1
|
Ramzan M, Duman D, Hendricks LCP, Guo S, Mutlu A, Kalcioglu MT, Seyhan S, Carranza C, Bonyadi M, Mahdieh N, Yildirim-Baylan M, Figueroa-Ildefonso E, Alper O, Atik T, Ayral A, Bozan N, Balta B, Rivas C, Manzoli GN, Huesca-Hernandez F, Kuchay RAH, Durgut M, Bademci G, Tekin M. Genome sequencing identifies coding and non-coding variants for non-syndromic hearing loss. J Hum Genet 2023; 68:657-669. [PMID: 37217689 DOI: 10.1038/s10038-023-01159-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 04/27/2023] [Accepted: 05/05/2023] [Indexed: 05/24/2023]
Abstract
Hearing loss (HL) is a common heterogeneous trait that involves variants in more than 200 genes. In this study, we utilized exome (ES) and genome sequencing (GS) to effectively identify the genetic cause of presumably non-syndromic HL in 322 families from South and West Asia and Latin America. Biallelic GJB2 variants were identified in 58 probands at the time of enrollment these probands were excluded. In addition, upon review of phenotypic findings, 38/322 probands were excluded based on syndromic findings at the time of ascertainment and no further evaluation was performed on those samples. We performed ES as a primary diagnostic tool on one or two affected individuals from 212/226 families. Via ES we detected a total of 78 variants in 30 genes and showed their co-segregation with HL in 71 affected families. Most of the variants were frameshift or missense and affected individuals were either homozygous or compound heterozygous in their respective families. We employed GS as a primary test on a subset of 14 families and a secondary tool on 22 families which were unsolved by ES. Although the cumulative detection rate of causal variants by ES and GS is 40% (89/226), GS alone has led to a molecular diagnosis in 7 of 14 families as the primary tool and 5 of 22 families as the secondary test. GS successfully identified variants present in deep intronic or complex regions not detectable by ES.
Collapse
Affiliation(s)
- Memoona Ramzan
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Duygu Duman
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
- Division of Genetics, Department of Pediatrics, Ankara University School of Medicine, Ankara, Turkey
| | - LeShon Chere Peart Hendricks
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Shengru Guo
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Ahmet Mutlu
- Department of Otorhinolaryngology, Istanbul Medeniyet University Faculty of Medicine, Istanbul, Turkey
- Goztepe Prof. Dr. Suleyman Yalcin City Hospital, Istanbul, Turkey
| | - Mahmut Tayyar Kalcioglu
- Department of Otorhinolaryngology, Istanbul Medeniyet University Faculty of Medicine, Istanbul, Turkey
- Goztepe Prof. Dr. Suleyman Yalcin City Hospital, Istanbul, Turkey
| | - Serhat Seyhan
- Department of Medical Genetics, Faculty of Medicine, Uskudar University, Istanbul, Turkey
| | - Claudia Carranza
- Institute for Research on Genetic and Metabolic Diseases, INVEGEM, Guatemala City, Guatemala
| | - Murtaza Bonyadi
- Faculty of Natural Sciences, Center of Excellence for Biodiversity, University of Tabriz, Tabriz, Iran
| | - Nejat Mahdieh
- Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
| | | | - Erick Figueroa-Ildefonso
- Neurogenetics Research Center, Instituto Nacional de Ciencias Neurológicas, Lima, Peru
- Universidad Peruana Cayetano Heredia, Lima, 15102, Peru
| | - Ozgul Alper
- Department of Medical Biology and Genetics, Faculty of Medicine, Akdeniz University, Antalya, Turkey
| | - Tahir Atik
- Division of Pediatric Genetics, Department of Pediatrics, School of Medicine, Ege University, Izmir, Turkey
| | - Abdurrahman Ayral
- Department of Otolaryngology, Faculty of Medicine, Yuzuncu Yıl University, Van, Turkey
| | - Nazim Bozan
- Department of Otolaryngology, Faculty of Medicine, Yuzuncu Yıl University, Van, Turkey
| | - Burhan Balta
- Department of Medical Genetics, Kayseri Training and Research Hospital, Kayseri, Turkey
| | | | - Gabrielle N Manzoli
- Gonçalo Moniz Research Center (CPqGM), Oswaldo Cruz Foundation (FIOCRUZ), Salvador, Bahia, Brazil
| | - Fabiola Huesca-Hernandez
- Genetics and Genomic Medicine Service. National Institute of Rehabilitation, Mexico City, Mexico
| | - Raja A H Kuchay
- Department of Biotechnology, Baba Ghulam Shah Badshah University, Rajouri, J&K, India
| | - Merve Durgut
- Kocaeli University Otorhinolaryngology Department- Audiology Unit, İzmit, Turkey
| | - Guney Bademci
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Mustafa Tekin
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA.
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA.
| |
Collapse
|
2
|
Manzoli GN, Bademci G, Acosta AX, Félix TM, Cengiz FB, Foster J, Da Silva DSD, Menendez I, Sanchez-Pena I, Tekin D, Blanton SH, Abe-Sandes K, Liu XZ, Tekin M. Targeted Resequencing of Deafness Genes Reveals a Founder MYO15A Variant in Northeastern Brazil. Ann Hum Genet 2016; 80:327-331. [PMID: 27870113 PMCID: PMC5127167 DOI: 10.1111/ahg.12177] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 08/23/2016] [Accepted: 10/06/2016] [Indexed: 11/29/2022]
Abstract
Identifying the genetic etiology in a person with hearing loss (HL) is challenging due to the extreme genetic heterogeneity in HL and the population-specific variability. In this study, after excluding GJB2 variants, targeted resequencing of 180 deafness-related genes revealed the causative variants in 11 of 19 (58%) Brazilian probands with autosomal recessive HL. Identified pathogenic variants were in MYO15A (10 families) and CLDN14 (one family). Remarkably, the MYO15A p.(Val1400Met) variant was identified in eight families from the city of Monte Santo in the northeast region of Brazil. Haplotype analysis of this variant was consistent with a single founder. No other cases with this variant were detected among 105 simplex cases from other cities of northeastern Brazil, suggesting that this variant is confined to a geographical region. This study suggests that it is feasible to develop population-specific screening for deafness variants once causative variants are identified in different geographical groups.
Collapse
Affiliation(s)
- Gabrielle N Manzoli
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
- Gonçalo Moniz Research Center (CPqGM), Oswaldo Cruz Foundation (FIOCRUZ), Salvador, Bahia, Brazil
| | - Guney Bademci
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Angelina X Acosta
- Gonçalo Moniz Research Center (CPqGM), Oswaldo Cruz Foundation (FIOCRUZ), Salvador, Bahia, Brazil
| | - Têmis M Félix
- Serviço de Genética Médica, Hospital de Clinicas de Porto Alegre, Brazil
| | - F Basak Cengiz
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Joseph Foster
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Danniel S Dias Da Silva
- Gonçalo Moniz Research Center (CPqGM), Oswaldo Cruz Foundation (FIOCRUZ), Salvador, Bahia, Brazil
| | - Ibis Menendez
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Isalis Sanchez-Pena
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Demet Tekin
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Susan H Blanton
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Kiyoko Abe-Sandes
- Gonçalo Moniz Research Center (CPqGM), Oswaldo Cruz Foundation (FIOCRUZ), Salvador, Bahia, Brazil
| | - Xue Zhong Liu
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Mustafa Tekin
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| |
Collapse
|
3
|
Manzoli GN, Abe-Sandes K, Bittles AH, da Silva DSD, Fernandes LDC, Paulon RMC, de Castro ICS, Padovani CMCA, Acosta AX. Non-syndromic hearing impairment in a multi-ethnic population of Northeastern Brazil. Int J Pediatr Otorhinolaryngol 2013; 77:1077-82. [PMID: 23684175 DOI: 10.1016/j.ijporl.2013.04.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/09/2012] [Revised: 03/30/2013] [Accepted: 04/01/2013] [Indexed: 01/28/2023]
Abstract
OBJECTIVE There are many hearing impaired individuals in Monte Santo, a rural municipality in the state of Bahia, Brazil, including multiple familial cases strongly suggestive of a genetic aetiology. METHODS The present study investigated 81 subjects with hearing impairment (HI) recruited from 36 families. Mutations often associated with HI, i.e. the DFNB1 mutations c.35delG in GJB2, deletions del(GJB6-D13S1830) and del(GJB6-D13S1854), and A1555G in the mitochondrial gene MTRNR1 were initially analyzed, with additional mutations in GJB2 identified by sequencing the coding region of the gene. RESULTS Seven different mutations were present in GJB2 with mutations c.35delG and p.Arg75Gln, which are known to be pathogenic, identified in 37.0% of the subjects. Individuals homozygous for the c.35delG mutation were diagnosed in eight families, corresponding to 24.7% of unrelated individuals with nonsyndromic hearing impairment (NSHI), and an additional heterozygote for this mutation was present in a single family. Ten individuals (12.4%) in another family were heterozygous for the mutation p.Arg75Gln. CONCLUSIONS Significant heterogeneity was observed in the alleles and patterns of NSHI inheritance among the subjects studied, probably due to the extensive inter-ethnic admixture that characterizes the peoples of Brazil, together with a high prevalence of community endogamy and consanguineous marriage.
Collapse
Affiliation(s)
- Gabrielle N Manzoli
- Advanced Laboratory of Public Health/Gonçalo Moniz Research Center (CPqGM), Oswaldo Cruz Foundation (FIOCRUZ), Salvador, Bahia, Brazil
| | | | | | | | | | | | | | | | | |
Collapse
|