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Alkhidir S, El-Akouri K, Al-Dewik N, Khodjet-El-Khil H, Okashah S, Islam N, Ben-Omran T, Al-Shafai M. The genetic basis and the diagnostic yield of genetic testing related to nonsyndromic hearing loss in Qatar. Sci Rep 2024; 14:4202. [PMID: 38378725 PMCID: PMC10879212 DOI: 10.1038/s41598-024-52784-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 01/23/2024] [Indexed: 02/22/2024] Open
Abstract
Hearing loss is the most predominant sensory defect occurring in pediatrics, of which, 66% cases are attributed to genetic factors. The prevalence of hereditary hearing loss increases in consanguineous populations, and the prevalence of hearing loss in Qatar is 5.2%. We aimed to investigate the genetic basis of nonsyndromic hearing loss (NSHL) in Qatar and to evaluate the diagnostic yield of different genetic tests available. A retrospective chart review was conducted for 59 pediatric patients with NSHL referred to the Department of Adult and Pediatric Medical Genetics at Hamad Medical Corporation in Qatar, and who underwent at least one genetic test. Out of the 59 patients, 39 were solved cases due to 19 variants in 11 genes and two copy number variants that explained the NSHL phenotype. Of them 2 cases were initially uncertain and were reclassified using familial segregation. Around 36.8% of the single variants were in GJB2 gene and c.35delG was the most common recurrent variant seen in solved cases. We detected the c.283C > T variant in FGF3 that was seen in a Qatari patient and found to be associated with NSHL for the first time. The overall diagnostic yield was 30.7%, and the diagnostic yield was significantly associated with genetic testing using GJB2 sequencing and using the hearing loss (HL) gene panel. The diagnostic yield for targeted familial testing was 60% (n = 3 patients) and for gene panel was 50% (n = 5). Thus, we recommend using GJB2 gene sequencing as a first-tier genetic test and HL gene panel as a second-tier genetic test for NSHL. Our work provided new insights into the genetic pool of NSHL among Arabs and highlights its unique diversity, this is believed to help further in the diagnostic and management options for NSHL Arab patients.
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Affiliation(s)
- Shaza Alkhidir
- Department of Biomedical Sciences, College of Health Sciences, QU Health, Qatar University, Doha, Qatar
- Department of Adult and Pediatric Medical Genetics, Hamad Medical Corporation, Doha, Qatar
| | - Karen El-Akouri
- Department of Adult and Pediatric Medical Genetics, Hamad Medical Corporation, Doha, Qatar
- Division of Genetic and Genomic Medicine, Sidra Medicine, Doha, Qatar
| | - Nader Al-Dewik
- Department of Adult and Pediatric Medical Genetics, Hamad Medical Corporation, Doha, Qatar
| | - Houssein Khodjet-El-Khil
- Department of Biomedical Sciences, College of Health Sciences, QU Health, Qatar University, Doha, Qatar
| | - Sarah Okashah
- Department of Adult and Pediatric Medical Genetics, Hamad Medical Corporation, Doha, Qatar
- Department of Public Health, College of Health Sciences, QU Health, Qatar University, Doha, Qatar
| | - Nazmul Islam
- Department of Public Health, College of Health Sciences, QU Health, Qatar University, Doha, Qatar
- Department of Health Research Methods, Evidence and Impact, McMaster University, Hamilton, Ontario, Canada
| | - Tawfeg Ben-Omran
- Department of Adult and Pediatric Medical Genetics, Hamad Medical Corporation, Doha, Qatar.
- Division of Genetic and Genomic Medicine, Sidra Medicine, Doha, Qatar.
| | - Mashael Al-Shafai
- Department of Biomedical Sciences, College of Health Sciences, QU Health, Qatar University, Doha, Qatar.
- Biomedical Research Center, Qatar University, Doha, Qatar.
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Kumar S, Borisov O, Maj C, Ralser DJ, Humbatova A, Hanneken S, Schmieder A, Groß J, Maintz L, Heineke A, Knuever J, Fagerberg C, Parmentier L, Anemüller W, Oji V, Tantcheva-Poór I, Fölster-Holst R, Wenzel J, Krawitz PM, Frank J, Betz RC. Founder Variants in KRT5 and POGLUT1 Are Implicated in Dowling-Degos Disease. J Invest Dermatol 2024; 144:181-184. [PMID: 37468035 DOI: 10.1016/j.jid.2023.04.036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 04/14/2023] [Indexed: 07/21/2023]
Affiliation(s)
- Sheetal Kumar
- Institute of Human Genetics, University of Bonn, Medical Faculty & University Hospital Bonn, Bonn, Germany
| | - Oleg Borisov
- Institute for Genomic Statistics and Bioinformatics, University of Bonn, Medical Faculty & University Hospital Bonn, Bonn, Germany
| | - Carlo Maj
- Institute for Genomic Statistics and Bioinformatics, University of Bonn, Medical Faculty & University Hospital Bonn, Bonn, Germany; Center for Human Genetics, University Hospital of Marburg, Marburg, Germany
| | - Damian J Ralser
- Institute of Human Genetics, University of Bonn, Medical Faculty & University Hospital Bonn, Bonn, Germany
| | - Aytaj Humbatova
- Institute of Human Genetics, University of Bonn, Medical Faculty & University Hospital Bonn, Bonn, Germany
| | | | - Astrid Schmieder
- Department of Dermatology, Venereology and Allergology, University Hospital Wuerzburg, Wuerzburg, Germany
| | - Janina Groß
- Department of Dermatology and Allergy, University Hospital Bonn, Bonn, Germany
| | - Laura Maintz
- Department of Dermatology and Allergy, University Hospital Bonn, Bonn, Germany; Christine Kuehne - Center for Allergy Research and Education Davos (CK-CARE), Davos, Switzerland
| | - Andre Heineke
- Dermatologist practice, Dr. Karches/Dr. Thielert, Hannover, Germany
| | - Jana Knuever
- Department of Dermatology, University of Cologne, Cologne, Germany
| | - Christina Fagerberg
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | | | - Waltraud Anemüller
- Department of Dermatology, Allergology and Venereology, University of Luebeck, Luebeck, Germany
| | - Vinzenz Oji
- Department of Dermatology, University of Muenster, Muenster, Germany
| | | | - Regina Fölster-Holst
- Department of Dermatology, Allergology and Venereology, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Joerg Wenzel
- Department of Dermatology, Venereology and Allergology, University Hospital Wuerzburg, Wuerzburg, Germany
| | - Peter M Krawitz
- Institute for Genomic Statistics and Bioinformatics, University of Bonn, Medical Faculty & University Hospital Bonn, Bonn, Germany
| | - Jorge Frank
- Department of Dermatology, Venereology and Allergology, University Medical Center Goettingen, Goettingen, Germany
| | - Regina C Betz
- Institute of Human Genetics, University of Bonn, Medical Faculty & University Hospital Bonn, Bonn, Germany.
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Pshennikova VG, Teryutin FM, Cherdonova AM, Borisova TV, Solovyev AV, Romanov GP, Morozov IV, Bondar AA, Posukh OL, Fedorova SA, Barashkov NA. The GJB2 (Cx26) Gene Variants in Patients with Hearing Impairment in the Baikal Lake Region (Russia). Genes (Basel) 2023; 14:genes14051001. [PMID: 37239361 DOI: 10.3390/genes14051001] [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: 03/25/2023] [Revised: 04/22/2023] [Accepted: 04/25/2023] [Indexed: 05/28/2023] Open
Abstract
The GJB2 (Cx26) gene pathogenic variants are associated with autosomal recessive deafness type 1A (DFNB1A, OMIM #220290). Direct sequencing of the GJB2 gene among 165 hearing-impaired individuals living in the Baikal Lake region of Russia identified 14 allelic variants: pathogenic/likely pathogenic-nine variants, benign-three variants, unclassified-one variant, and one novel variant. The contribution of the GJB2 gene variants to the etiology of hearing impairment (HI) in the total sample of patients was 15.8% (26 out of 165) and significantly differed in patients of different ethnicity (5.1% in Buryat patients and 28.9% in Russian patients). In patients with DFNB1A (n = 26), HIs were congenital/early onset (92.3%), symmetric (88.5%), sensorineural (100.0%), and variable in severity (moderate-11.6%, severe-26.9% or profound-61.5%). The reconstruction of the SNP haplotypes with three frequent GJB2 pathogenic variants (c.-23+1G>A, c.35delG or c.235delC), in comparison with previously published data, supports a major role of the founder effect in the expansion of the c.-23+1G>A and c.35delG variants around the world. Comparative analysis of the haplotypes with c.235delC revealed one major haplotype G A C T (97.5%) in Eastern Asians (Chinese, Japanese and Korean patients) and two haplotypes, G A C T (71.4%) and G A C C (28.6%), in Northern Asians (Altaians, Buryats and Mongols). The variable structure of the c.235delC-haplotypes in Northern Asians requires more studies to expand our knowledge about the origin of this pathogenic variant.
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Affiliation(s)
- Vera G Pshennikova
- Laboratory of Molecular Genetics, Yakut Science Centre of Complex Medical Problems, Yaroslavskogo 6/3, 677019 Yakutsk, Russia
| | - Fedor M Teryutin
- Laboratory of Molecular Genetics, Yakut Science Centre of Complex Medical Problems, Yaroslavskogo 6/3, 677019 Yakutsk, Russia
| | - Alexandra M Cherdonova
- Laboratory of Molecular Biology, Institute of Natural Sciences, M.K. Ammosov North-Eastern Federal University, Kulakovskogo 46, 677010 Yakutsk, Russia
| | - Tuyara V Borisova
- Laboratory of Molecular Biology, Institute of Natural Sciences, M.K. Ammosov North-Eastern Federal University, Kulakovskogo 46, 677010 Yakutsk, Russia
| | - Aisen V Solovyev
- Laboratory of Molecular Biology, Institute of Natural Sciences, M.K. Ammosov North-Eastern Federal University, Kulakovskogo 46, 677010 Yakutsk, Russia
| | - Georgii P Romanov
- Laboratory of Molecular Biology, Institute of Natural Sciences, M.K. Ammosov North-Eastern Federal University, Kulakovskogo 46, 677010 Yakutsk, Russia
| | - Igor V Morozov
- Novosibirsk State University, 630090 Novosibirsk, Russia
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Alexander A Bondar
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Olga L Posukh
- Novosibirsk State University, 630090 Novosibirsk, Russia
- Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Sardana A Fedorova
- Laboratory of Molecular Genetics, Yakut Science Centre of Complex Medical Problems, Yaroslavskogo 6/3, 677019 Yakutsk, Russia
- Laboratory of Molecular Biology, Institute of Natural Sciences, M.K. Ammosov North-Eastern Federal University, Kulakovskogo 46, 677010 Yakutsk, Russia
| | - Nikolay A Barashkov
- Laboratory of Molecular Genetics, Yakut Science Centre of Complex Medical Problems, Yaroslavskogo 6/3, 677019 Yakutsk, Russia
- Laboratory of Molecular Biology, Institute of Natural Sciences, M.K. Ammosov North-Eastern Federal University, Kulakovskogo 46, 677010 Yakutsk, Russia
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Aboagye ET, Adadey SM, Wonkam-Tingang E, Amenga-Etego L, Awandare GA, Wonkam A. Global Distribution of Founder Variants Associated with Non-Syndromic Hearing Impairment. Genes (Basel) 2023; 14:399. [PMID: 36833326 PMCID: PMC9957346 DOI: 10.3390/genes14020399] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 01/28/2023] [Accepted: 01/30/2023] [Indexed: 02/05/2023] Open
Abstract
The genetic etiology of non-syndromic hearing impairment (NSHI) is highly heterogeneous with over 124 distinct genes identified. The wide spectrum of implicated genes has challenged the implementation of molecular diagnosis with equal clinical validity in all settings. Differential frequencies of allelic variants in the most common NSHI causal gene, gap junction beta 2 (GJB2), has been described as stemming from the segregation of a founder variant and/or spontaneous germline variant hot spots. We aimed to systematically review the global distribution and provenance of founder variants associated with NSHI. The study protocol was registered on PROSPERO, the International Prospective Register of Systematic Reviews, with the registration number "CRD42020198573". Data from 52 reports, involving 27,959 study participants from 24 countries, reporting 56 founder pathogenic or likely pathogenic (P/LP) variants in 14 genes (GJB2, GJB6, GSDME, TMC1, TMIE, TMPRSS3, KCNQ4, PJVK, OTOF, EYA4, MYO15A, PDZD7, CLDN14, and CDH23), were reviewed. Varied number short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs) were used for haplotype analysis to identify the shared ancestral informative markers in a linkage disequilibrium and variants' origins, age estimates, and common ancestry computations in the reviewed reports. Asia recorded the highest number of NSHI founder variants (85.7%; 48/56), with variants in all 14 genes, followed by Europe (16.1%; 9/56). GJB2 had the highest number of ethnic-specific P/LP founder variants. This review reports on the global distribution of NSHI founder variants and relates their evolution to population migration history, bottleneck events, and demographic changes in populations linked with the early evolution of deleterious founder alleles. International migration and regional and cultural intermarriage, coupled to rapid population growth, may have contributed to re-shaping the genetic architecture and structural dynamics of populations segregating these pathogenic founder variants. We have highlighted and showed the paucity of data on hearing impairment (HI) variants in Africa, establishing unexplored opportunities in genetic traits.
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Affiliation(s)
- Elvis Twumasi Aboagye
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra LG Box 54, Ghana
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Samuel Mawuli Adadey
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra LG Box 54, Ghana
| | - Edmond Wonkam-Tingang
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Lucas Amenga-Etego
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra LG Box 54, Ghana
| | - Gordon A. Awandare
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra LG Box 54, Ghana
| | - Ambroise Wonkam
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
- McKusick-Nathans Institute and Department of Genetic Medicine, John Hopkins University School of Medicine, Baltimore, MD 21205, USA
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