ghent, Belgium
| | - Margriet Verstreken
- University Department Otolaryngology, St. Augustinus Hospital, Antwerp, Belgium
| | - Nicola Strenzke
- Inner Ear Lab, Department of Otolaryngology, University Medical Center Göttingen, Göttingen, Germany
| | - Friederike Predöhl
- Inner Ear Lab, Department of Otolaryngology, University Medical Center Göttingen, Göttingen, Germany
| | - Wim Wuyts
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium.,Antwerp University Hospital, Antwerp, Belgium
| | - Geert Mortier
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium.,Antwerp University Hospital, Antwerp, Belgium
| | - Maria Bitner-Glindzicz
- Clinical and Molecular Genetics Unit, UCL Institute of Child Health and Great Ormond Street Hospital NHS Trust, London, UK
| | - Tobias Moser
- Inner Ear Lab, Department of Otolaryngology, University Medical Center Göttingen, Göttingen, Germany.,Institute for Auditory Neuroscience and InnerEarLab, University Medical Center Göttingen, Göttingen, Germany
| | - Paul Coucke
- Center of Medical Genetics, Ghent University, Ghent, Belgium
| | - Matthew J Huentelman
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, Arizona
| | - Guy Van Camp
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
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Imtiaz A, Maqsood A, Rehman AU, Morell RJ, Holt JR, Friedman TB, Naz S. Recessive mutations of TMC1 associated with moderate to severe hearing loss. Neurogenetics 2016; 17:115-123. [PMID: 26879195 PMCID: PMC4795972 DOI: 10.1007/s10048-016-0477-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 02/09/2016] [Indexed: 12/12/2022]
Abstract
TMC1 encodes a protein required for the normal function of mechanically activated channels that enable sensory transduction in auditory and vestibular hair cells. TMC1 protein is localized at the tips of the hair cell stereocilia, the site of conventional mechanotransduction. In many populations, loss-of-function recessive mutations of TMC1 are associated with profound deafness across all frequencies tested. In six families reported here, variable moderate-to-severe or moderate-to-profound hearing loss co-segregated with STR (short tandem repeats) markers at the TMC1 locus DFNB7/11. Massively parallel and Sanger sequencing of genomic DNA revealed each family co-segregating hearing loss with a homozygous TMC1 mutation: two reported mutations (p.R34X and p.R389Q) and three novel mutations (p.S596R, p.N199I, and c.1404 + 1G > T). TMC1 cDNA sequence from affected subjects homozygous for the donor splice site transversion c.1404 + 1G > T revealed skipping of exon 16, deleting 60 amino acids from the TMC1 protein. Since the mutations in our study cause less than profound hearing loss, we speculate that there is hypo-functional TMC1 mechanotransduction channel activity and that other even less damaging variants of TMC1 may be associated with more common mild-to-severe sensorineural hearing loss.
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Affiliation(s)
- Ayesha Imtiaz
- School of Biological Sciences, University of the Punjab, Quaid-i-Azam Campus, Lahore 54590, Pakistan
- National Institute on Deafness and Other Communication Disorders, National Institutes of Health, USA 20892
| | - Azra Maqsood
- School of Biological Sciences, University of the Punjab, Quaid-i-Azam Campus, Lahore 54590, Pakistan
| | - Atteeq U. Rehman
- National Institute on Deafness and Other Communication Disorders, National Institutes of Health, USA 20892
| | - Robert J. Morell
- National Institute on Deafness and Other Communication Disorders, National Institutes of Health, USA 20892
| | - Jeffrey R. Holt
- Department of Otolaryngology, F. M. Kirby Neurobiology Center, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Thomas B. Friedman
- National Institute on Deafness and Other Communication Disorders, National Institutes of Health, USA 20892
| | - Sadaf Naz
- School of Biological Sciences, University of the Punjab, Quaid-i-Azam Campus, Lahore 54590, Pakistan
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Association of SNPs in EGR3 and ARC with Schizophrenia Supports a Biological Pathway for Schizophrenia Risk. PLoS One 2015; 10:e0135076. [PMID: 26474411 PMCID: PMC4608790 DOI: 10.1371/journal.pone.0135076] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Accepted: 07/17/2015] [Indexed: 02/07/2023] Open
Abstract
We have previously hypothesized a biological pathway of activity-dependent synaptic plasticity proteins that addresses the dual genetic and environmental contributions to schizophrenia. Accordingly, variations in the immediate early gene EGR3, and its target ARC, should influence schizophrenia susceptibility. We used a pooled Next-Generation Sequencing approach to identify variants across these genes in U.S. populations of European (EU) and African (AA) descent. Three EGR3 and one ARC SNP were selected and genotyped for validation, and three SNPs were tested for association in a replication cohort. In the EU group of 386 schizophrenia cases and 150 controls EGR3 SNP rs1877670 and ARC SNP rs35900184 showed significant associations (p = 0.0078 and p = 0.0275, respectively). In the AA group of 185 cases and 50 controls, only the ARC SNP revealed significant association (p = 0.0448). The ARC SNP did not show association in the Han Chinese (CH) population. However, combining the EU, AA, and CH groups revealed a highly significant association of ARC SNP rs35900184 (p = 2.353 x 10−7; OR [95% CI] = 1.54 [1.310–1.820]). These findings support previously reported associations between EGR3 and schizophrenia. Moreover, this is the first report associating an ARC SNP with schizophrenia and supports recent large-scale GWAS findings implicating the ARC complex in schizophrenia risk. These results support the need for further investigation of the proposed pathway of environmentally responsive, synaptic plasticity-related, schizophrenia genes.
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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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Nishio SY, Usami SI. Deafness gene variations in a 1120 nonsyndromic hearing loss cohort: molecular epidemiology and deafness mutation spectrum of patients in Japan. Ann Otol Rhinol Laryngol 2015; 124 Suppl 1:49S-60S. [PMID: 25788563 DOI: 10.1177/0003489415575059] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
OBJECTIVES To elucidate the molecular epidemiology of hearing loss in a large number of Japanese patients analyzed using massively parallel DNA sequencing (MPS) of target genes. METHODS We performed MPS of target genes using the Ion PGM system with the Ion AmpliSeq and HiSeq 2000 systems using SureSelect in 1389 samples (1120 nonsyndromic hearing loss cases and 269 normal hearing controls). We filtered the variants identified using allele frequencies in a large number of controls and 12 predication program scores. RESULTS We identified 8376 kinds of variants in the 1389 samples, and 409 835 total variants were detected. After filtering the variants, we selected 2631 kinds of candidate variants. The number of GJB2 mutations was exceptionally high among these variants, followed by those in CDH23, SLC26A4, MYO15A, COL11A2, MYO7A, and OTOF. CONCLUSIONS We performed a large number of MPS analyses and clarified the genetic background of Japanese patients with hearing loss. This data set will be a powerful tool to discover rare causative gene mutations in highly heterogeneous monogenic diseases and reveal the genetic epidemiology of deafness.
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Affiliation(s)
- Shin-Ya Nishio
- Department of Otorhinolaryngology, Shinshu University School of Medicine, Matsumoto, Japan Department of Hearing Implant Sciences, Shinshu University School of Medicine, Matsumoto, Japan
| | - Shin-Ichi Usami
- Department of Otorhinolaryngology, Shinshu University School of Medicine, Matsumoto, Japan Department of Hearing Implant Sciences, Shinshu University School of Medicine, Matsumoto, Japan
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Lu Y, Zhou X, Jin Z, Cheng J, Shen W, Ji F, Liu L, Zhang X, Zhang M, Cao Y, Han D, Choy K, Yuan H. Resolving the genetic heterogeneity of prelingual hearing loss within one family: Performance comparison and application of two targeted next generation sequencing approaches. J Hum Genet 2014; 59:599-607. [PMID: 25231367 PMCID: PMC4521291 DOI: 10.1038/jhg.2014.78] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Revised: 08/11/2014] [Accepted: 08/12/2014] [Indexed: 12/30/2022]
Abstract
Here, we report an unconventional Chinese pedigree consisting of three branches all segregating prelingual hearing loss (HL) with unclear inheritance pattern. After identifying the cause of one branch as maternally inherited aminoglycoside-induced HL, targeted next generation sequencing (NGS) was applied to identify the genetic causes for the other two branches. One affected subject from each branch was subject to targeted NGS whose genomic DNA was enriched either by whole-exome capture (Agilent SureSelect All Exon 50 Mb) or by candidate genes capture (Agilent SureSelect custom kit). By NGS analysis, we identified that patients from Branch A were compound heterozygous for p.E1006K and p.D1663V in the CDH23 (DFNB12) gene; and patients from Branch B were homozygous for IVS7-2A>G in the SLC26A4 (DFNB4) gene. Both CDH23 mutations altered conserved calcium binding sites of the extracellular cadherin domains. The co-occurrence of three different genetic causes in this family was exceedingly rare but fully compatible with the mutation spectrum of HL. Our study has also raised several technical and analytical issues when applying the NGS technique to genetic testing.
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Affiliation(s)
- Yu Lu
- Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, China
| | - Xueya Zhou
- 1] MOE Key Laboratory of Bioinformatics, Bioinformatics Division and Center for Synthetic and Systems Biology, TNLIST/Department of Automation, Tsinghua University, Beijing, China [2] Department of Psychiatry, The University of Hong Kong, Hong Kong, SAR, China
| | - Zhanguo Jin
- Department of Otolaryngology, Chinese PLA Air Force General Hospital, Beijing, China
| | - Jing Cheng
- Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, China
| | - Weidong Shen
- Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, China
| | - Fei Ji
- Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, China
| | - Liyang Liu
- MOE Key Laboratory of Bioinformatics, Bioinformatics Division and Center for Synthetic and Systems Biology, TNLIST/Department of Automation, Tsinghua University, Beijing, China
| | - Xuegong Zhang
- MOE Key Laboratory of Bioinformatics, Bioinformatics Division and Center for Synthetic and Systems Biology, TNLIST/Department of Automation, Tsinghua University, Beijing, China
| | - Michael Zhang
- 1] MOE Key Laboratory of Bioinformatics, Bioinformatics Division and Center for Synthetic and Systems Biology, TNLIST/Department of Automation, Tsinghua University, Beijing, China [2] MCB, Center for Systems Biology, The University of Texas at Dallas, Richardson, TX, USA
| | - Ye Cao
- 1] Department of Obstetrics and Gynaecology, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong, SAR, China [2] CUHK-University of Utrecht Joint Centre for Language, Mind and Brain, The Chinese University of Hong Kong, Shatin, Hong Kong, SAR, China
| | - Dongyi Han
- Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, China
| | - KwongWai Choy
- 1] Department of Obstetrics and Gynaecology, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong, SAR, China [2] CUHK-University of Utrecht Joint Centre for Language, Mind and Brain, The Chinese University of Hong Kong, Shatin, Hong Kong, SAR, China
| | - Huijun Yuan
- Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, China
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Gillespie RL, O'Sullivan J, Ashworth J, Bhaskar S, Williams S, Biswas S, Kehdi E, Ramsden SC, Clayton-Smith J, Black GC, Lloyd IC. Personalized diagnosis and management of congenital cataract by next-generation sequencing. Ophthalmology 2014; 121:2124-37.e1-2. [PMID: 25148791 DOI: 10.1016/j.ophtha.2014.06.006] [Citation(s) in RCA: 122] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Revised: 05/02/2014] [Accepted: 06/04/2014] [Indexed: 12/21/2022] Open
Abstract
PURPOSE To assess the utility of integrating genomic data from next-generation sequencing and phenotypic data to enhance the diagnosis of bilateral congenital cataract (CC). DESIGN Evaluation of diagnostic technology. PARTICIPANTS Thirty-six individuals diagnosed with nonsyndromic or syndromic bilateral congenital cataract were selected for investigation through a single ophthalmic genetics clinic. METHODS Participants underwent a detailed ophthalmic examination, accompanied by dysmorphology assessment where appropriate. Lenticular, ocular, and systemic phenotypes were recorded. Mutations were detected using a custom-designed target enrichment that permitted parallel analysis of 115 genes associated with CC by high-throughput, next-generation DNA sequencing (NGS). Thirty-six patients and a known positive control were tested. Suspected pathogenic variants were confirmed by bidirectional Sanger sequencing in relevant probands and other affected family members. MAIN OUTCOME MEASURES Molecular genetic results and details of clinical phenotypes were identified. RESULTS Next-generation DNA sequencing technologies are able to determine the precise genetic cause of CC in 75% of individuals, and 85% patients with nonsyndromic CC were found to have likely pathogenic mutations, all of which occurred in highly conserved domains known to be vital for normal protein function. The pick-up rate in patients with syndromic CC also was high, with 63% having potential disease-causing mutations. CONCLUSIONS This analysis demonstrates the clinical utility of this test, providing examples where it altered clinical management, directed care pathways, and enabled more accurate genetic counseling. This comprehensive screen will extend access to genetic testing and lead to improved diagnostic and management outcomes through a stratified medicine approach. Establishing more robust genotype-phenotype correlations will advance knowledge of cataract-forming mechanisms.
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Affiliation(s)
- Rachel L Gillespie
- Manchester Centre for Genomic Medicine, Institute of Human Development, Faculty of Medical and Human Sciences, University of Manchester, Manchester Academic Health Science Centre, Saint Mary's Hospital, Manchester, United Kingdom
| | - James O'Sullivan
- Manchester Centre for Genomic Medicine, Institute of Human Development, Faculty of Medical and Human Sciences, University of Manchester, Manchester Academic Health Science Centre, Saint Mary's Hospital, Manchester, United Kingdom
| | - Jane Ashworth
- Manchester Centre for Genomic Medicine, Institute of Human Development, Faculty of Medical and Human Sciences, University of Manchester, Manchester Academic Health Science Centre, Saint Mary's Hospital, Manchester, United Kingdom; Manchester Royal Eye Hospital, Manchester Academic Health Science Centre, The University of Manchester, Central Manchester Foundation Trust, Manchester, United Kingdom
| | - Sanjeev Bhaskar
- Manchester Centre for Genomic Medicine, Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Science Centre, Saint Mary's Hospital, Manchester, United Kingdom
| | - Simon Williams
- Manchester Centre for Genomic Medicine, Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Science Centre, Saint Mary's Hospital, Manchester, United Kingdom
| | - Susmito Biswas
- Manchester Centre for Genomic Medicine, Institute of Human Development, Faculty of Medical and Human Sciences, University of Manchester, Manchester Academic Health Science Centre, Saint Mary's Hospital, Manchester, United Kingdom; Manchester Royal Eye Hospital, Manchester Academic Health Science Centre, The University of Manchester, Central Manchester Foundation Trust, Manchester, United Kingdom
| | - Elias Kehdi
- Manchester Royal Eye Hospital, Manchester Academic Health Science Centre, The University of Manchester, Central Manchester Foundation Trust, Manchester, United Kingdom
| | - Simon C Ramsden
- Manchester Centre for Genomic Medicine, Institute of Human Development, Faculty of Medical and Human Sciences, University of Manchester, Manchester Academic Health Science Centre, Saint Mary's Hospital, Manchester, United Kingdom; Manchester Centre for Genomic Medicine, Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Science Centre, Saint Mary's Hospital, Manchester, United Kingdom
| | - Jill Clayton-Smith
- Manchester Centre for Genomic Medicine, Institute of Human Development, Faculty of Medical and Human Sciences, University of Manchester, Manchester Academic Health Science Centre, Saint Mary's Hospital, Manchester, United Kingdom; Manchester Centre for Genomic Medicine, Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Science Centre, Saint Mary's Hospital, Manchester, United Kingdom
| | - Graeme C Black
- Manchester Centre for Genomic Medicine, Institute of Human Development, Faculty of Medical and Human Sciences, University of Manchester, Manchester Academic Health Science Centre, Saint Mary's Hospital, Manchester, United Kingdom; Manchester Centre for Genomic Medicine, Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Science Centre, Saint Mary's Hospital, Manchester, United Kingdom.
| | - I Christopher Lloyd
- Manchester Centre for Genomic Medicine, Institute of Human Development, Faculty of Medical and Human Sciences, University of Manchester, Manchester Academic Health Science Centre, Saint Mary's Hospital, Manchester, United Kingdom; Manchester Royal Eye Hospital, Manchester Academic Health Science Centre, The University of Manchester, Central Manchester Foundation Trust, Manchester, United Kingdom
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Haas J, Barb I, Katus HA, Meder B. Targeted next-generation sequencing: the clinician's stethoscope for genetic disorders. Per Med 2014; 11:581-592. [PMID: 29758803 DOI: 10.2217/pme.14.40] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Genetic biomarkers are crucial for diagnosis, guiding of treatments and estimation of prognosis. In the past, clinical genetic diagnostics was limited by the sequencing information gained from selected exons and single genes. For genetically heterogeneous diseases, such as cardiomyopathies, where underlying mutations in more than 1000 exons are known, a Sanger-based comprehensive test would have been extremely expensive and labor intensive. Next-generation sequencing has overcome these problems in terms of costs, speed and throughput. In this review we discuss available methods for targeted next-generation sequencing that ease the introduction of this technology into routine clinical application. We further provide results of a study we have performed to compare two state-of-the-art methods for their enrichment efficiency and detection accuracy of variants in a clinical setting.
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Affiliation(s)
- Jan Haas
- Department of Internal Medicine III, University of Heidelberg, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), Germany
| | - Ioana Barb
- Department of Internal Medicine III, University of Heidelberg, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), Germany
| | - Hugo A Katus
- Department of Internal Medicine III, University of Heidelberg, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), Germany
| | - Benjamin Meder
- Department of Internal Medicine III, University of Heidelberg, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), Germany
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Yu Z, Cao K, Tischler T, Stolle CA, Santani AB. Mung bean nuclease treatment increases capture specificity of microdroplet-PCR based targeted DNA enrichment. PLoS One 2014; 9:e103491. [PMID: 25058678 PMCID: PMC4110027 DOI: 10.1371/journal.pone.0103491] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Accepted: 07/01/2014] [Indexed: 12/04/2022] Open
Abstract
Targeted DNA enrichment coupled with next generation sequencing has been increasingly used for interrogation of select sub-genomic regions at high depth of coverage in a cost effective manner. Specificity measured by on-target efficiency is a key performance metric for target enrichment. Non-specific capture leads to off-target reads, resulting in waste of sequencing throughput on irrelevant regions. Microdroplet-PCR allows simultaneous amplification of up to thousands of regions in the genome and is among the most commonly used strategies for target enrichment. Here we show that carryover of single-stranded template genomic DNA from microdroplet-PCR constitutes a major contributing factor for off-target reads in the resultant libraries. Moreover, treatment of microdroplet-PCR enrichment products with a nuclease specific to single-stranded DNA alleviates off-target load and improves enrichment specificity. We propose that nuclease treatment of enrichment products should be incorporated in the workflow of targeted sequencing using microdroplet-PCR for target capture. These findings may have a broad impact on other PCR based applications for which removal of template DNA is beneficial.
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Affiliation(s)
- Zhenming Yu
- Division of Genomic Diagnostics and Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
- * E-mail: (ZY) (ZY); (ABS) (AS)
| | - Kajia Cao
- Division of Genomic Diagnostics and Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Tanya Tischler
- Division of Genomic Diagnostics and Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Catherine A. Stolle
- Division of Genomic Diagnostics and Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Avni B. Santani
- Division of Genomic Diagnostics and Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- * E-mail: (ZY) (ZY); (ABS) (AS)
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Wang H, Jiang X, Wang X, Wei X, Zhu Y, Sun B, Su Y, He S, He Y. Hairpin DNA-Assisted Silicon/Silver-Based Surface-Enhanced Raman Scattering Sensing Platform for Ultrahighly Sensitive and Specific Discrimination of Deafness Mutations in a Real System. Anal Chem 2014; 86:7368-76. [DOI: 10.1021/ac501675d] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Hui Wang
- Institute of Functional Nano and
Soft Materials and Collaborative
Innovation Center of Suzhou Nano Science and Technology, Jiangsu Key
Laboratory for Carbon-Based Functional Materials and Devices, and ‡Cyrus Tang Hematology
Center, Jiangsu Institute of Hematology, First Affiliated Hospital,
and Collaborative Innovation Center of Hematology, Soochow University, Suzhou 215123, China
| | - Xiangxu Jiang
- Institute of Functional Nano and
Soft Materials and Collaborative
Innovation Center of Suzhou Nano Science and Technology, Jiangsu Key
Laboratory for Carbon-Based Functional Materials and Devices, and ‡Cyrus Tang Hematology
Center, Jiangsu Institute of Hematology, First Affiliated Hospital,
and Collaborative Innovation Center of Hematology, Soochow University, Suzhou 215123, China
| | - Xing Wang
- Institute of Functional Nano and
Soft Materials and Collaborative
Innovation Center of Suzhou Nano Science and Technology, Jiangsu Key
Laboratory for Carbon-Based Functional Materials and Devices, and ‡Cyrus Tang Hematology
Center, Jiangsu Institute of Hematology, First Affiliated Hospital,
and Collaborative Innovation Center of Hematology, Soochow University, Suzhou 215123, China
| | - Xinpan Wei
- Institute of Functional Nano and
Soft Materials and Collaborative
Innovation Center of Suzhou Nano Science and Technology, Jiangsu Key
Laboratory for Carbon-Based Functional Materials and Devices, and ‡Cyrus Tang Hematology
Center, Jiangsu Institute of Hematology, First Affiliated Hospital,
and Collaborative Innovation Center of Hematology, Soochow University, Suzhou 215123, China
| | - Ying Zhu
- Institute of Functional Nano and
Soft Materials and Collaborative
Innovation Center of Suzhou Nano Science and Technology, Jiangsu Key
Laboratory for Carbon-Based Functional Materials and Devices, and ‡Cyrus Tang Hematology
Center, Jiangsu Institute of Hematology, First Affiliated Hospital,
and Collaborative Innovation Center of Hematology, Soochow University, Suzhou 215123, China
| | - Bin Sun
- Institute of Functional Nano and
Soft Materials and Collaborative
Innovation Center of Suzhou Nano Science and Technology, Jiangsu Key
Laboratory for Carbon-Based Functional Materials and Devices, and ‡Cyrus Tang Hematology
Center, Jiangsu Institute of Hematology, First Affiliated Hospital,
and Collaborative Innovation Center of Hematology, Soochow University, Suzhou 215123, China
| | - Yuanyuan Su
- Institute of Functional Nano and
Soft Materials and Collaborative
Innovation Center of Suzhou Nano Science and Technology, Jiangsu Key
Laboratory for Carbon-Based Functional Materials and Devices, and ‡Cyrus Tang Hematology
Center, Jiangsu Institute of Hematology, First Affiliated Hospital,
and Collaborative Innovation Center of Hematology, Soochow University, Suzhou 215123, China
| | - Sudan He
- Institute of Functional Nano and
Soft Materials and Collaborative
Innovation Center of Suzhou Nano Science and Technology, Jiangsu Key
Laboratory for Carbon-Based Functional Materials and Devices, and ‡Cyrus Tang Hematology
Center, Jiangsu Institute of Hematology, First Affiliated Hospital,
and Collaborative Innovation Center of Hematology, Soochow University, Suzhou 215123, China
| | - Yao He
- Institute of Functional Nano and
Soft Materials and Collaborative
Innovation Center of Suzhou Nano Science and Technology, Jiangsu Key
Laboratory for Carbon-Based Functional Materials and Devices, and ‡Cyrus Tang Hematology
Center, Jiangsu Institute of Hematology, First Affiliated Hospital,
and Collaborative Innovation Center of Hematology, Soochow University, Suzhou 215123, China
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Pecci A, Verver EJJ, Schlegel N, Canzi P, Boccio CM, Platokouki H, Krause E, Benazzo M, Topsakal V, Greinacher A. Cochlear implantation is safe and effective in patients with MYH9-related disease. Orphanet J Rare Dis 2014; 9:100. [PMID: 24980457 PMCID: PMC4105151 DOI: 10.1186/1750-1172-9-100] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Accepted: 06/19/2014] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND MYH9-related disease (MYH9-RD) is a rare syndromic disorder deriving from mutations in MYH9, the gene for the heavy chain of non-muscle myosin IIA. Patients present with congenital thrombocytopenia and giant platelets and have a variable risk of developing sensorineural deafness, kidney damage, presenile cataract, and liver abnormalities. Almost all MYH9-RD patients develop the hearing defect, which, in many individuals, progresses to severe to profound deafness with high impact on quality of life. These patients are potential candidates for cochlear implantation (CI), however, no consistent data are available about the risk to benefit ratio of CI in MYH9-RD. The only reported patient who received CI experienced perisurgery complications that have been attributed to concurrent platelet defects and/or MYH9 protein dysfunction. METHODS By international co-operative study, we report the clinical outcome of 10 patients with MYH9-RD and severe to profound deafness who received a CI at 8 institutions. RESULTS Nine patients benefited from CI: in particular, eight of them obtained excellent performances with restoration of a practically normal hearing function and verbal communication abilities. One patient had a slightly worse performance that could be explained by the very long duration of severe deafness before CI. Finally, one patient did not significantly benefit from CI. No adverse events attributable to MYH9-RD syndrome were observed, in particular no perisurgery bleeding complications due to the platelet defects were seen. Patients' perioperative management is described and discussed. CONCLUSIONS CI is safe and effective in most patients with MYH9-RD and severe to profound deafness and should be offered to these subjects, possibly as soon as they develop the criteria for candidacy.
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Affiliation(s)
- Alessandro Pecci
- Department of Internal Medicine, IRCCS Policlinico San Matteo Foundation and University of Pavia, Piazzale Golgi, 27100 Pavia, Italy.
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Hearing impairment in Estonia: an algorithm to investigate genetic causes in pediatric patients. Adv Med Sci 2014; 58:419-28. [PMID: 24222258 DOI: 10.2478/ams-2013-0001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
PURPOSE The present study was initiated to establish the etiological causes of early onset hearing loss (HL) among Estonian children between 2000-2009. METHODS The study group consisted of 233 probands who were first tested with an arrayed primer extension assay, which covers 199 mutations in 7 genes (GJB2, GJB6, GJB3, SLC26A4, SLC26A5 genes, and two mitochondrial genes - 12S rRNA, tRNASer(UCN)). From probands whose etiology of HL remained unknown, DNA analysis of congenital cytomegalovirus (CMV) infection and G-banded karyotype and/or chromosomal microarray analysis (CMA) were performed. RESULTS In 110 (47%) cases, the etiology of HL was genetic and in 5 (2%) congenital CMV infection was diagnosed. We found mutations with clinical significance in GJB2 (100 children, 43%) and in 2 mitochondrial genes (2 patients, 1%). A single mutation in SLC26A4 gene was detected in 5 probands (2.2%) and was considered diagnostic. In 4 probands a heterozygous IVS2-2A>G change in the SLC26A5 gene was found. We did not find any instances of homozygosity for this splice variant in the probands. CMA identified in 4 probands chromosomal regions with the loss of one allele. In 2 of them we were able to conclude that the found abnormalities are definitely pathogenic (12q13.3-q14.2 and 17q22-23.2 microdeletion), but the pathogenity of 2 other findings (3p26.2 and 1p33 microdeletion) remained unknown. CONCLUSION This practical diagnostic algorithm confirmed the etiology of early onset HL for 115 Estonian patients (49%). This algorithm may be generalized to other populations for clinical application.
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Einführung in die Grundlagen der Hochdurchsatzsequenzierung. MED GENET-BERLIN 2014. [DOI: 10.1007/s11825-014-0447-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Zusammenfassung
Hintergrund
Next Generation Sequencing ist die neue Sequenziermethode für DNA. Aber was verbirgt sich eigentlich dahinter und was ist der Unterschied zur Sanger-Sequenzierung? In dieser Übersicht wird die neue Technologie ein wenig näher erläutert, und es wird erklärt, dass es sich hierbei nicht um eine einzige, sondern um viele neue Techniken handelt.
Technologie und Anwendung
Die momentan bekanntesten Sequenziergeräte und -techniken werden im Detail erklärt und die Gemeinsamkeiten der Maschinen, aber gerade auch die Unterschiede sowie Vor- und Nachteile dargestellt. Auf diese Weise soll der Leser erkennen, dass es nicht die perfekte Maschine für alle Applikationen gibt, sondern dass man für die jeweilige Fragestellung die Maschine aussuchen sollte, deren Spezifikationen sich hierfür am ehesten eignen. Auch die Möglichkeit des Outsourcings wird besprochen, die sicherlich für einige Laboratorien interessant sein könnte. Desweiteren wird kurz erklärt, dass, analog zur Polymerase-Kettenreaktion bei der Sanger-Sequenzierung, auch beim Next Generation Sequencing zuvor oft die zu untersuchenden Regionen anreichert werden. Hierfür existieren verschiedene Methoden, deren Wahl i. d. R. von der Anzahl der zu untersuchenden Patienten und Gene abhängt.
Ausblick
Es wird ein Ausblick auf neueste Entwicklungen gegeben, die deutlich anzeigen, dass das Ende der genetischen Revolution noch nicht in Sicht ist.
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Nakanishi H, Kurima K, Kawashima Y, Griffith AJ. Mutations of TMC1 cause deafness by disrupting mechanoelectrical transduction. Auris Nasus Larynx 2014; 41:399-408. [PMID: 24933710 DOI: 10.1016/j.anl.2014.04.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Accepted: 04/22/2014] [Indexed: 01/05/2023]
Abstract
OBJECTIVE Mutations of transmembrane channel-like 1 gene (TMC1) can cause dominant (DFNA36) or recessive (DFNB7/B11) deafness. In this article, we describe the characteristics of DFNA36 and DFNB7/B11 deafness, the features of the Tmc1 mutant mouse strains, and recent advances in our understanding of TMC1 function. METHODS Publications related to TMC1, DFNA36, or DFNB7/B11 were identified through PubMed. RESULTS All affected DFNA36 subjects showed post-lingual, progressive, sensorineural hearing loss (HL), initially affecting high frequencies. In contrast, almost all affected DFNB7/B11 subjects demonstrated congenital or prelingual severe to profound sensorineural HL. The mouse Tmc1 gene also has dominant and recessive mutant alleles that cause HL in mutant strains, including Beethoven, deafness, and Tmc1 knockout mice. These mutant mice have been instrumental for revealing that Tmc1 and its closely related paralog Tmc2 are expressed in cochlear and vestibular hair cells, and are required for hair cell mechanoelectrical transduction (MET). Recent studies suggest that TMC1 and TMC2 may be components of the long-sought hair cell MET channel. CONCLUSION TMC1 mutations disrupt hair cell MET.
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Affiliation(s)
- Hiroshi Nakanishi
- Molecular Biology and Genetics Section, National Institute on Deafness and Other Communication Disorders (NIDCD), NIH, 35A Convent Dr, Bethesda, MD 20892, USA
| | - Kiyoto Kurima
- Molecular Biology and Genetics Section, National Institute on Deafness and Other Communication Disorders (NIDCD), NIH, 35A Convent Dr, Bethesda, MD 20892, USA
| | - Yoshiyuki Kawashima
- Department of Otolaryngology, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8519, Japan
| | - Andrew J Griffith
- Molecular Biology and Genetics Section, National Institute on Deafness and Other Communication Disorders (NIDCD), NIH, 35A Convent Dr, Bethesda, MD 20892, USA.
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De Wilde B, Lefever S, Dong W, Dunne J, Husain S, Derveaux S, Hellemans J, Vandesompele J. Target enrichment using parallel nanoliter quantitative PCR amplification. BMC Genomics 2014; 15:184. [PMID: 24612714 PMCID: PMC4234423 DOI: 10.1186/1471-2164-15-184] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Accepted: 02/25/2014] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Next generation targeted resequencing is replacing Sanger sequencing at high pace in routine genetic diagnosis. The need for well validated, high quality enrichment platforms to complement the bench-top next generation sequencing devices is high. RESULTS We used the WaferGen Smartchip platform to perform highly parallelized PCR based target enrichment for a set of known cancer genes in a well characterized set of cancer cell lines from the NCI60 panel. Optimization of PCR assay design and cycling conditions resulted in a high enrichment efficiency. We provide proof of a high mutation rediscovery rate and have included technical replicates to enable SNP calling validation demonstrating the high reproducibility of our enrichment platform. CONCLUSIONS Here we present our custom developed quantitative PCR based target enrichment platform. Using highly parallel nanoliter singleplex PCR reactions makes this a flexible and efficient platform. The high mutation validation rate shows this platform's promise as a targeted resequencing method for multi-gene routine sequencing diagnostics.
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Affiliation(s)
- Bram De Wilde
- Center of Medical Genetics Ghent, Ghent University, Ghent, Belgium
| | - Steve Lefever
- Center of Medical Genetics Ghent, Ghent University, Ghent, Belgium
| | - Wes Dong
- WaferGen Biosystems Inc, Fremont, USA
| | | | | | | | | | - Jo Vandesompele
- Center of Medical Genetics Ghent, Ghent University, Ghent, Belgium
- Biogazelle, Zwijnaarde, Belgium
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Abstract
Genetics has been revolutionised by recent technologies. The latest addition to these advances is next-generation sequencing, which is set to transform clinical diagnostics in every branch of medicine. In the research arena this has already been instrumental in identifying hundreds of novel genetic syndromes, making a molecular diagnosis possible for the first time in numerous refractory cases. However, the pace of change has left many clinicians bewildered by new terminology and the implications of next-generation sequencing for their clinical practice. The rapid developments have also left many diagnostic laboratories struggling to implement these new technologies with limited resources. This review explains the basic concepts of next-generation sequencing, gives examples of its role in clinically applied research and examines the challenges of its introduction into clinical practice.
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Altmüller J, Budde BS, Nürnberg P. Enrichment of target sequences for next-generation sequencing applications in research and diagnostics. Biol Chem 2014; 395:231-7. [DOI: 10.1515/hsz-2013-0199] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Accepted: 08/30/2013] [Indexed: 12/21/2022]
Abstract
Abstract
Targeted re-sequencing such as gene panel sequencing (GPS) has become very popular in medical genetics, both for research projects and in diagnostic settings. The technical principles of the different enrichment methods have been reviewed several times before; however, new enrichment products are constantly entering the market, and researchers are often puzzled about the requirement to take decisions about long-term commitments, both for the enrichment product and the sequencing technology. This review summarizes important considerations for the experimental design and provides helpful recommendations in choosing the best sequencing strategy for various research projects and diagnostic applications.
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Bonnefond A, Philippe J, Durand E, Muller J, Saeed S, Arslan M, Martínez R, De Graeve F, Dhennin V, Rabearivelo I, Polak M, Cavé H, Castaño L, Vaxillaire M, Mandel JL, Sand O, Froguel P. Highly sensitive diagnosis of 43 monogenic forms of diabetes or obesity through one-step PCR-based enrichment in combination with next-generation sequencing. Diabetes Care 2014; 37:460-7. [PMID: 24041679 DOI: 10.2337/dc13-0698] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
OBJECTIVE Accurate etiological diagnosis of monogenic forms of diabetes and obesity is useful as it can lead to marked improvements in patient care and genetic counseling. Currently, molecular diagnosis based on Sanger sequencing is restricted to only a few genes, as this technology is expensive, time-consuming, and labor-intensive. High-throughput next-generation sequencing (NGS) provides an opportunity to develop innovative cost-efficient methods for sensitive diabetes and obesity multigene screening. RESEARCH DESIGN AND METHODS We assessed a new method based on PCR enrichment in microdroplets (RainDance Technologies) and NGS using the Illumina HiSeq2000 for the molecular diagnosis of 43 forms of monogenic diabetes or obesity. Forty patients carrying a known causal mutation for those subtypes according to diagnostic laboratories were blindly reanalyzed. RESULTS Except for one variant, we reidentified all causal mutations in each patient associated with an almost-perfect sequencing of the targets (mean of 98.6%). We failed to call one highly complex indel, although we identified a dramatic drop of coverage at this locus. In three patients, we detected other mutations with a putatively deleterious effect in addition to those reported by the genetic diagnostic laboratories. CONCLUSIONS Our NGS approach provides an efficient means of highly sensitive screening for mutations in genes associated with monogenic forms of diabetes and obesity. As cost and time to deliver results have been key barriers to uncovering a molecular cause in the many undiagnosed cases likely to exist, the present methodology should be considered in patients displaying features of monogenic diabetes or obesity.
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Németh AH, Kwasniewska AC, Lise S, Parolin Schnekenberg R, Becker EBE, Bera KD, Shanks ME, Gregory L, Buck D, Zameel Cader M, Talbot K, de Silva R, Fletcher N, Hastings R, Jayawant S, Morrison PJ, Worth P, Taylor M, Tolmie J, O’Regan M, Valentine R, Packham E, Evans J, Seller A, Ragoussis J. Next generation sequencing for molecular diagnosis of neurological disorders using ataxias as a model. Brain 2013; 136:3106-18. [PMID: 24030952 PMCID: PMC3784284 DOI: 10.1093/brain/awt236] [Citation(s) in RCA: 134] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Revised: 05/28/2013] [Accepted: 06/20/2013] [Indexed: 12/23/2022] Open
Abstract
Many neurological conditions are caused by immensely heterogeneous gene mutations. The diagnostic process is often long and complex with most patients undergoing multiple invasive and costly investigations without ever reaching a conclusive molecular diagnosis. The advent of massively parallel, next-generation sequencing promises to revolutionize genetic testing and shorten the 'diagnostic odyssey' for many of these patients. We performed a pilot study using heterogeneous ataxias as a model neurogenetic disorder to assess the introduction of next-generation sequencing into clinical practice. We captured 58 known human ataxia genes followed by Illumina Next-Generation Sequencing in 50 highly heterogeneous patients with ataxia who had been extensively investigated and were refractory to diagnosis. All cases had been tested for spinocerebellar ataxia 1-3, 6, 7 and Friedrich's ataxia and had multiple other biochemical, genetic and invasive tests. In those cases where we identified the genetic mutation, we determined the time to diagnosis. Pathogenicity was assessed using a bioinformatics pipeline and novel variants were validated using functional experiments. The overall detection rate in our heterogeneous cohort was 18% and varied from 8.3% in those with an adult onset progressive disorder to 40% in those with a childhood or adolescent onset progressive disorder. The highest detection rate was in those with an adolescent onset and a family history (75%). The majority of cases with detectable mutations had a childhood onset but most are now adults, reflecting the long delay in diagnosis. The delays were primarily related to lack of easily available clinical testing, but other factors included the presence of atypical phenotypes and the use of indirect testing. In the cases where we made an eventual diagnosis, the delay was 3-35 years (mean 18.1 years). Alignment and coverage metrics indicated that the capture and sequencing was highly efficient and the consumable cost was ∼£400 (€460 or US$620). Our pathogenicity interpretation pathway predicted 13 different mutations in eight different genes: PRKCG, TTBK2, SETX, SPTBN2, SACS, MRE11, KCNC3 and DARS2 of which nine were novel including one causing a newly described recessive ataxia syndrome. Genetic testing using targeted capture followed by next-generation sequencing was efficient, cost-effective, and enabled a molecular diagnosis in many refractory cases. A specific challenge of next-generation sequencing data is pathogenicity interpretation, but functional analysis confirmed the pathogenicity of novel variants showing that the pipeline was robust. Our results have broad implications for clinical neurology practice and the approach to diagnostic testing.
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Affiliation(s)
- Andrea H. Németh
- 1 Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford OX3 9DU, UK
- 2 Department of Clinical Genetics, Churchill Hospital, Oxford University Hospitals NHS Trust, Oxford, OX3 7LJ, UK
- 3 Wellcome Trust Centre for Human Genetics, University of Oxford, OX3 7BN, UK
| | - Alexandra C. Kwasniewska
- 1 Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford OX3 9DU, UK
- 3 Wellcome Trust Centre for Human Genetics, University of Oxford, OX3 7BN, UK
| | - Stefano Lise
- 3 Wellcome Trust Centre for Human Genetics, University of Oxford, OX3 7BN, UK
| | - Ricardo Parolin Schnekenberg
- 3 Wellcome Trust Centre for Human Genetics, University of Oxford, OX3 7BN, UK
- 4 School of Medicine, Universidade Positivo, Curitiba, Brazil
| | - Esther B. E. Becker
- 5 Department of Physiology, Anatomy and Genetics, MRC Functional Genomics Unit, University of Oxford, OX1 3QX, UK
| | - Katarzyna D. Bera
- 5 Department of Physiology, Anatomy and Genetics, MRC Functional Genomics Unit, University of Oxford, OX1 3QX, UK
| | - Morag E. Shanks
- 3 Wellcome Trust Centre for Human Genetics, University of Oxford, OX3 7BN, UK
| | - Lorna Gregory
- 3 Wellcome Trust Centre for Human Genetics, University of Oxford, OX3 7BN, UK
| | - David Buck
- 3 Wellcome Trust Centre for Human Genetics, University of Oxford, OX3 7BN, UK
| | - M. Zameel Cader
- 1 Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford OX3 9DU, UK
| | - Kevin Talbot
- 1 Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford OX3 9DU, UK
| | - Rajith de Silva
- 6 Department of Neurology, Essex Centre for Neurological Sciences, Queen's Hospital, Romford, UK
| | | | - Rob Hastings
- 8 Department of Clinical Genetics, St Michael's Hospital, Bristol, BS2 8EG, UK
| | - Sandeep Jayawant
- 9 Department of Paediatrics, Oxford University Hospitals NHS Trust, Oxford, OX3 7LJ, UK
| | - Patrick J. Morrison
- 10 School of Medicine, Dentistry and Biomedical Sciences, Queens University, Belfast, BT9 7BL, Northern Ireland, UK
| | - Paul Worth
- 11 Department of Neurology, Norfolk and Norwich University Hospital, Norwich, UK
| | - Malcolm Taylor
- 12 School of Cancer Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - John Tolmie
- 13 Department of Clinical Genetics, Southern General Hospital, Glasgow G51 4TF, UK
| | - Mary O’Regan
- 14 Fraser of Allander Neurosciences Unit, Royal Hospital for Sick Children, Glasgow G3 8SJ, UK
| | | | - Ruth Valentine
- 15 Thames Valley Dementia and Neurodegenerative Diseases Network, Oxford, UK
| | - Emily Packham
- 16 Oxford Regional Molecular Genetics Laboratories, Oxford University Hospitals NHS Trust
| | - Julie Evans
- 16 Oxford Regional Molecular Genetics Laboratories, Oxford University Hospitals NHS Trust
| | - Anneke Seller
- 16 Oxford Regional Molecular Genetics Laboratories, Oxford University Hospitals NHS Trust
| | - Jiannis Ragoussis
- 3 Wellcome Trust Centre for Human Genetics, University of Oxford, OX3 7BN, UK
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