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Olono A, Mitesser V, Happi A, Happi C. Building genomic capacity for precision health in Africa. Nat Med 2024; 30:1856-1864. [PMID: 38961224 DOI: 10.1038/s41591-024-03081-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 05/21/2024] [Indexed: 07/05/2024]
Abstract
The African continent is poised to have a pivotal role in the global population landscape, with the United Nations projecting a population of 2.5 billion (more than 25% of the global population) by 2050. Amid this demographic shift, Africa faces a unique healthcare challenge-navigating a complex landscape of infectious and non-communicable diseases. This necessitates a departure from the conventional 'one-size-fits-all' medical model toward precision approaches that are efficient and sustainable. Genomic capacity is a pillar of precision health; however, access to up-to-date genetic testing in African countries is limited, compounded by a startling lack of representation of data from populations of African descent in gene discovery studies. In this Review, we delve into the challenges impeding the development of genomic capacity in Africa, such as the lack of electronic clinical and epidemiological records, infrastructural challenges, high supply chain costs and the 'dependency trap' that jeopardizes long-term sustainability. We emphasize the need for strategies hinged on true partnerships, robust infrastructure, workforce development and well-crafted policies. Finally, we outline recent progress and existing initiatives that should be considered as role models for future capacity-building initiatives.
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Affiliation(s)
- Alhaji Olono
- The African Centre of Excellence for Genomics and Infectious Diseases, ACEGID, Ede, Nigeria
| | - Vera Mitesser
- The African Centre of Excellence for Genomics and Infectious Diseases, ACEGID, Ede, Nigeria
| | - Anise Happi
- The African Centre of Excellence for Genomics and Infectious Diseases, ACEGID, Ede, Nigeria
| | - Christian Happi
- The African Centre of Excellence for Genomics and Infectious Diseases, ACEGID, Ede, Nigeria.
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Yalcouyé A, Esoh K, Guida L, Wonkam A. Current profile of Charcot-Marie-Tooth disease in Africa: A systematic review. J Peripher Nerv Syst 2022; 27:100-112. [PMID: 35383421 PMCID: PMC9322329 DOI: 10.1111/jns.12489] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 01/17/2022] [Accepted: 02/25/2022] [Indexed: 12/21/2022]
Abstract
BACKGROUND AND AIMS Charcot-Marie-Tooth disease (CMT) is the most common inherited peripheral neuropathy characterised by a high clinical and genetic heterogeneity. While most cases were described in populations with Caucasian ancestry, genetic research on CMT in Africa is scant. Only a few cases of CMT have been reported, mainly from North Africa. The current study aimed to summarise available data on CMT in Africa, with emphasis on the epidemiological, clinical, and genetic features. METHODS We searched PubMed, Scopus, Web of Sciences, and the African Journal Online for articles published from the database inception until April 2021 using specific keywords. A total of 398 articles were screened, and 28 fulfilled our selection criteria. RESULTS A total of 107 families totalling 185 patients were reported. Most studies were reported from North Africa (n = 22). The demyelinating form of CMT was the commonest subtype, and the phenotype varied greatly between families, and one family (1%) of CMT associated with hearing impairment was reported. The inheritance pattern was autosomal recessive in 91.2% (n = 97/107) of families. CMT-associated variants were reported in 11 genes: LMNA, GDAP1, GJB1, MPZ, MTMR13, MTMR2, PRX, FGD4/FRABIN, PMP22, SH3TC2, and GARS. The most common genes reported are LMNA, GDAP1, and SH3TC2 and have been found mostly in Northern African populations. INTERPRETATION This study reveals that CMT is not rare in Africa, and describes the current clinical and genetic profile. The review emphasised the urgent need to invest in genetic research to inform counselling, prevention, and care for CMT in numerous settings on the continent.
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Affiliation(s)
- Abdoulaye Yalcouyé
- Faculté de Médecine et d'Odontostomatologie, USTTB, Bamako, Mali.,Division of Human Genetics, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Kevin Esoh
- Division of Human Genetics, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Landouré Guida
- Faculté de Médecine et d'Odontostomatologie, USTTB, Bamako, Mali.,Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, Bethesda, Maryland, USA.,Service de Neurologie, Centre Hospitalier Universitaire du Point "G", Bamako, Mali
| | - Ambroise Wonkam
- Division of Human Genetics, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.,McKusick-Nathans Institute, and Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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Dia Y, Adadey SM, Diop JPD, Aboagye ET, Ba SA, De Kock C, Ly CAT, Oluwale OG, Sène ARG, Sarr PD, Diallo BK, Diallo RN, Wonkam A. GJB2 Is a Major Cause of Non-Syndromic Hearing Impairment in Senegal. BIOLOGY 2022; 11:795. [PMID: 35625523 PMCID: PMC9138795 DOI: 10.3390/biology11050795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 05/16/2022] [Accepted: 05/17/2022] [Indexed: 11/29/2022]
Abstract
This study aimed to investigate GJB2 (MIM: 121011) and GJB6 (MIM: 604418) variants associated with familial non-syndromic hearing impairment (HI) in Senegal. We investigated a total of 129 affected and 143 unaffected individuals from 44 multiplex families by segregating autosomal recessive non-syndromic HI, 9 sporadic HI cases of putative genetic origin, and 148 control individuals without personal or family history of HI. The DNA samples were screened for GJB2 coding-region variants and GJB6-D3S1830 deletions. The mean age at the medical diagnosis of the affected individuals was 2.93 ± 2.53 years [range: 1−15 years]. Consanguinity was present in 40 out of 53 families (75.47%). Variants in GJB2 explained HI in 34.1% (n = 15/44) of multiplex families. A bi-allelic pathogenic variant, GJB2: c.94C>T: p.(Arg32Cys) accounted for 25% (n = 11/44 families) of familial cases, of which 80% (n = 12/15) were consanguineous. Interestingly, the previously reported “Ghanaian” founder variant, GJB2: c.427C>T: p.(Arg143Trp), accounted for 4.5% (n = 2/44 families) of the families investigated. Among the normal controls, the allele frequency of GJB2: c.94C>T and GJB2: c.427C>T was estimated at 1% (2/148 ∗ 2) and 2% (4/148 ∗ 2), respectively. No GJB6-D3S1830 deletion was identified in any of the HI patients. This is the first report of a genetic investigation of HI in Senegal, and suggests that GJB2: c.94C>T: p.(Arg32Cys) and GJB2: c.427C>T: p.(Arg143Trp) should be tested in clinical practice for congenital HI in Senegal.
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Affiliation(s)
- Yacouba Dia
- Division of Human Genetics, Faculty of Medicine, Pharmacy and Odontology, University Cheikh Anta Diop (UCAD), Dakar 10700, Senegal; (Y.D.); (J.P.D.D.); (S.A.B.); (C.A.T.L.); (A.R.G.S.); (P.D.S.), (R.N.D.)
| | - Samuel Mawuli Adadey
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa; (S.M.A.); (E.T.A.); (C.D.K.); (O.G.O.)
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Legon, Accra P.O. Box LG 54, Ghana
| | - Jean Pascal Demba Diop
- Division of Human Genetics, Faculty of Medicine, Pharmacy and Odontology, University Cheikh Anta Diop (UCAD), Dakar 10700, Senegal; (Y.D.); (J.P.D.D.); (S.A.B.); (C.A.T.L.); (A.R.G.S.); (P.D.S.), (R.N.D.)
| | - Elvis Twumasi Aboagye
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa; (S.M.A.); (E.T.A.); (C.D.K.); (O.G.O.)
| | - Seydi Abdoul Ba
- Division of Human Genetics, Faculty of Medicine, Pharmacy and Odontology, University Cheikh Anta Diop (UCAD), Dakar 10700, Senegal; (Y.D.); (J.P.D.D.); (S.A.B.); (C.A.T.L.); (A.R.G.S.); (P.D.S.), (R.N.D.)
| | - Carmen De Kock
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa; (S.M.A.); (E.T.A.); (C.D.K.); (O.G.O.)
| | - Cheikh Ahmed Tidjane Ly
- Division of Human Genetics, Faculty of Medicine, Pharmacy and Odontology, University Cheikh Anta Diop (UCAD), Dakar 10700, Senegal; (Y.D.); (J.P.D.D.); (S.A.B.); (C.A.T.L.); (A.R.G.S.); (P.D.S.), (R.N.D.)
| | - Oluwafemi Gabriel Oluwale
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa; (S.M.A.); (E.T.A.); (C.D.K.); (O.G.O.)
| | - Andrea Regina Gnilane Sène
- Division of Human Genetics, Faculty of Medicine, Pharmacy and Odontology, University Cheikh Anta Diop (UCAD), Dakar 10700, Senegal; (Y.D.); (J.P.D.D.); (S.A.B.); (C.A.T.L.); (A.R.G.S.); (P.D.S.), (R.N.D.)
| | - Pierre Diaga Sarr
- Division of Human Genetics, Faculty of Medicine, Pharmacy and Odontology, University Cheikh Anta Diop (UCAD), Dakar 10700, Senegal; (Y.D.); (J.P.D.D.); (S.A.B.); (C.A.T.L.); (A.R.G.S.); (P.D.S.), (R.N.D.)
| | - Bay Karim Diallo
- Department of Oto-Rhino-Laryngology, Albert Royer Children’s Hospital, Dakar 10700, Senegal;
| | - Rokhaya Ndiaye Diallo
- Division of Human Genetics, Faculty of Medicine, Pharmacy and Odontology, University Cheikh Anta Diop (UCAD), Dakar 10700, Senegal; (Y.D.); (J.P.D.D.); (S.A.B.); (C.A.T.L.); (A.R.G.S.); (P.D.S.), (R.N.D.)
| | - Ambroise Wonkam
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa; (S.M.A.); (E.T.A.); (C.D.K.); (O.G.O.)
- McKusick-Nathans Institute and Department of Genetic Medicine, Johns-Hopskins University School of Medicine, Baltimore, MD 21205, USA
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Manyisa N, Adadey SM, Wonkam-Tingang E, Yalcouye A, Wonkam A. Hearing Impairment in South Africa and the Lessons Learned for Planetary Health Genomics: A Systematic Review. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2022; 26:2-18. [PMID: 35041532 PMCID: PMC8792495 DOI: 10.1089/omi.2021.0181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Hearing impairment (HI) is a silent planetary health crisis that requires attention worldwide. The prevalence of HI in South Africa is estimated as 5.5 in 100 live births, which is about 5 times higher than the prevalence in high-income countries. This also offers opportunity to drive progressive science, technology and innovation policy, and health systems. We present here a systematic analysis and review on the prevalence, etiologies, clinical patterns, and genetics/genomics of HI in South Africa. We searched PubMed, Scopus, African Journals Online, AFROLIB, and African Index Medicus to identify the pertinent studies on HI in South Africa, published from inception to April 30, 2021, and the data were summarized narratively. We screened 944 records, of which 27 studies were included in the review. The age at diagnosis is ∼3 years of age and the most common factor associated with acquired HI was middle ear infections. There were numerous reports on medication toxicity, with kanamycin-induced ototoxicity requiring specific attention when considering the high burden of tuberculosis in South Africa. The Waardenburg Syndrome is the most common reported syndromic HI. The Usher Syndrome is the only syndrome with genetic investigations, whereby a founder mutation was identified among black South Africans (MYO7A-c.6377delC). GJB2 and GJB6 genes are not major contributors to nonsyndromic HI among Black South Africans. Furthermore, emerging data using targeted panel sequencing have shown a low resolution rate in Black South Africans in known HI genes. Importantly, mutations in known nonsyndromic HI genes are infrequent in South Africa. Therefore, whole-exome sequencing appears as the most effective way forward to identify variants associated with HI in South Africa. Taken together, this article contributes to the emerging field of planetary health genomics with a focus on HI and offers new insights and lessons learned for future roadmaps on genomics/multiomics and clinical studies of HI around the world.
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Affiliation(s)
- Noluthando Manyisa
- Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Samuel Mawuli Adadey
- Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.,West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
| | - Edmond Wonkam-Tingang
- Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Abdoulaye Yalcouye
- Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.,Department of Neurology, Point G Teaching Hospital, University of Sciences, Techniques and Technology, Bamako, Mali
| | - Ambroise Wonkam
- Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
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Wonkam-Tingang E, Kengne Kamga K, Adadey SM, Nguefack S, De Kock C, Munung NS, Wonkam A. Knowledge and Challenges Associated With Hearing Impairment in Affected Individuals From Cameroon (Sub-Saharan Africa). FRONTIERS IN REHABILITATION SCIENCES 2021; 2:726761. [PMID: 36188771 PMCID: PMC9397862 DOI: 10.3389/fresc.2021.726761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 10/22/2021] [Indexed: 11/13/2022]
Abstract
Background: This study aimed to gain an understanding of the challenges faced by people with hearing impairment (HI) in Cameroon, their understanding of the causes of HI, and how challenges could be remedied to improve the quality of life of persons with HI. Methods: Semi-structured one-on-one in-depth interviews and observation of participant behaviour when answering questions were used to collect data from 10 HI professionals (healthcare workers and educationists), and 10 persons affected by HI (including caregivers). Results: The results show that the different groups associate the causes of HI to genetics, environmental factors, and a spiritual curse. There were reported cases of stigma and discrimination of persons with HI, with people sometimes referring to HI as an “intellectual disorder.” Interviewees also highlighted the difficulty persons with HI have in accessing education and healthcare services and suggested the need for the government and health researchers to develop strategies for the prevention and early diagnosis of HI. These strategies include (1) the awareness of the general population regarding HI, (2) the development of facilities for the proper management and new-born screening of HI, and (3) the implementation of a premarital screening to reduce the burden of HI of genetic origin. Conclusions: This study confirms the difficult social interaction and access to proper management faced by persons with HI in Cameroon and further highlights the need to educate populations on the causes of HI for a better acceptance of individuals with HI in the Cameroonian society.
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Affiliation(s)
- Edmond Wonkam-Tingang
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Karen Kengne Kamga
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Samuel Mawuli Adadey
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana
| | - Seraphin Nguefack
- Department of Paediatrics, University of Yaounde 1, Yaounde, Cameroon
| | - Carmen De Kock
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Nchangwi Syntia Munung
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Ambroise Wonkam
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- *Correspondence: Ambroise Wonkam
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Comprehensive functional network analysis and screening of deleterious pathogenic variants in non-syndromic hearing loss causative genes. Biosci Rep 2021; 41:230001. [PMID: 34714320 PMCID: PMC8559308 DOI: 10.1042/bsr20211865] [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: 08/05/2021] [Revised: 10/12/2021] [Accepted: 10/15/2021] [Indexed: 11/17/2022] Open
Abstract
Hearing loss (HL) is a significant public health problem and causes the most frequent congenital disability in developed societies. The genetic analysis of non-syndromic hearing loss (NSHL) may be considered as a complement to the existent plethora of diagnostic modalities available. The present study focuses on exploring more target genes with respective non-synonymous single nucleotide polymorphisms (nsSNPs) involved in the development of NSHL. The functional network analysis and variant study have successfully been carried out from the gene pool retrieved from reported research articles of the last decade. The analyses have been done through STRING. According to predicted biological processes, various variant analysis tools have successfully classified the NSHL causative genes and identified the deleterious nsSNPs, respectively. Among the predicted pathogenic nsSNPs with rsIDs rs80356586 (I515T), rs80356596 (L1011P), rs80356606 (P1987R) in OTOF have been reported in NSHL earlier. The rs121909642 (P722S), rs267606805 (P722H) in FGFR1, rs121918506 (E565A) and rs121918509 (A628T, A629T) in FGFR2 have not been reported in NSHL yet, which should be clinically experimented in NSHL. This also indicates this variant's novelty as its association in NSHL. The findings and the analyzed data have delivered some vibrant genetic pathogenesis of NSHL. These data might be used in the diagnostic and prognostic purposes in non-syndromic congenitally deaf children.
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Adadey SM, Wonkam-Tingang E, Aboagye ET, Quaye O, Awandare GA, Wonkam A. Hearing loss in Africa: current genetic profile. Hum Genet 2021; 141:505-517. [PMID: 34609590 PMCID: PMC9034983 DOI: 10.1007/s00439-021-02376-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 09/21/2021] [Indexed: 01/03/2023]
Abstract
Hearing impairment (HI) is highly heterogeneous with over 123 associated genes reported to date, mostly from studies among Europeans and Asians. Here, we performed a systematic review of literature on the genetic profile of HI in Africa. The study protocol was registered on PROSPERO, International Prospective Register of Systematic Reviews with the registration number “CRD42021240852”. Literature search was conducted on PubMed, Scopus, Africa-Wide Information, and Web of Science databases. A total of 89 full-text records was selected and retrieved for data extraction and analyses. We found reports from only 17/54 (31.5%) African countries. The majority (61/89; 68.5%) of articles were from North Africa, with few reports found from sub-Saharan Africa. The most common method used in these publications was targeted gene sequencing (n = 66/111; 59.5%), and only 13.5% (n = 15/111) used whole-exome sequencing. More than half of the studies were performed in families segregating HI (n = 51/89). GJB2 was the most investigated gene, with GJB2: p.(R143W) founder variant only reported in Ghana, while GJB2: c.35delG was common in North African countries. Variants in MYO15A were the second frequently reported in both North and Central Africa, followed by ATP6V1B1 only reported from North Africa. Usher syndrome was the main syndromic HI molecularly investigated, with variants in five genes reported: USH2A, USH1G, USH1C, MYO7A, and PCDH15. MYO7A: p.(P1780S) founder variant was reported as the common Usher syndrome variant among Black South Africans. This review provides the most comprehensive data on HI gene variants in the largely under-investigated African populations. Future exomes studies particularly in multiplex families will likely provide opportunities for the discovery of the next sets of novel HI genes, and well as unreported variants in known genes to further our understanding of HI pathobiology, globally.
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Affiliation(s)
- Samuel Mawuli Adadey
- Department of Biochemistry, Cell and Molecular Biology, West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, P.O. Box LG 54, Legon, Accra, Ghana.,Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Anzio Road, Observatory, Cape Town, 7925, South Africa
| | - Edmond Wonkam-Tingang
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Anzio Road, Observatory, Cape Town, 7925, South Africa
| | - Elvis Twumasi Aboagye
- Department of Biochemistry, Cell and Molecular Biology, West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, P.O. Box LG 54, Legon, Accra, Ghana
| | - Osbourne Quaye
- Department of Biochemistry, Cell and Molecular Biology, West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, P.O. Box LG 54, Legon, Accra, Ghana
| | - Gordon A Awandare
- Department of Biochemistry, Cell and Molecular Biology, West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, P.O. Box LG 54, Legon, Accra, Ghana
| | - Ambroise Wonkam
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Anzio Road, Observatory, Cape Town, 7925, South Africa.
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Cai L, Liu Y, Xu Y, Yang H, Lv L, Li Y, Chen Q, Lin X, Yang Y, Hu G, Zheng G, Zhou J, Qian Q, Xu MA, Fang J, Ding J, Chen W, Gao J. Multi-Center in-Depth Screening of Neonatal Deafness Genes: Zhejiang, China. Front Genet 2021; 12:637096. [PMID: 34276761 PMCID: PMC8282931 DOI: 10.3389/fgene.2021.637096] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 05/07/2021] [Indexed: 11/13/2022] Open
Abstract
Purpose The conventional genetic screening for deafness involves 9-20 variants from four genes. This study expands screening to analyze the mutation types and frequency of hereditary deafness genes in Zhejiang, China, and explore the significance of in-depth deafness genetic screening in newborns. Methods This was a multi-centre study conducted in 5,120 newborns from 12 major hospitals in the East-West (including mountains and islands) of Zhejiang Province. Concurrent hearing and genetic screening was performed. For genetic testing, 159 variants of 22 genes were screened, including CDH23, COL11A1, DFNA5, DFNB59, DSPP, GJB2, GJB3, KCNJ10, MT-RNR1, MT-TL1, MT-TS1, MYO15A, MYO7A, OTOF, PCDH15, SLC26A4, SOX10, TCOF1, TMC1, USH1G, WFS1, and WHRN using next-generation sequencing. Newborns who failed to have genetic mutations or hearing screening were diagnosed audiologically at the age of 6 months. Results A total of 4,893 newborns (95.57%) have passed the initial hearing screening, and 7 (0.14%) have failed in repeated screening. Of these, 446 (8.71%) newborns carried at least one genetic deafness-associated variant. High-risk pathogenic variants were found in 11 newborns (0.21%) (nine homozygotes and two compound heterozygotes), and eight of these infants have passed the hearing screening. The frequency of mutations in GJB2, GJB3, SLC26A4, 12SrRNA, and TMC1 was 5.43%, 0.59%, 1.91%, 0.98%, and 0.02%, respectively. The positive rate of in-depth screening was significantly increased when compared with 20 variants in four genes of traditional testing, wherein GJB2 was increased by 97.2%, SLC26A4 by 21% and MT-RNR1 by 150%. The most common mutation variants were GJB2c.235delC and SLC26A4c.919-2A > G, followed by GJB2c.299_300delAT. Homoplasmic mutation in MT-RNR1 was the most common, including m.1555A > G, m.961T > C, m.1095T > C. All these infants have passed routine hearing screening. The positive rate of MT-RNR1 mutation was significantly higher in newborns with high-risk factors of maternal pregnancy. Conclusion The positive rate of deafness gene mutations in the Zhejiang region is higher than that of the database, mainly in GJB2c.235delC, SLC26A4 c.919-2A > G, and m.1555A > G variants. The expanded genetic screening in the detection rate of diseasecausing variants was significantly improved. It is helpful in identifying high-risk children for follow-up intervention.
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Affiliation(s)
- Luhang Cai
- Department of Otorhinolaryngology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Ya Liu
- Department of Otorhinolaryngology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yaping Xu
- Department of Otorhinolaryngology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Hang Yang
- Department of Otorhinolaryngology, Jiangshan People's Hospital, Quzhou, China
| | - Lihui Lv
- Department of Otorhinolaryngology, Fenghua People's Hospital, Ningbo, China
| | - Yang Li
- Department of Obstetrics, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Qiongqiong Chen
- Department of Otorhinolaryngology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiaojiang Lin
- Department of Otorhinolaryngology, Kaihua People's Hospital, Quzhou, China
| | - Yihui Yang
- Department of Otorhinolaryngology, Ningbo Women and Children's Hospital, Ningbo, China
| | - Guangwei Hu
- Department of Otorhinolaryngology, Zhoushan Hospital, Zhoushan, China
| | - Guofeng Zheng
- Department of Otorhinolaryngology, Shaoxing Second Hospital, Shaoxing, China
| | - Jing Zhou
- Department of Otorhinolaryngology, Ruian People's Hospital, Wenzhou, China
| | - Qiyong Qian
- Department of Otorhinolaryngology, Shengzhou People's Hospital, Shaoxing, China
| | - Mei-Ai Xu
- Department of Otorhinolaryngology, Sanmen People's Hospital, Taizhou, China
| | - Jin Fang
- Department of Otorhinolaryngology, Zhejiang Xin'an International Hospital, Jiaxing, China
| | - Jianjun Ding
- Department of Otorhinolaryngology, Linhai First People's Hospital, Taizhou, China
| | - Wei Chen
- Department of Otorhinolaryngology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jiong Gao
- Beijing Genomics Institute, Shenzhen, China
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Wonkam-Tingang E, Schrauwen I, Esoh KK, Bharadwaj T, Nouel-Saied LM, Acharya A, Nasir A, Leal SM, Wonkam A. A novel variant in DMXL2 gene is associated with autosomal dominant non-syndromic hearing impairment (DFNA71) in a Cameroonian family. Exp Biol Med (Maywood) 2021; 246:1524-1532. [PMID: 33715530 DOI: 10.1177/1535370221999746] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Approximately half of congenital hearing impairment cases are inherited, with non-syndromic hearing impairment (NSHI) being the most frequent clinical entity of genetic hearing impairment cases. A family from Cameroon with NSHI was investigated by performing exome sequencing using DNA samples obtained from three family members, followed by direct Sanger sequencing in additional family members and controls participants. We identified an autosomal dominantly inherited novel missense variant [NM_001174116.2:c.918G>T; p.(Q306H)] in DMXL2 gene (MIM:612186) that co-segregates with mild to profound non-syndromic sensorineural hearing impairment . The p.(Q306H) variant which substitutes a highly conserved glutamine residue is predicted deleterious by various bioinformatics tools and is absent from several genome databases. This variant was also neither found in 121 apparently healthy controls without a family history of hearing impairment , nor 112 sporadic NSHI cases from Cameroon. There is one previous report of a large Han Chinese NSHI family that segregates a missense variant in DMXL2. The present study provides additional evidence that DMXL2 is involved in hearing impairment etiology, and we suggest DMXL2 should be considered in diagnostic hearing impairment panels.
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Affiliation(s)
- Edmond Wonkam-Tingang
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Isabelle Schrauwen
- Center for Statistical Genetics, Sergievsky Center, Taub Institute for Alzheimer's Disease and the Aging Brain, and the Department of Neurology, Columbia University Medical Centre, New York, NY 10032, USA
| | - Kevin K Esoh
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Thashi Bharadwaj
- Center for Statistical Genetics, Sergievsky Center, Taub Institute for Alzheimer's Disease and the Aging Brain, and the Department of Neurology, Columbia University Medical Centre, New York, NY 10032, USA
| | - Liz M Nouel-Saied
- Center for Statistical Genetics, Sergievsky Center, Taub Institute for Alzheimer's Disease and the Aging Brain, and the Department of Neurology, Columbia University Medical Centre, New York, NY 10032, USA
| | - Anushree Acharya
- Center for Statistical Genetics, Sergievsky Center, Taub Institute for Alzheimer's Disease and the Aging Brain, and the Department of Neurology, Columbia University Medical Centre, New York, NY 10032, USA
| | - Abdul Nasir
- Synthetic Protein Engineering Lab (SPEL), Department of Molecular Science and Technology, Ajou University, Suwon 443-749, Korea
| | - Suzanne M Leal
- Center for Statistical Genetics, Sergievsky Center, Taub Institute for Alzheimer's Disease and the Aging Brain, and the Department of Neurology, Columbia University Medical Centre, New York, NY 10032, USA
| | - Ambroise Wonkam
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
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Wonkam A, Lebeko K, Mowla S, Noubiap JJ, Chong M, Pare G. Whole exome sequencing reveals a biallelic frameshift mutation in GRXCR2 in hearing impairment in Cameroon. Mol Genet Genomic Med 2021; 9:e1609. [PMID: 33528103 PMCID: PMC8104159 DOI: 10.1002/mgg3.1609] [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: 11/11/2020] [Revised: 01/06/2021] [Accepted: 01/11/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Hearing impairment (HI) genes are poorly studied in African populations. METHODS We used whole exome sequencing (WES) to investigate pathogenic and likely pathogenic (PLP) variants in 10 individuals with HI, from four multiplex families from Cameroon, two of which were previously unresolved with a targeted gene enrichment (TGE) panel of 116 genes. In silico protein modelling, western blotting and live imaging of transfected HEK293 cells were performed to study protein structure and functions. RESULTS All PLP variants previously identified with TGE were replicated. In one previously unresolved family, we found a homozygous frameshift PLP variant in GRXCR2 (OMIM: 615762), NM_001080516.1(GRXCR2):c.251delC p.(Ile85SerfsTer33), in two affected siblings; and additionally, in 1/80 unrelated individuals affected with non-syndromic hearing impairment (NSHI). The GRXCR2-c.251delC variant introduced a premature stop codon, leading to truncation and loss of a zinc-finger domain. Fluorescence confocal microscopy tracked the wild-type GRXCR2 protein to the cellular membrane, unlike the mutated GRXCR2 protein. CONCLUSION This study confirms GRXCR2 as a HI-associated gene. GRXCR2 should be included to the currently available TGE panels for HI diagnosis.
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Affiliation(s)
- Ambroise Wonkam
- Department of Medicine, Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.,Institute of Infectious Diseases and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Kamogelo Lebeko
- Department of Medicine, Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Shaheen Mowla
- Department of Pathology, Division of Haematology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Jean Jacques Noubiap
- Centre for Heart Rhythm Disorders, South Australian Health and Medical Research Institute (SAHMRI, University of Adelaide and Royal Adelaide Hospital, Adelaide, Australia
| | - Mike Chong
- Population Health Research Institute, Hamilton Health Sciences and McMaster University, Hamilton, ON, Canada
| | - Guillaume Pare
- Population Health Research Institute, Hamilton Health Sciences and McMaster University, Hamilton, ON, Canada
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11
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Oluwole OG, Esoh KK, Wonkam-Tingang E, Manyisa N, Noubiap JJ, Chimusa ER, Wonkam A. Whole exome sequencing identifies rare coding variants in novel human-mouse ortholog genes in African individuals diagnosed with non-syndromic hearing impairment. Exp Biol Med (Maywood) 2021; 246:197-206. [PMID: 32996353 PMCID: PMC7871117 DOI: 10.1177/1535370220960388] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 08/28/2020] [Indexed: 01/08/2023] Open
Abstract
Physiologically, the human and murine hearing systems are very similar, justifying the extensive use of mice in experimental models for hearing impairment (HI). About 340 murine HI genes have been reported; however, whether variants in all human-mouse ortholog genes contribute to HI has been rarely investigated. In humans, nearly 120 HI genes have been identified to date, with GJB2 and GJB6 variants accounting for half of congenital HI cases, of genetic origin, in populations of European and Asian ancestries, but not in most African populations. The contribution of variants in other known genes of HI among the populations of African ancestry is poorly studied and displays the lowest pick-up rate. We used whole exome sequencing (WES) to investigate pathogenic and likely pathogenic (PLP) variants in 34 novel human-mouse orthologs HI genes, in 40 individuals from Cameroon and South Africa diagnosed with non-syndromic hearing impairment (NSHI), and compared the data to WES data of 129 ethnically matched controls. In addition, protein modeling for selected PLP gene variants, gene enrichment, and network analyses were performed. A total of 4/38 murine genes, d6wsu163e, zfp719, grp152 and minar2, had no human orthologs. WES identified three rare PLP variants in 3/34 human-mouse orthologs genes in three unrelated Cameroonian patients, namely: OCM2, c.227G>C p.(Arg76Thr) and LRGI1, c.1657G>A p.(Gly533Arg) in a heterozygous state, and a PLP variant MCPH1, c.2311C>G p.(Pro771Ala) in a homozygous state. In silico functional analyses suggest that these human-mouse ortholog genes functionally co-expressed interactions with well-established HI genes: GJB2 and GJB6. The study found one homozygous variant in MCPH1, likely to explain HI in one patient, and suggests that human-mouse ortholog variants could contribute to the understanding of the physiology of hearing in humans.
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Affiliation(s)
- Oluwafemi G Oluwole
- Division of Human Genetics, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town 7935, South Africa
| | - Kevin K Esoh
- Division of Human Genetics, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town 7935, South Africa
| | - Edmond Wonkam-Tingang
- Division of Human Genetics, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town 7935, South Africa
| | - Noluthando Manyisa
- Division of Human Genetics, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town 7935, South Africa
| | - Jean Jacques Noubiap
- Centre for Heart Rhythm Disorders, South Australian Health and Medical Research Institute (SAHMRI), University of Adelaide and Royal Adelaide Hospital, Adelaide 5000, Australia
| | - Emile R Chimusa
- Division of Human Genetics, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town 7935, South Africa
| | - Ambroise Wonkam
- Division of Human Genetics, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town 7935, South Africa
- Department of Medicine, University of Cape Town, Cape Town 7925, South Africa
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12
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Adadey SM, Wonkam-Tingang E, Twumasi Aboagye E, Nayo-Gyan DW, Boatemaa Ansong M, Quaye O, Awandare GA, Wonkam A. Connexin Genes Variants Associated with Non-Syndromic Hearing Impairment: A Systematic Review of the Global Burden. Life (Basel) 2020; 10:life10110258. [PMID: 33126609 PMCID: PMC7693846 DOI: 10.3390/life10110258] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 10/18/2020] [Accepted: 10/27/2020] [Indexed: 12/21/2022] Open
Abstract
Mutations in connexins are the most common causes of hearing impairment (HI) in many populations. Our aim was to review the global burden of pathogenic and likely pathogenic (PLP) variants in connexin genes associated with HI. We conducted a systematic review of the literature based on targeted inclusion/exclusion criteria of publications from 1997 to 2020. The databases used were PubMed, Scopus, Africa-Wide Information, and Web of Science. The protocol was registered on PROSPERO, the International Prospective Register of Systematic Reviews, with the registration number “CRD42020169697”. The data extracted were analyzed using Microsoft Excel and SPSS version 25 (IBM, Armonk, New York, United States). A total of 571 independent studies were retrieved and considered for data extraction with the majority of studies (47.8% (n = 289)) done in Asia. Targeted sequencing was found to be the most common technique used in investigating connexin gene mutations. We identified seven connexin genes that were associated with HI, and GJB2 (520/571 publications) was the most studied among the seven. Excluding PLP in GJB2, GJB6, and GJA1 the other connexin gene variants (thus GJB3, GJB4, GJC3, and GJC1 variants) had conflicting association with HI. Biallelic GJB2 PLP variants were the most common and widespread variants associated with non-syndromic hearing impairment (NSHI) in different global populations but absent in most African populations. The most common GJB2 alleles found to be predominant in specific populations include; p.Gly12ValfsTer2 in Europeans, North Africans, Brazilians, and Americans; p.V37I and p.L79Cfs in Asians; p.W24X in Indians; p.L56Rfs in Americans; and the founder mutation p.R143W in Africans from Ghana, or with putative Ghanaian ancestry. The present review suggests that only GJB2 and GJB3 are recognized and validated HI genes. The findings call for an extensive investigation of the other connexin genes in many populations to elucidate their contributions to HI, in order to improve gene-disease pair curations, globally.
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Affiliation(s)
- Samuel Mawuli Adadey
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, P.O. Box LG 54, Legon GA184, Accra, Greater Accra Region, Ghana; (S.M.A.); (O.Q.); (G.A.A.)
- Department of Biochemistry, Cell and Molecular Biology, University of Ghana, P.O. Box LG 54, Legon Accra GA184, Greater Accra Region, Ghana; (E.T.A.); (M.B.A.)
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Anzio Road, Observatory, Cape Town 7925, South Africa;
| | - Edmond Wonkam-Tingang
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Anzio Road, Observatory, Cape Town 7925, South Africa;
| | - Elvis Twumasi Aboagye
- Department of Biochemistry, Cell and Molecular Biology, University of Ghana, P.O. Box LG 54, Legon Accra GA184, Greater Accra Region, Ghana; (E.T.A.); (M.B.A.)
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Anzio Road, Observatory, Cape Town 7925, South Africa;
| | - Daniel Wonder Nayo-Gyan
- Department of Applied Chemistry and Biochemistry, C. K. Tedam University of Technology and Applied Sciences, P.O. Box 24, Navrongo 00000, Upper East Region, Ghana;
| | - Maame Boatemaa Ansong
- Department of Biochemistry, Cell and Molecular Biology, University of Ghana, P.O. Box LG 54, Legon Accra GA184, Greater Accra Region, Ghana; (E.T.A.); (M.B.A.)
| | - Osbourne Quaye
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, P.O. Box LG 54, Legon GA184, Accra, Greater Accra Region, Ghana; (S.M.A.); (O.Q.); (G.A.A.)
- Department of Biochemistry, Cell and Molecular Biology, University of Ghana, P.O. Box LG 54, Legon Accra GA184, Greater Accra Region, Ghana; (E.T.A.); (M.B.A.)
| | - Gordon A. Awandare
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, P.O. Box LG 54, Legon GA184, Accra, Greater Accra Region, Ghana; (S.M.A.); (O.Q.); (G.A.A.)
- Department of Biochemistry, Cell and Molecular Biology, University of Ghana, P.O. Box LG 54, Legon Accra GA184, Greater Accra Region, Ghana; (E.T.A.); (M.B.A.)
| | - Ambroise Wonkam
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Anzio Road, Observatory, Cape Town 7925, South Africa;
- Correspondence: ; Tel.: +27-21-4066307
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13
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Wonkam-Tingang E, Schrauwen I, Esoh KK, Bharadwaj T, Nouel-Saied LM, Acharya A, Nasir A, Adadey SM, Mowla S, Leal SM, Wonkam A. Bi-Allelic Novel Variants in CLIC5 Identified in a Cameroonian Multiplex Family with Non-Syndromic Hearing Impairment. Genes (Basel) 2020; 11:genes11111249. [PMID: 33114113 PMCID: PMC7690789 DOI: 10.3390/genes11111249] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 10/20/2020] [Accepted: 10/20/2020] [Indexed: 11/16/2022] Open
Abstract
DNA samples from five members of a multiplex non-consanguineous Cameroonian family, segregating prelingual and progressive autosomal recessive non-syndromic sensorineural hearing impairment, underwent whole exome sequencing. We identified novel bi-allelic compound heterozygous pathogenic variants in CLIC5. The variants identified, i.e., the missense [NM_016929.5:c.224T>C; p.(L75P)] and the splicing (NM_016929.5:c.63+1G>A), were validated using Sanger sequencing in all seven available family members and co-segregated with hearing impairment (HI) in the three hearing impaired family members. The three affected individuals were compound heterozygous for both variants, and all unaffected individuals were heterozygous for one of the two variants. Both variants were absent from the genome aggregation database (gnomAD), the Single Nucleotide Polymorphism Database (dbSNP), and the UK10K and Greater Middle East (GME) databases, as well as from 122 apparently healthy controls from Cameroon. We also did not identify these pathogenic variants in 118 unrelated sporadic cases of non-syndromic hearing impairment (NSHI) from Cameroon. In silico analysis showed that the missense variant CLIC5-p.(L75P) substitutes a highly conserved amino acid residue (leucine), and is expected to alter the stability, the structure, and the function of the CLIC5 protein, while the splicing variant CLIC5-(c.63+1G>A) is predicted to disrupt a consensus donor splice site and alter the splicing of the pre-mRNA. This study is the second report, worldwide, to describe CLIC5 involvement in human hearing impairment, and thus confirms CLIC5 as a novel non-syndromic hearing impairment gene that should be included in targeted diagnostic gene panels.
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Affiliation(s)
- Edmond Wonkam-Tingang
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa; (E.W.-T.); (K.K.E.); (S.M.A.)
| | - Isabelle Schrauwen
- Center for Statistical Genetics, Sergievsky Center, Taub Institute for Alzheimer’s Disease and the Aging Brain, and the Department of Neurology, Columbia University Medical Centre, New York, NY 10032, USA; (I.S.); (T.B.); (L.M.N.-S.); (A.A.); (S.M.L.)
| | - Kevin K. Esoh
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa; (E.W.-T.); (K.K.E.); (S.M.A.)
| | - Thashi Bharadwaj
- Center for Statistical Genetics, Sergievsky Center, Taub Institute for Alzheimer’s Disease and the Aging Brain, and the Department of Neurology, Columbia University Medical Centre, New York, NY 10032, USA; (I.S.); (T.B.); (L.M.N.-S.); (A.A.); (S.M.L.)
| | - Liz M. Nouel-Saied
- Center for Statistical Genetics, Sergievsky Center, Taub Institute for Alzheimer’s Disease and the Aging Brain, and the Department of Neurology, Columbia University Medical Centre, New York, NY 10032, USA; (I.S.); (T.B.); (L.M.N.-S.); (A.A.); (S.M.L.)
| | - Anushree Acharya
- Center for Statistical Genetics, Sergievsky Center, Taub Institute for Alzheimer’s Disease and the Aging Brain, and the Department of Neurology, Columbia University Medical Centre, New York, NY 10032, USA; (I.S.); (T.B.); (L.M.N.-S.); (A.A.); (S.M.L.)
| | - Abdul Nasir
- Synthetic Protein Engineering Lab (SPEL), Department of Molecular Science and Technology, Ajou University, Suwon 443-749, Korea;
| | - Samuel M. Adadey
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa; (E.W.-T.); (K.K.E.); (S.M.A.)
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra LG 54, Ghana
| | - Shaheen Mowla
- Division of Haematology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa;
| | - Suzanne M. Leal
- Center for Statistical Genetics, Sergievsky Center, Taub Institute for Alzheimer’s Disease and the Aging Brain, and the Department of Neurology, Columbia University Medical Centre, New York, NY 10032, USA; (I.S.); (T.B.); (L.M.N.-S.); (A.A.); (S.M.L.)
| | - Ambroise Wonkam
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa; (E.W.-T.); (K.K.E.); (S.M.A.)
- Correspondence: ; Tel.: +27-21-4066-307
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14
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Wonkam A, Manyisa N, Bope CD, Dandara C, Chimusa ER. Whole exome sequencing reveals pathogenic variants in MYO3A, MYO15A and COL9A3 and differential frequencies in ancestral alleles in hearing impairment genes among individuals from Cameroon. Hum Mol Genet 2020; 29:3729-3743. [PMID: 33078831 PMCID: PMC7861016 DOI: 10.1093/hmg/ddaa225] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 10/01/2020] [Accepted: 10/12/2020] [Indexed: 12/30/2022] Open
Abstract
There is scarcity of known gene variants of hearing impairment (HI) in African populations. This knowledge deficit is ultimately affecting the development of genetic diagnoses. We used whole exome sequencing to investigate gene variants, pathways of interactive genes and the fractions of ancestral overderived alleles for 159 HI genes among 18 Cameroonian patients with non-syndromic HI (NSHI) and 129 ethnically matched controls. Pathogenic and likely pathogenic (PLP) variants were found in MYO3A, MYO15A and COL9A3, with a resolution rate of 50% (9/18 patients). The study identified significant genetic differentiation in novel population-specific gene variants at FOXD4L2, DHRS2L6, RPL3L and VTN between HI patients and controls. These gene variants are found in functional/co-expressed interactive networks with other known HI-associated genes and in the same pathways with VTN being a hub protein, that is, focal adhesion pathway and regulation of the actin cytoskeleton (P-values <0.05). The results suggest that these novel population-specific gene variants are possible modifiers of the HI phenotypes. We found a high proportion of ancestral allele versus derived at low HI patients-specific minor allele frequency in the range of 0.0–0.1. The results showed a relatively low pickup rate of PLP variants in known genes in this group of Cameroonian patients with NSHI. In addition, findings may signal an evolutionary enrichment of some variants of HI genes in patients, as the result of polygenic adaptation, and suggest the possibility of multigenic influence on the phenotype of congenital HI, which deserves further investigations.
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Affiliation(s)
- Ambroise Wonkam
- Division of Human Genetics, Department of Pathology, University of Cape Town, Cape Town 7925, South Africa.,Department of Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Noluthando Manyisa
- Division of Human Genetics, Department of Pathology, University of Cape Town, Cape Town 7925, South Africa
| | - Christian D Bope
- Department of Mathematics and Department of Computer Science, Faculty of Sciences, University of Kinshasa, Kinshasa, Democratic Republic of Congo
| | - Collet Dandara
- Division of Human Genetics, Department of Pathology, University of Cape Town, Cape Town 7925, South Africa
| | - Emile R Chimusa
- Division of Human Genetics, Department of Pathology, University of Cape Town, Cape Town 7925, South Africa
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Adadey SM, Esoh KK, Quaye O, Amedofu GK, Awandare GA, Wonkam A. GJB4 and GJC3 variants in non-syndromic hearing impairment in Ghana. Exp Biol Med (Maywood) 2020; 245:1355-1367. [PMID: 32524838 PMCID: PMC7441344 DOI: 10.1177/1535370220931035] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 05/11/2020] [Indexed: 12/13/2022] Open
Abstract
IMPACT STATEMENT Although connexins are known to be the major genetic factors associated with HI, only a few studies have investigated GJB4 and GJC3 variants among hearing-impaired patients. This study is the first to report GJB4 and GJC3 variants from an African HI cohort. We have demonstrated that GJB4 and GJC3 genes may not contribute significantly to HI in Ghana, hence these genes should not be considered for routine clinical screening in Ghana. However, it is important to study a larger population to determine the association of GJB4 and GJC3 variants with HI.
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Affiliation(s)
- Samuel M Adadey
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra LG 54, Ghana
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
| | | | - Osbourne Quaye
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra LG 54, Ghana
| | | | - Gordon A Awandare
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra LG 54, Ghana
| | - Ambroise Wonkam
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
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Abstract
The incidence of hearing impairment (HI) is higher in low- and middle-income countries when compared to high-income countries. There is therefore a necessity to estimate the burden of this condition in developing world. The aim of our study was to use a systematic approach to provide summarized data on the prevalence, etiologies, clinical patterns and genetics of HI in Cameroon. We searched PubMed, Scopus, African Journals Online, AFROLIB and African Index Medicus to identify relevant studies on HI in Cameroon, published from inception to 31 October, 2019, with no language restrictions. Reference lists of included studies were also scrutinized, and data were summarized narratively. This study is registered with PROSPERO, number CRD42019142788. We screened 333 records, of which 17 studies were finally included in the review. The prevalence of HI in Cameroon ranges from 0.9% to 3.6% in population-based studies and increases with age. Environmental factors contribute to 52.6% to 62.2% of HI cases, with meningitis, impacted wax and age-related disorder being the most common ones. Hereditary HI comprises 0.8% to 14.8% of all cases. In 32.6% to 37% of HI cases, the origin remains unknown. Non-syndromic hearing impairment (NSHI) is the most frequent clinical entity and accounts for 86.1% to 92.5% of cases of HI of genetic origin. Waardenburg and Usher syndromes account for 50% to 57.14% and 8.9% to 42.9% of genetic syndromic cases, respectively. No pathogenic mutation was described in GJB6 gene, and the prevalence of pathogenic mutations in GJB2 gene ranged from 0% to 0.5%. The prevalence of pathogenic mutations in other known NSHI genes was <10% in Cameroonian probands. Environmental factors are the leading etiology of HI in Cameroon, and mutations in most important HI genes are infrequent in Cameroon. Whole genome sequencing therefore appears as the most effective way to identify variants associated with HI in Cameroon and sub-Saharan Africa in general.
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17
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Wonkam Tingang E, Noubiap JJ, F. Fokouo JV, Oluwole OG, Nguefack S, Chimusa ER, Wonkam A. Hearing Impairment Overview in Africa: the Case of Cameroon. Genes (Basel) 2020; 11:genes11020233. [PMID: 32098311 PMCID: PMC7073999 DOI: 10.3390/genes11020233] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Revised: 02/15/2020] [Accepted: 02/19/2020] [Indexed: 01/27/2023] Open
Abstract
The incidence of hearing impairment (HI) is higher in low- and middle-income countries when compared to high-income countries. There is therefore a necessity to estimate the burden of this condition in developing world. The aim of our study was to use a systematic approach to provide summarized data on the prevalence, etiologies, clinical patterns and genetics of HI in Cameroon. We searched PubMed, Scopus, African Journals Online, AFROLIB and African Index Medicus to identify relevant studies on HI in Cameroon, published from inception to 31 October, 2019, with no language restrictions. Reference lists of included studies were also scrutinized, and data were summarized narratively. This study is registered with PROSPERO, number CRD42019142788. We screened 333 records, of which 17 studies were finally included in the review. The prevalence of HI in Cameroon ranges from 0.9% to 3.6% in population-based studies and increases with age. Environmental factors contribute to 52.6% to 62.2% of HI cases, with meningitis, impacted wax and age-related disorder being the most common ones. Hereditary HI comprises 0.8% to 14.8% of all cases. In 32.6% to 37% of HI cases, the origin remains unknown. Non-syndromic hearing impairment (NSHI) is the most frequent clinical entity and accounts for 86.1% to 92.5% of cases of HI of genetic origin. Waardenburg and Usher syndromes account for 50% to 57.14% and 8.9% to 42.9% of genetic syndromic cases, respectively. No pathogenic mutation was described in GJB6 gene, and the prevalence of pathogenic mutations in GJB2 gene ranged from 0% to 0.5%. The prevalence of pathogenic mutations in other known NSHI genes was <10% in Cameroonian probands. Environmental factors are the leading etiology of HI in Cameroon, and mutations in most important HI genes are infrequent in Cameroon. Whole genome sequencing therefore appears as the most effective way to identify variants associated with HI in Cameroon and sub-Saharan Africa in general.
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Affiliation(s)
- Edmond Wonkam Tingang
- Division of Human Genetics, Department of Pathology, University of Cape Town, Cape Town 7925, South Africa; (E.W.T.); (O.G.O.); (E.R.C.)
| | - Jean Jacques Noubiap
- Centre for Heart Rhythm Disorders, South Australian Health and Medical Research Institute (SAHMRI), University of Adelaide and Royal Adelaide Hospital, Adelaide 5000, Australia;
| | | | - Oluwafemi Gabriel Oluwole
- Division of Human Genetics, Department of Pathology, University of Cape Town, Cape Town 7925, South Africa; (E.W.T.); (O.G.O.); (E.R.C.)
| | - Séraphin Nguefack
- Department of Paediatrics, Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, Yaoundé 1364, Cameroon;
- Paediatrics unit, Gynaeco-Obstetric and Paediatric Hospital, Yaoundé 4362, Cameroon
| | - Emile R. Chimusa
- Division of Human Genetics, Department of Pathology, University of Cape Town, Cape Town 7925, South Africa; (E.W.T.); (O.G.O.); (E.R.C.)
| | - Ambroise Wonkam
- Division of Human Genetics, Department of Pathology, University of Cape Town, Cape Town 7925, South Africa; (E.W.T.); (O.G.O.); (E.R.C.)
- Department of Medicine, University of Cape Town, Cape Town 7925, South Africa
- Correspondence: ; Tel.: +27-21-4066-307
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