Mutation analysis of the Cx26, Cx30, and Cx31 genes in autosomal recessive nonsyndromic hearing impairment

Genetic analysis of 106 sporadic cases with hearing loss in the UAE population

BACKGROUND

Hereditary hearing loss is a rare hereditary condition that has a significant presence in consanguineous populations. Despite its prevalence, hearing loss is marked by substantial genetic diversity, which poses challenges for diagnosis and screening, particularly in cases with no clear family history or when the impact of the genetic variant requires functional analysis, such as in the case of missense mutations and UTR variants. The advent of next-generation sequencing (NGS) has transformed the identification of genes and variants linked to various conditions, including hearing loss. However, there remains a high proportion of undiagnosed patients, attributable to various factors, including limitations in sequencing coverage and gaps in our knowledge of the entire genome, among other factors. In this study, our objective was to comprehensively identify the spectrum of genes and variants associated with hearing loss in a cohort of 106 affected individuals from the UAE.

RESULTS

In this study, we investigated 106 sporadic cases of hearing impairment and performed genetic analyses to identify causative mutations. Screening of the GJB2 gene in these cases revealed its involvement in 24 affected individuals, with specific mutations identified. For individuals without GJB2 mutations, whole exome sequencing (WES) was conducted. WES revealed 33 genetic variants, including 6 homozygous and 27 heterozygous DNA changes, two of which were previously implicated in hearing loss, while 25 variants were novel. We also observed multiple potential pathogenic heterozygous variants across different genes in some cases. Notably, a significant proportion of cases remained without potential pathogenic variants.

CONCLUSIONS

Our findings confirm the complex genetic landscape of hearing loss and the limitations of WES in achieving a 100% diagnostic rate, especially in conditions characterized by genetic heterogeneity. These results contribute to our understanding of the genetic basis of hearing loss and emphasize the need for further research and comprehensive genetic analyses to elucidate the underlying causes of this condition.

Next-generation sequencing for genetic testing of hearing loss populations

BACKGROUND AND AIMS

Hearing loss is a common sensorineural disease with genetic heterogeneity. More than 140 genes are known to cause hereditary hearing loss. We aim to uncover the etiologies of hearing loss and provide patients with reasonable reproductive choices.

MATERIALS AND METHODS

Total 825 participants were recruited, including 74 individuals, 47 couples, and 219 families, to identify the molecular etiologies of hearing loss using next-generation sequencing (NGS). Novel mutations were verified with a minigene splicing assay and the construction of three-dimensional protein models.

RESULTS

A positive molecular diagnosis was obtained for 244 patients, a rate of 63.05 %. Total 470 mutations were identified in 18 causative genes in positive patients. The most common genes mutated were GJB2 and SLC26A4. 47 novel mutations were identified. Further analysis predicted that two splicing mutations would cause abnormal mRNA splicing and three missense mutations would affect the protein structure. The results of prenatal diagnosis showed that the genotypes of 15 fetuses were the same as the probands.

CONCLUSION

Our findings expand the mutation spectrum of hearing loss and highlight the importance of genetic diagnosis and prenatal diagnosis to allow accurate and personalized guidance for those at high risk of deafness.

Mitochondrial mutations in non-syndromic hearing loss at UAE

INTRODUCTION

Hearing loss (HL) is a common sensory disorder over the world, and it has been estimated that genetic etiology is involved in more than 50% of the cases in developed countries. Both nuclear and mitochondrial genes were reported as responsible for hereditary HL. Mitochondrial mutations leading to HL have so far been reported in the MT-RNR1 gene, mitochondrially encoded 12S rRNA.

METHODS

To study the molecular contribution of mitochondrial 12S rRNA gene mutations in UAE-HL, a cohort of 74 unrelated UAE patients with no gap junction protein beta 2 (GJB2) mutations were selected for mitochondrial 12S rRNA gene mutational screening using Sanger sequencing and whole-exome sequencing. Detected DNA variants were analyzed by bioinformatics tools to predict their pathogenic effects.

RESULTS

Our analysis revealed the presence of two known deafness mutations; m.669T > C and m.827A > G in two different deaf individuals. Furthermore, whole-exome sequencing was done for these two patients and showed the absence of any nuclear mutations. Our study supports the pathogenic effect of the m.669T > C and m.827A > G mutations and showed that mitochondrial mutations have a contribution of 2.7% in our cohort.

CONCLUSIONS

This is the first report of mtDNA mutations in the UAE which revealed that both variants m.669T > C and m.827A > G should be included in the molecular diagnosis of patients with maternally inherited HL in UAE.

Analyses of del(GJB6-D13S1830) and del(GJB6-D13S1834) deletions in a large cohort with hearing loss: Caveats to interpretation of molecular test results in multiplex families

BACKGROUND

Mutations involving the closely linked GJB2 and GJB6 at the DFNB1 locus are a common genetic cause of profound congenital hearing loss in many populations. In some deaf GJB2 heterozygotes, a 309 kb deletion involving the GJB6 has been found to be the cause for hearing loss when inherited in trans to a GJB2 mutation.

METHODS

We screened 2,376 probands from a National DNA Repository of deaf individuals.

RESULTS

Fifty-two of 318 heterozygous probands with pathogenic GJB2 sequence variants had a GJB6 deletion. Additionally, eight probands had an isolated heterozygous GJB6 deletion that did not explain their hearing loss. In two deaf subjects, including one proband, a homozygous GJB6 deletion was the cause for their hearing loss, a rare occurrence not reported to date.

CONCLUSION

This study represents the largest US cohort of deaf individuals harboring GJB2 and GJB6 variants, including unique subsets of families with deaf parents. Testing additional members to clarify the phase of GJB2/GJB6 variants in multiplex families was crucial in interpreting clinical significance of the variants in the proband. It highlights the importance of determining the phase of GJB2/GJB6 variants when interpreting molecular test results especially in multiplex families with assortative mating.

A Novel Nonsense Mutation (c.414G>A; p.Trp138*) in CLDN14 Causes Hearing Loss in Yemeni Families: A Case Report

Non-syndromic hearing loss (NSHL) is a hereditary disorder that affects many populations. Many genes are involved in NSHL and the mutational load of these genes often differs among ethnic groups. Claudin-14 (CLDN14), a tight junction protein, is known to be associated with NSHL in many populations. In this study, we aimed to identify the responsible variants in 3 different Yemeni families affected with NSHL. Firstly, clinical exome sequencing (CES) performed for 3 affected patients from these different families identified a new nonsense variant (c.414G > A) in CLDN14. This variant was then confirmed by Sanger sequencing and PCR-RFLP. Subsequently, four microsatellite markers were used to genotype these families, which revealed a founder effect for this variant. Overall, this study illustrates the implication of the CLDN14 gene in the Yemeni population with NSHL and identifies a new founder variant.

The Application of Next-Generation Sequencing for Mutation Detection in Autosomal-Dominant Hereditary Hearing Impairment

OBJECTIVE

Identification of the causative mutation using next-generation sequencing in autosomal-dominant hereditary hearing impairment, as mutation analysis in hereditary hearing impairment by classic genetic methods, is hindered by the high heterogeneity of the disease.

PATIENTS

Two Swiss families with autosomal-dominant hereditary hearing impairment.

INTERVENTION

Amplified DNA libraries for next-generation sequencing were constructed from extracted genomic DNA, derived from peripheral blood, and enriched by a custom-made sequence capture library. Validated, pooled libraries were sequenced on an Illumina MiSeq instrument, 300 cycles and paired-end sequencing. Technical data analysis was performed with SeqMonk, variant analysis with GeneTalk or VariantStudio. The detection of mutations in genes related to hearing loss by next-generation sequencing was subsequently confirmed using specific polymerase-chain-reaction and Sanger sequencing.

MAIN OUTCOME MEASURE

Mutation detection in hearing-loss-related genes.

RESULTS

The first family harbored the mutation c.5383+5delGTGA in the TECTA-gene. In the second family, a novel mutation c.2614-2625delCATGGCGCCGTG in the WFS1-gene and a second mutation TCOF1-c.1028G>A were identified.

CONCLUSION

Next-generation sequencing successfully identified the causative mutation in families with autosomal-dominant hereditary hearing impairment. The results helped to clarify the pathogenic role of a known mutation and led to the detection of a novel one. NGS represents a feasible approach with great potential future in the diagnostics of hereditary hearing impairment, even in smaller labs.

Mutation detection in GJB2 gene among Malays with non-syndromic hearing loss

OBJECTIVES

To identify the mutations in the GJB2 gene and to determine its association with non-syndromic hearing loss in Malays.

METHODS

A comparative cross sectional study was conducted on a group of children from the deaf schools and the normal schools. A total of 91 buccal cell samples of non-syndromic hearing loss and 91 normal hearing children were taken. Polymerase chain reaction was used to amplify the coding region of GJB2 gene. The PCR product of GJB2 coding region was preceded with screening for mutations using denaturing high performance liquid chromatography (dHPLC) and mutations detected were confirmed by DNA sequencing.

RESULTS

Twelve sequence variations including mutations and polymorphisms were found in 32 patients and 37 control subjects. The variations were G4D, V27I, E114G, T123N, V37I and R127H in both groups, W24X, R32H, 257_259 del CGC and M34L in patients only and I203T and V153I in control subjects only. There were no association between homozygous (P=0.368) or heterozygous (P=0.164) GJB2 gene and non-syndromic hearing loss.

CONCLUSIONS

The types of GJB2 gene mutation were different and vary in Malay non-syndromic hearing loss as compared to the other races. Furthermore, the mutation did not associate with hearing loss in the population. Other related genes are believed to be involved and need to be sought in this group of patients.

Searching for digenic inheritance in deaf Brazilian individuals using the multiplex ligation-dependent probe amplification technique

Mutations in the genes coding for connexin 26 (Cx26), connexin 30 (Cx30), and connexin 31 (Cx31) are the main cause of autosomal recessive nonsyndromic sensorineural hearing loss (AR-NSNHL). The 35delG mutation is the most frequent in the majority of Caucasian populations and may account for up to 70% of all GJB2 mutations. As a large number of affected individuals (10%-40%) with GJB2 mutations carry only one mutant allele, it has been postulated that the presence of additional mutations in the GJB6 gene (Cx30) explains the deafness condition found in these patients. In the present study, we screened the c.35delG mutation in ~600 unrelated Brazilian patients, with moderate to profound AR-NSNHL. Other point mutations in the coding region of the GJB2 gene were screened by sequencing analysis as well as the IVS 1+1 G>A splice site mutation in the same gene. Digenic mutations including large deletions and duplications were investigated in the Cx26, 30, and 31 genes in monoallelic individuals for mutations in the GJB2 gene. Large deletions and duplications were assessed by multiplex ligation-dependent probe amplification. We found 46 patients with mutations in only one GJB2 allele. Different pathogenic mutations associated with c.35delG were found in 13 patients. Two patients were identified with digenic heterozygous mutations. Our findings contributed to more accurate diagnosis and more appropriate genetic counseling in 28% of patients studied (13/46).

Gap junctions in inherited human disease

Gap junctions (GJ) provide direct intercellular communication. The structures underlying these cell junctions are membrane-associated channels composed of six integral membrane connexin (Cx) proteins, which can form communicating channels connecting the cytoplasms of adjacent cells. This provides coupled cells with a direct pathway for sharing ions, nutrients, or small metabolites to establish electrical coupling or balancing metabolites in various tissues. Genetic approaches have uncovered a still growing number of mutations in Cxs related to human diseases including deafness, skin disease, peripheral and central neuropathies, cataracts, or cardiovascular dysfunctions. The discovery of a growing number of inherited human disorders provides an unequivocal demonstration that gap junctional communication is crucial for diverse physiological processes.