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Lebeko K, Sloan-Heggen CM, Noubiap JJN, Dandara C, Kolbe DL, Ephraim SS, Booth KT, Azaiez H, Santos-Cortez RLP, Leal SM, Smith RJH, Wonkam A. Targeted genomic enrichment and massively parallel sequencing identifies novel nonsyndromic hearing impairment pathogenic variants in Cameroonian families. Clin Genet 2016; 90:288-90. [PMID: 27246798 DOI: 10.1111/cge.12799] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 04/19/2016] [Accepted: 05/01/2016] [Indexed: 01/22/2023]
Abstract
In sub-Saharan Africa GJB2-related nonsyndromic hearing impairment (NSHI) is rare. Ten Cameroonian families was studied using a platform (OtoSCOPE®) with 116 genes. In seven of 10 families (70%), 12 pathogenic variants were identified in six genes. Five of the 12 (41.6%) variants are novel. These results confirm the efficiency of comprehensive genetic testing in defining the causes of NSHI in sub-Saharan Africa.
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Affiliation(s)
- K Lebeko
- Division of Human Genetics, Department of Pathology, Faculty of Health Sciences University of Cape Town, Cape Town, South Africa
| | - C M Sloan-Heggen
- Department of Otolaryngology, Molecular Otolaryngology and Renal Research Laboratories, The University of Iowa, Iowa City, IA, USA
| | - J J N Noubiap
- Department of Medicine, Faculty of Health Sciences University of Cape Town, Cape Town, South Africa
| | - C Dandara
- Division of Human Genetics, Department of Pathology, Faculty of Health Sciences University of Cape Town, Cape Town, South Africa
| | - D L Kolbe
- Department of Otolaryngology, Molecular Otolaryngology and Renal Research Laboratories, The University of Iowa, Iowa City, IA, USA
| | - S S Ephraim
- Department of Otolaryngology, Molecular Otolaryngology and Renal Research Laboratories, The University of Iowa, Iowa City, IA, USA
| | - K T Booth
- Department of Otolaryngology, Molecular Otolaryngology and Renal Research Laboratories, The University of Iowa, Iowa City, IA, USA
| | - H Azaiez
- Department of Otolaryngology, Molecular Otolaryngology and Renal Research Laboratories, The University of Iowa, Iowa City, IA, USA
| | - R L P Santos-Cortez
- Center for Statistical Genetics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - S M Leal
- Center for Statistical Genetics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - R J H Smith
- Department of Otolaryngology, Molecular Otolaryngology and Renal Research Laboratories, The University of Iowa, Iowa City, IA, USA
| | - A Wonkam
- Division of Human Genetics, Department of Pathology, Faculty of Health Sciences University of Cape Town, Cape Town, South Africa.,Department of Medicine, Faculty of Health Sciences University of Cape Town, Cape Town, South Africa
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Moteki H, Azaiez H, Booth KT, Shearer AE, Sloan CM, Kolbe DL, Nishio S, Hattori M, Usami S, Smith RJH. Comprehensive genetic testing with ethnic-specific filtering by allele frequency in a Japanese hearing-loss population. Clin Genet 2015; 89:466-472. [PMID: 26346818 DOI: 10.1111/cge.12677] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 09/06/2015] [Accepted: 09/06/2015] [Indexed: 12/31/2022]
Abstract
Recent advances in targeted genomic enrichment with massively parallel sequencing (TGE+MPS) have made comprehensive genetic testing for non-syndromic hearing loss (NSHL) possible. After excluding NSHL subjects with causative mutations in GJB2 and the MT-RNR1 (1555A>G) variant by Sanger sequencing, we completed TGE+MPS on 194 probands with presumed NSHL identified across Japan. We used both publicly available minor allele frequency (MAF) datasets and ethnic-specific MAF filtering against an in-house database of 200 normal-hearing Japanese controls. Ethnic-specific MAF filtering allowed us to re-categorize as common 203 variants otherwise annotated as rare or novel in non-Japanese ethnicities. This step minimizes false-positive results and improves the annotation of identified variants. Causative variants were identified in 27% of probands with solve rates of 35%, 35% and 19% for dominant, recessive and sporadic NSHL, respectively. Mutations in MYO15A and CDH23 follow GJB2 as the frequent causes of recessive NSHL; copy number variations in STRC are a major cause of mild-to-moderate NSHL. Ethnic-specific filtering by allele frequency is essential to optimize the interpretation of genetic data.
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Affiliation(s)
- H Moteki
- Department of Otolaryngology-Head and Neck Surgery, Molecular Otolaryngology & Renal Research Labs, University of Iowa Hospitals and Clinics, Iowa City, IA, USA.,Department of Otorhinolaryngology, Shinshu University School of Medicine, Matsumoto, Japan
| | - H Azaiez
- Department of Otolaryngology-Head and Neck Surgery, Molecular Otolaryngology & Renal Research Labs, University of Iowa Hospitals and Clinics, Iowa City, IA, USA
| | - K T Booth
- Department of Otolaryngology-Head and Neck Surgery, Molecular Otolaryngology & Renal Research Labs, University of Iowa Hospitals and Clinics, Iowa City, IA, USA
| | - A E Shearer
- Department of Otolaryngology-Head and Neck Surgery, Molecular Otolaryngology & Renal Research Labs, University of Iowa Hospitals and Clinics, Iowa City, IA, USA
| | - C M Sloan
- Department of Otolaryngology-Head and Neck Surgery, Molecular Otolaryngology & Renal Research Labs, University of Iowa Hospitals and Clinics, Iowa City, IA, USA
| | - D L Kolbe
- Department of Otolaryngology-Head and Neck Surgery, Molecular Otolaryngology & Renal Research Labs, University of Iowa Hospitals and Clinics, Iowa City, IA, USA
| | - S Nishio
- Department of Otorhinolaryngology, Shinshu University School of Medicine, Matsumoto, Japan
| | - M Hattori
- Department of Otorhinolaryngology, Shinshu University School of Medicine, Matsumoto, Japan
| | - S Usami
- Department of Otorhinolaryngology, Shinshu University School of Medicine, Matsumoto, Japan
| | - R J H Smith
- Department of Otolaryngology-Head and Neck Surgery, Molecular Otolaryngology & Renal Research Labs, University of Iowa Hospitals and Clinics, Iowa City, IA, USA
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Messaoud O, Ben Rekaya M, Ouragini H, Benfadhel S, Azaiez H, Kefi R, Gouider-Khouja N, Mokhtar I, Amouri A, Boubaker MS, Zghal M, Abdelhak S. Severe phenotypes in two Tunisian families with novel XPA mutations: evidence for a correlation between mutation location and disease severity. Arch Dermatol Res 2011; 304:171-6. [DOI: 10.1007/s00403-011-1190-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2011] [Revised: 10/30/2011] [Accepted: 11/01/2011] [Indexed: 02/04/2023]
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Wilch E, Azaiez H, Fisher RA, Elfenbein J, Murgia A, Birkenhäger R, Bolz H, Da Silva-Costa SM, Del Castillo I, Haaf T, Hoefsloot L, Kremer H, Kubisch C, Le Marechal C, Pandya A, Sartorato EL, Schneider E, Van Camp G, Wuyts W, Smith RJH, Friderici KH. A novel DFNB1 deletion allele supports the existence of a distant cis-regulatory region that controls GJB2 and GJB6 expression. Clin Genet 2010; 78:267-74. [PMID: 20236118 DOI: 10.1111/j.1399-0004.2010.01387.x] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Eleven affected members of a large German-American family segregating recessively inherited, congenital, non-syndromic sensorineural hearing loss (SNHL) were found to be homozygous for the common 35delG mutation of GJB2, the gene encoding the gap junction protein Connexin 26. Surprisingly, four additional family members with bilateral profound SNHL carried only a single 35delG mutation. Previously, we demonstrated reduced expression of both GJB2 and GJB6 mRNA from the allele carried in trans with that bearing the 35delG mutation in these four persons. Using array comparative genome hybridization (array CGH), we have now identified on this allele a deletion of 131.4 kb whose proximal breakpoint lies more than 100 kb upstream of the transcriptional start sites of GJB2 and GJB6. This deletion, del(chr13:19,837,344-19,968,698), segregates as a completely penetrant DFNB1 allele in this family. It is not present in 528 persons with SNHL and monoallelic mutation of GJB2 or GJB6, and we have not identified any other candidate pathogenic copy number variation by arrayCGH in a subset of 10 such persons. Characterization of distant GJB2/GJB6 cis-regulatory regions evidenced by this allele may be required to find the 'missing' DFNB1 mutations that are believed to exist.
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Affiliation(s)
- E Wilch
- Genetics Program, Michigan State University, East Lansing, MI 48824, USA
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del Castillo FJ, Rodríguez-Ballesteros M, Alvarez A, Hutchin T, Leonardi E, de Oliveira CA, Azaiez H, Brownstein Z, Avenarius MR, Marlin S, Pandya A, Shahin H, Siemering KR, Weil D, Wuyts W, Aguirre LA, Martín Y, Moreno-Pelayo MA, Villamar M, Avraham KB, Dahl HHM, Kanaan M, Nance WE, Petit C, Smith RJH, Van Camp G, Sartorato EL, Murgia A, Moreno F, del Castillo I. A novel deletion involving the connexin-30 gene, del(GJB6-d13s1854), found in trans with mutations in the GJB2 gene (connexin-26) in subjects with DFNB1 non-syndromic hearing impairment. J Med Genet 2006; 42:588-94. [PMID: 15994881 PMCID: PMC1736094 DOI: 10.1136/jmg.2004.028324] [Citation(s) in RCA: 250] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Ben Zina Z, Chaabouni S, Azaiez H, Ellouze D, Ayadi H, Feki J. 253 Colobome oculaire isolé familial. J Fr Ophtalmol 2005. [DOI: 10.1016/s0181-5512(05)74651-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Cryns K, Orzan E, Murgia A, Huygen PLM, Moreno F, del Castillo I, Chamberlin GP, Azaiez H, Prasad S, Cucci RA, Leonardi E, Snoeckx RL, Govaerts PJ, Van de Heyning PH, Van de Heyning CM, Smith RJH, Van Camp G. A genotype-phenotype correlation for GJB2 (connexin 26) deafness. J Med Genet 2004; 41:147-54. [PMID: 14985372 PMCID: PMC1735685 DOI: 10.1136/jmg.2003.013896] [Citation(s) in RCA: 161] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
INTRODUCTION Mutations in GJB2 are the most common cause of non-syndromic autosomal recessive hearing impairment, ranging from mild to profound. Mutation analysis of this gene is widely available as a genetic diagnostic test. OBJECTIVE To assess a possible genotype-phenotype correlation for GJB2. DESIGN Retrospective analysis of audiometric data from people with hearing impairment, segregating two GJB2 mutations. SUBJECTS Two hundred and seventy seven unrelated patients with hearing impairment who were seen at the ENT departments of local and university hospitals from Italy, Belgium, Spain, and the United States, and who harboured bi-allelic GJB2 mutations. RESULTS We found that 35delG homozygotes have significantly more hearing impairment, compared with 35delG/non-35delG compound heterozygotes. People with two non-35delG mutations have even less hearing impairment. We observed a similar gradient of hearing impairment when we categorised mutations as inactivating (that is, stop mutations or frame shifts) or non-inactivating (that is, missense mutations). We demonstrated that certain mutation combinations (including the combination of 35delG with the missense mutations L90P, V37I, or the splice-site mutation IVS1+1G>A, and the V37I/V37I genotype) are associated with significantly less hearing impairment compared with 35delG homozygous genotypes. CONCLUSIONS This study is the first large systematic analysis indicating that the GJB2 genotype has a major impact on the degree of hearing impairment, and identifying mild genotypes. Furthermore, this study shows that it will be possible to refine this correlation and extend it to additional genotypes. These data will be useful in evaluating habilitation options for people with GJB2 related deafness.
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Affiliation(s)
- K Cryns
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
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