1
|
Toure M, Amalou G, Raise IA, Mobio NMA, Malki A, Barakat A. First report of an Ivorian family with nonsyndromic hearing loss caused by GJB2 compound heterozygous variants. Ann Hum Genet 2024. [PMID: 39092543 DOI: 10.1111/ahg.12574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 07/19/2024] [Accepted: 07/24/2024] [Indexed: 08/04/2024]
Abstract
The primary etiology of congenital hearing loss is attributed to genetic factors, with GJB2 identified as a pivotal gene across diverse ethnic groups. Additionally, nonsyndromic hearing loss is predominantly inherited in an autosomal recessive manner. We used Sanger sequencing to analyze GJB2 in 17 deaf children from 13 unrelated Ivory Coast families. One family had two children born with severe congenital deafness and exhibited pathogenic compound heterozygous variants. These variants included a nonsense substitution (c.132G > A or p.Trp44Ter) and a newly discovered duplication of 7 base pairs (c.205_211dupTTCCCCA or p.Ser72ProfsTer32). Segregation testing confirmed these variants, marking the first identification of GJB2 in an Ivorian family with congenital hearing loss.
Collapse
Affiliation(s)
- Madoussou Toure
- Genomics and Human Genetics Laboratory, Institut Pasteur du Maroc, Casablanca, Morocco
- Ben M'Sik Faculty of science, Hassan II University of Casablanca, Casablanca, Morocco
| | - Ghita Amalou
- Genomics and Human Genetics Laboratory, Institut Pasteur du Maroc, Casablanca, Morocco
| | - Imane Ait Raise
- Genomics and Human Genetics Laboratory, Institut Pasteur du Maroc, Casablanca, Morocco
| | - N'kan Max Ange Mobio
- ENT department at the University Hospital Medical Center of Treichville, Abidjan, Ivory Coast
| | - Abderrahim Malki
- Ben M'Sik Faculty of science, Hassan II University of Casablanca, Casablanca, Morocco
| | - Abdelhamid Barakat
- Genomics and Human Genetics Laboratory, Institut Pasteur du Maroc, Casablanca, Morocco
| |
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
3
|
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: 7] [Impact Index Per Article: 3.5] [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.
Collapse
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
| |
Collapse
|
4
|
Sharma N, Kumari D, Panigrahi I, Khetarpal P. A systematic review of the monogenic causes of Non-Syndromic Hearing Loss (NSHL) and discussion of Current Diagnosis and Treatment options. Clin Genet 2023; 103:16-34. [PMID: 36089522 DOI: 10.1111/cge.14228] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 09/02/2022] [Accepted: 09/06/2022] [Indexed: 12/13/2022]
Abstract
Hearing impairment is one of the most widespread inheritable sensory disorder affecting at least 1 in every 1000 born. About two-third of hereditary hearing loss (HHL) disorders are non-syndromic. To provide comprehensive update of monogenic causes of non-syndromic hearing loss (NSHL), literature search has been carried out with appropriate keywords in the following databases-PubMed, Google Scholar, Cochrane library, and Science Direct. Out of 2214 papers, 271 papers were shortlisted after applying inclusion and exclusion criterion. Data extracted from selected papers include information about gene name, identified pathogenic variants, ethnicity of the patient, age of onset, gender, title, authors' name, and year of publication. Overall, pathogenic variants in 98 different genes have been associated with NSHL. These genes have important role to play during early embryonic development in ear structure formation and hearing development. Here, we also review briefly the recent information about diagnosis and treatment approaches. Understanding pathogenic genetic variants are helpful in the management of affected and may offer targeted therapies in future.
Collapse
Affiliation(s)
- Nandita Sharma
- Department of Human Genetics and Molecular Medicine, School of Health Sciences, Central University of Punjab, Bathinda, India
| | - Divya Kumari
- Department of Pediatrics Medicine, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Inusha Panigrahi
- Department of Pediatrics Medicine, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Preeti Khetarpal
- Department of Human Genetics and Molecular Medicine, School of Health Sciences, Central University of Punjab, Bathinda, India
| |
Collapse
|
5
|
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: 6] [Impact Index Per Article: 2.0] [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.
Collapse
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
| |
Collapse
|
6
|
Agent-Based Modeling of Autosomal Recessive Deafness 1A (DFNB1A) Prevalence with Regard to Intensity of Selection Pressure in Isolated Human Population. BIOLOGY 2022; 11:biology11020257. [PMID: 35205123 PMCID: PMC8869167 DOI: 10.3390/biology11020257] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/28/2022] [Accepted: 02/03/2022] [Indexed: 01/09/2023]
Abstract
An increase in the prevalence of autosomal recessive deafness 1A (DFNB1A) in populations of European descent was shown to be promoted by assortative marriages among deaf people. Assortative marriages became possible with the widespread introduction of sign language, resulting in increased genetic fitness of deaf individuals and, thereby, relaxing selection against deafness. However, the effect of this phenomenon was not previously studied in populations with different genetic structures. We developed an agent-based computer model for the analysis of the spread of DFNB1A. Using this model, we tested the impact of different intensities of selection pressure against deafness in an isolated human population over 400 years. Modeling of the "purifying" selection pressure on deafness ("No deaf mating" scenario) resulted in a decrease in the proportion of deaf individuals and the pathogenic allele frequency. Modeling of the "relaxed" selection ("Assortative mating" scenario) resulted in an increase in the proportion of deaf individuals in the first four generations, which then quickly plateaued with a subsequent decline and a decrease in the pathogenic allele frequency. The results of neutral selection pressure modeling ("Random mating" scenario) showed no significant changes in the proportion of deaf individuals or the pathogenic allele frequency after 400 years.
Collapse
|
7
|
Arias S, Paradisi I, Hernández A, Kanzler D. Undescribed GJB2 c.35dupG homozygous prelingual distinguished from c.35delG homozygous/compound heterozygous deafs, dwelling a German ancestry Venezuelan isolate. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2021. [DOI: 10.1186/s43042-021-00159-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Among ten hearing-impaired (HI) families mostly of German descent dwelling the Venezuelan isolate Colonia Tovar, which were initially studied several decades ago to assess the etiology of their profound/prelingual nonsyndromic deafness phenotype, an undescribed genotype/phenotype was found. Forty-eight subjects, including 8 of the still living 143 originally searched with audiograms 4 decades ago, were retested and their DNA collected. A genomic search of 27 loci involved in HI was performed on a randomly chosen prelingual deaf patient. Subsequently, GJB2 sequencing was performed in all subjects from each pedigree. Haplotypes were constructed with five intragenic GJB2 SNPs (rs117685390, rs7994748, rs2274084, rs2274083, and rs3751385). Audiograms performed along 5 decades were compared to evaluate age-related hearing loss in the different genotypes found in the population.
Results
Three prelingual deaf siblings, having the highest recorded symmetrical hearing loss of all the known affected in the isolate, carried the very rare mutation c.35dupG (p.V13Cfs*35) at GJB2 in a homozygous condition. Two additional GJB2 mutations were identified (p.W77R and c.35delG) in the isolate. Allelic disequilibrium in both c.35dupG and p.W77R carriers (with in-phase haplotype T;T;G;A;C) were found, although not so in the 2 other found c.35delG independent haplotypes. A compound heterozygote in trans (c.35delG/c.35dupG) was audiometrically distinguishable from both the c.35dupG and c.35delG homozygotes.
Conclusions
A relatively higher frequency of mutation of c.35dupG found than elsewhere was retrospectively inferred for the ancient population of the Kaiserstuhl region in Germany, having an opposite epidemiological situation to the one found with the contiguous and very frequent c.35delG. Haplotype analysis suggests founder phenomena and independent occurrence, hundreds of generations back in Caucasoid populations for both mutations.
Collapse
|
8
|
A common founder effect of the splice site variant c.-23 + 1G > A in GJB2 gene causing autosomal recessive deafness 1A (DFNB1A) in Eurasia. Hum Genet 2021; 141:697-707. [PMID: 34839402 DOI: 10.1007/s00439-021-02405-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 11/21/2021] [Indexed: 10/19/2022]
Abstract
Mutations in the GJB2 gene are known to be a major cause of autosomal recessive deafness 1A (OMIM 220290). The most common pathogenic variants of the GJB2 gene have a high ethno-geographic specificity in their distribution, being attributed to a founder effect related to the Neolithic migration routes of Homo sapiens. The c.-23 + 1G > A splice site variant is frequently found among deaf patients of both Caucasian and Asian origins. It is currently unknown whether the spread of this mutation across Eurasia is a result of the founder effect or if it could have multiple local centers of origin. To determine the origin of c.-23 + 1G > A, we reconstructed haplotypes by genotyping SNPs on an Illumina OmniExpress 730 K platform of 23 deaf individuals homozygous for this variant from different populations of Eurasia. The analyses revealed the presence of common regions of homozygosity in different individual genomes in the sample. These data support the hypothesis of the common founder effect in the distribution of the c.-23 + 1G > A variant of the GJB2 gene. Based on the published data on the c.-23 + 1G > A prevalence among 16,177 deaf people and the calculation of the TMRCA of the modified f2-haplotypes carrying this variant, we reconstructed the potential migration routes of the carriers of this mutation around the world. This analysis indicates that the c.-23 + 1G > A variant in the GJB2 gene may have originated approximately 6000 years ago in the territory of the Caucasus or the Middle East then spread throughout Europe, South and Central Asia and other regions of the world.
Collapse
|
9
|
Lezirovitz K, Mingroni-Netto RC. Genetic etiology of non-syndromic hearing loss in Latin America. Hum Genet 2021; 141:539-581. [PMID: 34652575 DOI: 10.1007/s00439-021-02354-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 08/23/2021] [Indexed: 12/16/2022]
Abstract
Latin America comprises all countries from South and Central America, in addition to Mexico. It is characterized by a complex mosaic of regions with heterogeneous genetic profiles regarding the geographical origin of the ancestors and proportions of admixture between the Native American, European and African components. In the first years following the findings of the role of the GJB2/GJB6 genes in the etiology of hearing loss, most scientific investigations about the genetics of hearing loss in Latin America focused on assessing the frequencies of pathogenic variants in these genes. More recently, modern techniques allowed researchers in Latin America to make exciting contributions to the finding of new candidate genes, novel mechanisms of inheritance in previously known genes, and characterize a wide diversity of variants, many of them unique to Latin America. This review aimed to provide a general landscape of the genetic studies about non-syndromic hearing loss in Latin America and their main scientific contributions. It allows the conclusion that, although there are similar contributions of some genes, such as GJB2/GJB6, when compared to European and North American countries, Latin American populations revealed some peculiarities that indicate the need for tailored strategies of screening and diagnosis to specific geographic regions.
Collapse
Affiliation(s)
- Karina Lezirovitz
- Laboratório de Otorrinolaringologia/LIM32, Faculdade de Medicina, Hospital das Clínicas, Universidade de São Paulo, São Paulo, SP, Brazil.
| | - Regina Célia Mingroni-Netto
- Departamento de Genética e Biologia Evolutiva, Centro de Pesquisas sobre o Genoma Humano e Células-Tronco, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| |
Collapse
|
10
|
Batissoco AC, Pedroso-Campos V, Pardono E, Sampaio-Silva J, Sonoda CY, Vieira-Silva GA, da Silva de Oliveira Longati EU, Mariano D, Hoshino ACH, Tsuji RK, Jesus-Santos R, Abath-Neto O, Bento RF, Oiticica J, Lezirovitz K. Molecular and genetic characterization of a large Brazilian cohort presenting hearing loss. Hum Genet 2021; 141:519-538. [PMID: 34599368 DOI: 10.1007/s00439-021-02372-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 09/15/2021] [Indexed: 12/16/2022]
Abstract
Hearing loss is one of the most common sensory defects, affecting 5.5% of the worldwide population and significantly impacting health and social life. It is mainly attributed to genetic causes, but their relative contribution reflects the geographical region's socio-economic development. Extreme genetic heterogeneity with hundreds of deafness genes involved poses challenges for molecular diagnosis. Here we report the investigation of 542 hearing-impaired subjects from all Brazilian regions to search for genetic causes. Biallelic GJB2/GJB6 causative variants were identified in 12.9% (the lowest frequency was found in the Northern region, 7.7%), 0.4% carried GJB2 dominant variants, and 0.6% had the m.1555A > G variant (one aminoglycoside-related). In addition, other genetic screenings, employed in selected probands according to clinical presentation and presumptive inheritance patterns, identified causative variants in 2.4%. Ear malformations and auditory neuropathy were diagnosed in 10.8% and 3.5% of probands, respectively. In 3.8% of prelingual/perilingual cases, Waardenburg syndrome was clinically diagnosed, and in 71.4%, these diagnoses were confirmed with pathogenic variants revealed; seven out of them were novel, including one CNV. All these genetic screening strategies revealed causative variants in 16.2% of the cases. Based on causative variants in the molecular diagnosis and genealogy analyses, a probable genetic etiology was found in ~ 50% of the cases. The present study highlights the relevance of GJB2/GJB6 as a cause of hearing loss in all Brazilian regions and the importance of screening unselected samples for estimating frequencies. Moreover, when a comprehensive screening is not available, molecular diagnosis can be enhanced by selecting probands for specific screenings.
Collapse
Affiliation(s)
- Ana Carla Batissoco
- Laboratório de Otorrinolaringologia/LIM 32, Hospital das Clínicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo, SP, Brasil
- ENT Department, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP, Brasil
| | - Vinicius Pedroso-Campos
- Laboratório de Otorrinolaringologia/LIM 32, Hospital das Clínicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo, SP, Brasil
| | - Eliete Pardono
- Laboratório de Otorrinolaringologia/LIM 32, Hospital das Clínicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo, SP, Brasil
- Instituto de Ciências de Saúde da UNIP, São Paulo, SP, Brasil
| | - Juliana Sampaio-Silva
- Laboratório de Otorrinolaringologia/LIM 32, Hospital das Clínicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo, SP, Brasil
| | - Cindy Yukimi Sonoda
- Laboratório de Otorrinolaringologia/LIM 32, Hospital das Clínicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo, SP, Brasil
| | - Gleiciele Alice Vieira-Silva
- Laboratório de Otorrinolaringologia/LIM 32, Hospital das Clínicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo, SP, Brasil
| | | | - Diego Mariano
- Department of Computer Science, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brasil
| | - Ana Cristina Hiromi Hoshino
- ENT Department, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP, Brasil
| | - Robinson Koji Tsuji
- ENT Department, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP, Brasil
| | - Rafaela Jesus-Santos
- Laboratório de Otorrinolaringologia/LIM 32, Hospital das Clínicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo, SP, Brasil
| | - Osório Abath-Neto
- Departamento de Neurologia, Faculdade de Medicina FMUSP, Universidade de São Paulo, São Paulo, SP, Brasil
| | - Ricardo Ferreira Bento
- Laboratório de Otorrinolaringologia/LIM 32, Hospital das Clínicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo, SP, Brasil
- ENT Department, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP, Brasil
| | - Jeanne Oiticica
- Laboratório de Otorrinolaringologia/LIM 32, Hospital das Clínicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo, SP, Brasil
- ENT Department, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP, Brasil
| | - Karina Lezirovitz
- Laboratório de Otorrinolaringologia/LIM 32, Hospital das Clínicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo, SP, Brasil.
- ENT Department, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP, Brasil.
| |
Collapse
|
11
|
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: 16] [Impact Index Per Article: 3.2] [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.
Collapse
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
| |
Collapse
|
12
|
High Rates of Three Common GJB2 Mutations c.516G>C, c.-23+1G>A, c.235delC in Deaf Patients from Southern Siberia Are Due to the Founder Effect. Genes (Basel) 2020; 11:genes11070833. [PMID: 32708339 PMCID: PMC7397271 DOI: 10.3390/genes11070833] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 07/10/2020] [Accepted: 07/17/2020] [Indexed: 11/17/2022] Open
Abstract
The mutations in the GJB2 gene (13q12.11, MIM 121011) encoding transmembrane protein connexin 26 (Cx26) account for a significant portion of hereditary hearing loss worldwide. Earlier we found a high prevalence of recessive GJB2 mutations c.516G>C, c.-23+1G>A, c.235delC in indigenous Turkic-speaking Siberian peoples (Tuvinians and Altaians) from the Tyva Republic and Altai Republic (Southern Siberia, Russia) and proposed the founder effect as a cause for their high rates in these populations. To reconstruct the haplotypes associated with each of these mutations, the genotyping of polymorphic genetic markers both within and flanking the GJB2 gene was performed in 28 unrelated individuals homozygous for c.516G>C (n = 18), c.-23+1G>A (n = 6), or c.235delC (n = 4) as well as in the ethnically matched controls (62 Tuvinians and 55 Altaians) without these mutations. The common haplotypes specific for mutations c.516G>C, c.-23+1G>A, or c.235delC were revealed implying a single origin of each of these mutations. The age of mutations estimated by the DMLE+ v2.3 software and the single marker method is discussed in relation to ethnic history of Tuvinians and Altaians. The data obtained in this study support a crucial role of the founder effect in the high prevalence of GJB2 mutations c.516G>C, c.-23+1G>A, c.235delC in indigenous populations of Southern Siberia.
Collapse
|
13
|
Bouzaher MH, Worden CP, Jeyakumar A. Systematic Review of Pathogenic GJB2 Variants in the Latino Population. Otol Neurotol 2020; 41:e182-e191. [PMID: 31834214 DOI: 10.1097/mao.0000000000002505] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
OBJECTIVES Define the extent to which GJB2-related hearing loss is responsible for non-syndromic hearing loss (NSHL) in the Latino population. METHODS Preferred Reporting Items for Systematic Reviews and Meta-Analysis guidelines were followed. PubMed and MEDLINE were accessed from 1966 to 2019 using permutations of the MeSH terms: "Hearing Loss," "Hearing Impairment," "Deafness," "Latin American," "Latino," "GJB2," and "Genetic." Additionally, countries designated as Latino by the US Office of Management and Bureau were cross-referenced as key terms against the aforementioned search criteria. Exclusion criteria included non-English publications, a non-Latino study population, and literature not investigating GJB2. An allele frequency analysis of pathogenic GJB2 variants in the Latino population was performed and stratified by country of origin and reported ethnicity. RESULTS One hundred twenty two unique studies were identified of which 64 met our inclusion criteria. Forty three studies were included in the GJB2 systematic review. A total of 38 pathogenic GJB2 variants were identified across 20 countries in the Latino population. The prevalence of pathogenic GJB2 variants varied by country; however, were generally uncommon with the exception of c.35delG (p.Gly12Valfs*) which displayed an allele frequency of 3.1% in the combined Latino population; ranging from 21% in Colombia to 0% in Guatemala. CONCLUSION Variation in the prevalence of pathogenic GJB2 variants by country likely reflect the heterogeneous nature of ethnic ancestral contributions to the Latino population. Additional research utilizing next generation sequencing might aid in the development of assays for high throughput diagnosis of inherited hearing loss in the multitude of ethnic sub-groups that comprise this and other traditionally marginalized populations.
Collapse
Affiliation(s)
| | | | - Anita Jeyakumar
- Division of Otolaryngology, Department of Surgery, Akron Children's Hospital, Akron, Ohio
| |
Collapse
|
14
|
Posukh OL, Zytsar MV, Bady-Khoo MS, Danilchenko VY, Maslova EA, Barashkov NA, Bondar AA, Morozov IV, Maximov VN, Voevoda MI. Unique Mutational Spectrum of the GJB2 Gene and its Pathogenic Contribution to Deafness in Tuvinians (Southern Siberia, Russia): A High Prevalence of Rare Variant c.516G>C (p.Trp172Cys). Genes (Basel) 2019; 10:E429. [PMID: 31195736 PMCID: PMC6627114 DOI: 10.3390/genes10060429] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 05/30/2019] [Accepted: 06/03/2019] [Indexed: 01/09/2023] Open
Abstract
Mutations in the GJB2 gene are the main cause for nonsyndromic autosomal recessive deafness 1A (DFNB1A) in many populations. GJB2 mutational spectrum and pathogenic contribution are widely varying in different populations. Significant efforts have been made worldwide to define DFNB1A molecular epidemiology, but this issue still remains open for some populations. The main aim of study is to estimate the DFNB1A prevalence and GJB2 mutational spectrum in Tuvinians-an indigenous population of the Tyva Republic (Southern Siberia, Russia). Sanger sequencing was applied to analysis of coding (exon 2) and non-coding regions of GJB2 in a cohort of Tuvinian patients with hearing impairments (n = 220) and ethnically matched controls (n = 157). Diagnosis of DFNB1A was established for 22.3% patients (28.8% of familial vs 18.6% of sporadic cases). Our results support that patients with monoallelic GJB2 mutations (8.2%) are coincidental carriers. Recessive mutations p.Trp172Cys, c.-23+1G>A, c.235delC, c.299_300delAT, p.Val37Ile and several benign variants were found in examined patients. A striking finding was a high prevalence of rare variant p.Trp172Cys (c.516G>C) in Tuvinians accounting for 62.9% of all mutant GJB2 alleles and a carrier frequency of 3.8% in controls. All obtained data provide important targeted information for genetic counseling of affected Tuvinian families and enrich current information on variability of GJB2 worldwide.
Collapse
Affiliation(s)
- Olga L Posukh
- Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia.
- Novosibirsk State University, 630090 Novosibirsk, Russia.
| | - Marina V Zytsar
- Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia.
| | - Marita S Bady-Khoo
- Research Institute of Medical-Social Problems and Management of the Republic of Tyva, 667000 Kyzyl, Russia.
- Perinatal Center of the Republic of Tyva, 667000 Kyzyl, Russia.
| | - Valeria Yu Danilchenko
- Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia.
| | - Ekaterina A Maslova
- Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia.
- Novosibirsk State University, 630090 Novosibirsk, Russia.
| | - Nikolay A Barashkov
- Yakut Scientific Centre of Complex Medical Problems, 677019 Yakutsk, Russia.
- M.K. Ammosov North-Eastern Federal University, 677027 Yakutsk, Russia.
| | - Alexander A Bondar
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, 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.
| | - Vladimir N Maximov
- Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia.
- Novosibirsk State University, 630090 Novosibirsk, Russia.
| | - Michael I Voevoda
- Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia.
- Novosibirsk State University, 630090 Novosibirsk, Russia.
| |
Collapse
|
15
|
Soares-Souza G, Borda V, Kehdy F, Tarazona-Santos E. Admixture, Genetics and Complex Diseases in Latin Americans and US Hispanics. CURRENT GENETIC MEDICINE REPORTS 2018. [DOI: 10.1007/s40142-018-0151-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
|
16
|
Zytsar MV, Barashkov NA, Bady-Khoo MS, Shubina-Olejnik OA, Danilenko NG, Bondar AA, Morozov IV, Solovyev AV, Danilchenko VY, Maximov VN, Posukh OL. Updated carrier rates for c.35delG (GJB2) associated with hearing loss in Russia and common c.35delG haplotypes in Siberia. BMC MEDICAL GENETICS 2018; 19:138. [PMID: 30086704 PMCID: PMC6081885 DOI: 10.1186/s12881-018-0650-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 07/20/2018] [Indexed: 01/18/2023]
Abstract
Background Mutations in GJB2 gene are a major causes of deafness and their spectrum and prevalence are specific for various populations. The well-known mutation c.35delG is more frequent in populations of Caucasian origin. Data on the c.35delG prevalence in Russia are mainly restricted to the European part of this country. We aimed to estimate the carrier frequency of c.35delG in Western Siberia and thereby update current data on the c.35delG prevalence in Russia. According to a generally accepted hypothesis, c.35delG originated from a common ancestor in the Middle East or the Mediterranean ~ 10,000–14,000 years ago and spread throughout Europe with Neolithic migrations. To test the c.35delG common origin hypothesis, we have reconstructed haplotypes bearing c.35delG and evaluated the approximate age of c.35delG in Siberia. Methods The carrier frequency of c.35delG was estimated in 122 unrelated hearing individuals living in Western Siberia. For reconstruction of haplotypes bearing c.35delG, polymorphic D13S141, D13S175, D13S1853 flanking the GJB2 gene, and intragenic rs3751385 were genotyped in deaf patients homozygous for c.35delG (n = 24) and in unrelated healthy individuals negative for c.35delG (n = 67) living in Siberia. Results We present updated carrier rates for c.35delG in Russia complemented by new data on c.35delG carrier frequency in Russians living in Western Siberia (4.1%). Two common D13S141-c.35delG-D13S175-D13S1853 haplotypes, 126-c.35delG-105-202 and 124-c.35delG-105-202, were reconstructed in the c.35delG homozygotes from Siberia. Moreover, identical allelic composition of the two most frequent c.35delG haplotypes restricted by D13S141 and D13S175 was established in geographically remote regions: Siberia and Volga-Ural region (Russia) and Belarus (Eastern Europe). Conclusions Distribution of the c.35delG carrier frequency in Russia is characterized by pronounced ethno-geographic specificity with a downward trend from west to east. Comparative analysis of the c.35delG haplotypes supports a common origin of c.35delG in some regions of Russia (Volga-Ural region and Siberia) and in Eastern Europe (Belarus). A rough estimation of the c.35delG age in Siberia (about 4800 to 8100 years ago) probably reflects the early formation stages of the modern European population (including the European part of the contemporary territory of Russia) since the settlement of Siberia by Russians started only at the end of sixteenth century. Electronic supplementary material The online version of this article (10.1186/s12881-018-0650-5) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Marina V Zytsar
- Federal Research Center Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia.,Novosibirsk State University, Novosibirsk, Russia
| | - Nikolay A Barashkov
- Yakut Scientific Centre of Complex Medical Problems, Yakutsk, Russia.,M.K. Ammosov North-Eastern Federal University, Yakutsk, Russia
| | - Marita S Bady-Khoo
- Scientific Research Institute of Medical-Social Problems and Management of the Republic of Tuva, Kyzyl, Russia
| | | | - Nina G Danilenko
- Institute of Genetics and Cytology, National Academy of Sciences, Minsk, Belarus
| | - Alexander A Bondar
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia
| | - Igor V Morozov
- Novosibirsk State University, Novosibirsk, Russia.,Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia
| | - Aisen V Solovyev
- Yakut Scientific Centre of Complex Medical Problems, Yakutsk, Russia.,M.K. Ammosov North-Eastern Federal University, Yakutsk, Russia
| | - Valeriia Yu Danilchenko
- Federal Research Center Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia.,Novosibirsk State University, Novosibirsk, Russia
| | - Vladimir N Maximov
- Federal Research Center Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
| | - Olga L Posukh
- Federal Research Center Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia. .,Novosibirsk State University, Novosibirsk, Russia.
| |
Collapse
|
17
|
Barashkov NA, Pshennikova VG, Posukh OL, Teryutin FM, Solovyev AV, Klarov LA, Romanov GP, Gotovtsev NN, Kozhevnikov AA, Kirillina EV, Sidorova OG, Vasilyevа LM, Fedotova EE, Morozov IV, Bondar AA, Solovyevа NA, Kononova SK, Rafailov AM, Sazonov NN, Alekseev AN, Tomsky MI, Dzhemileva LU, Khusnutdinova EK, Fedorova SA. Spectrum and Frequency of the GJB2 Gene Pathogenic Variants in a Large Cohort of Patients with Hearing Impairment Living in a Subarctic Region of Russia (the Sakha Republic). PLoS One 2016; 11:e0156300. [PMID: 27224056 PMCID: PMC4880331 DOI: 10.1371/journal.pone.0156300] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 05/12/2016] [Indexed: 11/29/2022] Open
Abstract
Pathogenic variants in the GJB2 gene, encoding connexin 26, are known to be a major cause of hearing impairment (HI). More than 300 allelic variants have been identified in the GJB2 gene. Spectrum and allelic frequencies of the GJB2 gene vary significantly among different ethnic groups worldwide. Until now, the spectrum and frequency of the pathogenic variants in exon 1, exon 2 and the flanking intronic regions of the GJB2 gene have not been described thoroughly in the Sakha Republic (Yakutia), which is located in a subarctic region in Russia. The complete sequencing of the non-coding and coding regions of the GJB2 gene was performed in 393 patients with HI (Yakuts—296, Russians—51, mixed and other ethnicities—46) and in 187 normal hearing individuals of Yakut (n = 107) and Russian (n = 80) populations. In the total sample (n = 580), we revealed 12 allelic variants of the GJB2 gene, 8 of which were recessive pathogenic variants. Ten genotypes with biallelic recessive pathogenic variants in the GJB2 gene (in a homozygous or a compound heterozygous state) were found in 192 out of 393 patients (48.85%). We found that the most frequent GJB2 pathogenic variant in the Yakut patients was c.-23+1G>A (51.82%) and that the second most frequent was c.109G>A (2.37%), followed by c.35delG (1.64%). Pathogenic variants с.35delG (22.34%), c.-23+1G>A (5.31%), and c.313_326del14 (2.12%) were found to be the most frequent among the Russian patients. The carrier frequencies of the c.-23+1G>A and с.109G>A pathogenic variants in the Yakut control group were 10.20% and 2.80%, respectively. The carrier frequencies of с.35delG and c.101T>C were identical (2.5%) in the Russian control group. We found that the contribution of the GJB2 gene pathogenic variants in HI in the population of the Sakha Republic (48.85%) was the highest among all of the previously studied regions of Asia. We suggest that extensive accumulation of the c.-23+1G>A pathogenic variant in the indigenous Yakut population (92.20% of all mutant chromosomes in patients) and an extremely high (10.20%) carrier frequency in the control group may indicate a possible selective advantage for the c.-23+1G>A carriers living in subarctic climate.
Collapse
Affiliation(s)
- Nikolay A. Barashkov
- Department of Molecular Genetics, Federal State Budgetary Scientific Institution “Yakut Science Centre of Complex Medical Problems,” Yakutsk, Russian Federation
- Laboratory of Molecular Biology, Institute of Natural Sciences, M.K. Ammosov North-Eastern Federal University, Yakutsk, Russian Federation
- * E-mail:
| | - Vera G. Pshennikova
- Department of Molecular Genetics, Federal State Budgetary Scientific Institution “Yakut Science Centre of Complex Medical Problems,” Yakutsk, Russian Federation
- Laboratory of Molecular Biology, Institute of Natural Sciences, M.K. Ammosov North-Eastern Federal University, Yakutsk, Russian Federation
| | - Olga L. Posukh
- Laboratory of Human Molecular Genetics, Federal Research Center, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation
- Novosibirsk State University, Novosibirsk, Russian Federation
| | - Fedor M. Teryutin
- Department of Molecular Genetics, Federal State Budgetary Scientific Institution “Yakut Science Centre of Complex Medical Problems,” Yakutsk, Russian Federation
- Laboratory of Molecular Biology, Institute of Natural Sciences, M.K. Ammosov North-Eastern Federal University, Yakutsk, Russian Federation
| | - Aisen V. Solovyev
- Department of Molecular Genetics, Federal State Budgetary Scientific Institution “Yakut Science Centre of Complex Medical Problems,” Yakutsk, Russian Federation
- Laboratory of Molecular Biology, Institute of Natural Sciences, M.K. Ammosov North-Eastern Federal University, Yakutsk, Russian Federation
| | - Leonid A. Klarov
- Department of Molecular Genetics, Federal State Budgetary Scientific Institution “Yakut Science Centre of Complex Medical Problems,” Yakutsk, Russian Federation
- Department of Radiology, Republican Hospital # 2 –Center of Emergency Medicine, Ministry of Public Health of the Sakha Republic, Yakutsk, Russian Federation
| | - Georgii P. Romanov
- Department of Molecular Genetics, Federal State Budgetary Scientific Institution “Yakut Science Centre of Complex Medical Problems,” Yakutsk, Russian Federation
- Laboratory of Molecular Biology, Institute of Natural Sciences, M.K. Ammosov North-Eastern Federal University, Yakutsk, Russian Federation
| | - Nyurgun N. Gotovtsev
- Department of Molecular Genetics, Federal State Budgetary Scientific Institution “Yakut Science Centre of Complex Medical Problems,” Yakutsk, Russian Federation
- Laboratory of Molecular Biology, Institute of Natural Sciences, M.K. Ammosov North-Eastern Federal University, Yakutsk, Russian Federation
| | - Andrey A. Kozhevnikov
- Republican Centre of Professional Pathology, Republican Hospital # 2 –Center of Emergency Medicine, Ministry of Public Health of the Sakha Republic, Yakutsk, Russian Federation
| | - Elena V. Kirillina
- Institute of Foreign Philology and Regional Studies, M.K. Ammosov North-Eastern Federal University, Yakutsk, Russian Federation
| | - Oksana G. Sidorova
- Department of Molecular Genetics, Federal State Budgetary Scientific Institution “Yakut Science Centre of Complex Medical Problems,” Yakutsk, Russian Federation
| | - Lena M. Vasilyevа
- Audiology-Logopaedic Centre, Republican Hospital #1– National Medical Centre, Ministry of Public Health of the Sakha Republic, Yakutsk, Russian Federation
| | - Elvira E. Fedotova
- Audiology-Logopaedic Centre, Republican Hospital #1– National Medical Centre, Ministry of Public Health of the Sakha Republic, Yakutsk, Russian Federation
| | - Igor V. Morozov
- Novosibirsk State University, Novosibirsk, Russian Federation
- SB RAS Genomics Core Facility, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation
| | - Alexander A. Bondar
- SB RAS Genomics Core Facility, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation
| | - Natalya A. Solovyevа
- Department of Molecular Genetics, Federal State Budgetary Scientific Institution “Yakut Science Centre of Complex Medical Problems,” Yakutsk, Russian Federation
- Laboratory of Molecular Biology, Institute of Natural Sciences, M.K. Ammosov North-Eastern Federal University, Yakutsk, Russian Federation
| | - Sardana K. Kononova
- Department of Molecular Genetics, Federal State Budgetary Scientific Institution “Yakut Science Centre of Complex Medical Problems,” Yakutsk, Russian Federation
- Laboratory of Molecular Biology, Institute of Natural Sciences, M.K. Ammosov North-Eastern Federal University, Yakutsk, Russian Federation
| | - Adyum M. Rafailov
- Laboratory of Molecular Biology, Institute of Natural Sciences, M.K. Ammosov North-Eastern Federal University, Yakutsk, Russian Federation
| | - Nikolay N. Sazonov
- Department of Biochemistry and Biotechnology, Institute of Natural Sciences, M.K. Ammosov North-Eastern Federal University, Yakutsk, Russian Federation
| | - Anatoliy N. Alekseev
- Institute of Humanitarian Research and Indigenous Peoples of the North, Siberian Branch of the Russian Academy of Sciences, Yakutsk, Russian Federation
| | - Mikhail I. Tomsky
- Department of Molecular Genetics, Federal State Budgetary Scientific Institution “Yakut Science Centre of Complex Medical Problems,” Yakutsk, Russian Federation
| | - Lilya U. Dzhemileva
- Laboratory of Human Molecular Genetics, Institute of Biochemistry and Genetics, Ufa Scientific Centre, Russian Academy of Sciences, Ufa, Russian Federation
- Department of Immunology and Human Reproductive Health, Bashkir State Medical University, Ufa, Russian Federation
| | - Elza K. Khusnutdinova
- Laboratory of Human Molecular Genetics, Institute of Biochemistry and Genetics, Ufa Scientific Centre, Russian Academy of Sciences, Ufa, Russian Federation
- Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa, Russian Federation
| | - Sardana A. Fedorova
- Department of Molecular Genetics, Federal State Budgetary Scientific Institution “Yakut Science Centre of Complex Medical Problems,” Yakutsk, Russian Federation
- Laboratory of Molecular Biology, Institute of Natural Sciences, M.K. Ammosov North-Eastern Federal University, Yakutsk, Russian Federation
| |
Collapse
|