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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.
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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.
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