Genetic testing for deafness--GJB2 and SLC26A4 as causes of deafness

Epidemiology, etiology, genetic variants in non- syndromic hearing loss in Iran: A systematic review and meta-analysis

OBJECTIVES

Hearing loss is one of the most common heterogeneous complicated disorders worldwide. We previously analyzed the results of published data on non-syndromic hearing loss in the Iranian population systematically. A broad range of genes is a challenge for molecular screening and clinical diagnosis in our populations on the ground of distinct genetics. The aim of this study was to analyze the role and frequency of the variants accountable for non-syndromic hearing loss (NSHL) in the Iranian population. These were identified with different methods including whole exome sequencing (WES), next-generation sequencing (NGS), targeted genomic enrichment and massively parallel sequencing (TGE + MPS), autozygosity mapping, STR markers, linkage analysis, and direct sequencing. This is the comprehensively study focusing on classifying 13 common NSHL genes according to their frequencies. Previous studies have not studied different regions and the Iranian population, and this is the definitive study on the topic.

METHODS

We searched Scopus, PubMed, Science Direct databases, and Google Scholar. After a systematic review of the evidence 95 studies were considered then 31 studies were eligible for meta-analysis. In total, 6995 families, 358 variants, and 117 novel variants were included. Statistical analyses were conducted using Stata SE version 11 software. The inverse variance method enjoyed combining data. Heterogeneity of the preliminary results was assessed using Q (Cochrane test), and I square index. Random effects or fixed models were applied to combine the results, relying on the degree of heterogeneity. Point and pooled prevalence of variants acting on different regions were illustrated by forest plots.

RESULTS

The total prevalence of at least one variant of GJB2 and SLC26A genes was estimated at 26% and 5%, respectively. Variant c.35delG accounted for 18% of the GJB2 variants while 1% of these variants were novel ones. The next most common variants in the GJB2 gene were c.109G>A at 3.5% and c.-23+1G>A at 2.3%. Moreover, the prevalence of GJB2 gene variants varied on average 0.002% from one region to another in Iran (p=0.849). Our meta-analysis also showed that the frequency of at least one variant of MYO15A varied between 1.2% and 12.5%. Corresponding prevalences for the other variants were as follows: ILDR1 (3.5%-3.7%), CDH23 (2%-10%), PJVK (1.4%-33%), TECTA (1.3%-6.7%), MYO6 (2%-4.8%), TMC1 (1.8%-2%), MYO7A (0.7%-5%), MARVELD2 (0.7-5%), OTOF (0.7%-4%), LRTOMT (0.7%-2.5%). Finally, we did not find any relationship between geographic area and the presence of these variants.

CONCLUSION

GJB2 gene variants were the most common cause of NSHL in Iran. Understanding the prevalence of NSHL gene frequency in Iran may be the foundation for future studies in an Iranian population which may lead to future NSHL therapy.

Study on the relationship between the pathogenic mutations of SLC26A4 and CT phenotypes of inner ear in patient with sensorineural hearing loss

To investigate the possible association of pathogenic mutations of SLC26A4 and computerized tomography (CT) phenotypes of inner ear, and explore the feasibility of using the method of gene sequence analysis. A total of 155 patients with bilateral hearing loss carrying SLC26A4 gene mutations were further subjected to high-resolution temporal bone CT and thyroid B ultrasound tests. The potential relationship between the pathogenic mutations of gene and the CT phenotypes were analyzed. As a result, 65 patients (41.9%, 65/155) carried SLC26A4 gene mutations, and 27 cases were detected with pathogenic mutations of SLC26A4 where IVS7-2A>G (55.6%, 15/27) was the most common pathogenic mutation. Amongst them, 19 patients carrying bi-allelic SLC26A4 mutations were all confirmed to have inner ear malformation by CT scan including four cases of enlarged vestibular aqueduct (EVA) and 15 cases of Mondini dysplasia (MD). However, there was only one in eight cases of single allele pathogenic mutation who was confirmed to have EVA by CT scan. Further, only one patient with EVA was confirmed to be slightly higher of total T3 than normal by thyroid ultrasound scan and thyroid hormone assays. These findings suggested that CT detection and SLC26A4 gene detection are efficient methods to diagnose EVA, which can complement each other. Also, the bi-allelic pathogenic mutations of SLC26A4 are more likely to induce inner ear malformation than single allele pathogenic mutation.

[Genetic hearing loss]

Deafness is the most common sensory disability in developed countries affecting more than 2 births in 1000. Eighty percent of congenital deafness is genetic. Universal newborn hearing screening has been in place since 2012 in France. All genetic hearing losses are not congenital and all congenital hearing losses are not genetic. Genetic hearing loss may be syndromic (associated with other symptoms) (10 %) or non-syndromic (isolated) (90 %). Hearing loss may initially be the only symptom of syndromic deafness. A genetic origin can be diagnosed and must therefore be evoked systematically even in the adult.

Genotyping data and novel haplotype diversity of STR markers in the SLC26A4 gene region in five ethnic groups of the Iranian population

BACKGROUND AND AIMS

SLC26A4 gene mutations are the second currently identifiable genetic cause of autosomal recessive nonsyndromic hearing loss after GJB2 mutations. Because of the extensive size of the SLC26A4 gene and the variety of mutations, indirect diagnosis using linkage analysis has been suggested. Therefore, in this investigation three potential short tandem repeat (STR) markers related to this region including D7S2420, D7S496, and D7S2459 were selected for further analysis.

METHODS

The characteristics and haplotype frequency of the markers were examined for the first time in five ethnic groups of the Iranian population including Fars, Azari, Turkmen, Gilaki, and Arab using the polymerase chain reaction followed by fluorescent capillary electrophoresis. RESULTS were analyzed by GeneMarker HID Human STR Identity, GenePop, Microsatellite tools, PowerMarker 3.25, and Arlequin 3.5 software.

RESULTS

Analysis of the allelic frequency revealed the presence of 11, 10, and 8 alleles for D7S2420, D7S496, and D7S2459 markers, respectively, in the Iranian population. The detailed analysis of each ethnic group was reported. Calculated polymorphism information content values were above 0.7 in the Iranian population. Pairwise linkage disequilibrium (LD) revealed a significant LD in pairing markers of D7S2420-D7S496 and in D7S496-D7S2459. Estimation of the haplotype frequency showed the presence of 20, 13, 15, 15, and 20 informative haplotypes in Fars, Azari, Turkmen, Gilaki, and Arabian ethnics, respectively.

CONCLUSION

Together, the investigated markers could be suggested as powerful tools for linkage analysis of SLC26A4 gene mutations in the Iranian population.

A novel mutation in the TECTA gene in a Chinese family with autosomal dominant nonsyndromic hearing loss

TECTA-related deafness can be inherited as autosomal-dominant nonsyndromic deafness (designated DFNA) or as the autosomal-recessive version. The α-tectorin protein, which is encoded by the TECTA gene, is one of the major components of the tectorial membrane in the inner ear. Using targeted DNA capture and massively parallel sequencing (MPS), we screened 42 genes known to be responsible for human deafness in a Chinese family (Family 3187) in which common deafness mutations had been ruled out as the cause, and identified a novel mutation, c.257-262CCTTTC>GCT (p. Ser86Cys; p. Pro88del) in exon 3 of the TECTA gene in the proband and his extended family. All affected individuals in this family had moderate down-sloping hearing loss across all frequencies. To our knowledge, this is the second TECTA mutation identified in Chinese population. This study demonstrates that targeted genomic capture, MPS, and barcode technology might broaden the availability of genetic testing for individuals with undiagnosed DFNA.

Sensorineural hearing loss caused by mutations in two alleles of both GJB2 and SLC26A4 genes

BACKGROUND

Most studies of the molecular etiology of sensorineural hearing loss have described deafness as a monogenic disease encompassing double-allele mutations for patients with autosomal recessive deafness. Here, we report the first case of autosomal recessive genetic deafness in an enlarged vestibular aqueduct syndrome (EVAS) patient with biallelic mutations in two deafness genes.

METHODS

Temporal computed tomography (CT), complete physical and otoscopic examinations, and an audiological study, including tympanometry, pure-tone audiometry or auditory steady-state response (ASSR), were carried out. Exon 2 of GJB2 and the coding exons of SLC26A4 were sequenced.

RESULTS

A patient with an enlarged vestibular aqueduct was found to carry c.1229C>T/c.1079C>T compound heterozygous mutations in SLC26A4.This individual also carried c.257C>G/c.299-300delAT compound heterozygous mutations in GJB2. As a result, the recurrent risk of the patient's siblings increased significantly from 25% for typical autosomal recessive deafness to 43.75%.

CONCLUSIONS

The findings of the present study challenge the traditional diagnostic strategy in which testing is generally considered complete upon identification of a double-allele mutation within one gene, with significant implications for genetic counseling and risk prediction. Our results suggest that, with advances in sequencing technology, it will be possible and necessary to test all known deafness genes in the near future, as this will likely allow more accurate genetic counseling of patients.

The ethics of abortions for fetuses with congenital abnormalities

Abortion remains a highly contentious moral issue, with the debate usually framed as a battle between the fetus's right to life and the woman's right to choose. Often overlooked in this debate is the impact of the concurrent legalization of abortion and the development of new prenatal screening tests on the birth prevalence of many inherited diseases. Most proponents of abortion support abortion for fetuses with severe congenital diseases, but there has unfortunately been, in our opinion, too little debate over the moral appropriateness of abortion for much less severe congenital conditions such as Down's syndrome, deafness, and dwarfism. Due to scientific advances, we are looking at a future in which prenatal diagnosis will be safer and more accurate, raising the specter, and the concomitant ethical concerns, of wholesale abortions. Herein, we present a reframing of the abortion debate that better encompasses these conditions and offers a more nuanced position.

Intrafamilial variability of the deafness and goiter phenotype in Pendred syndrome caused by a T416P mutation in the SLC26A4 gene

Pendred syndrome (PS) is the most common cause of syndromic deafness, accounting for more than 5% of all autosomal-recessive hearing loss cases. It is characterized by bilateral sensorineural hearing loss and by goiter with or without hypothyroidism. Mutations in the SLC26A4 gene cause both classical PS and deafness associated with an enlarged vestibular aqueduct without goiter. To investigate a possible genotype-phenotype correlation in PS, we performed a detailed clinical and genetic study in three adult German sibs with typical PS caused by a common homozygous SLC26A4 mutation, T416P. An audiological long-term follow-up of 23 yr showed that the mutation T416P is associated with a distinct type of hearing loss in each of the three sibs: moderate-to-profound progressive deafness, profound nonprogressive deafness, and a milder but more rapidly progressing form. We show that these phenotypic differences are not caused by either different degrees of inner ear malformations or sequence variations in the GJB2/connexin 26 gene. Because the thyroid phenotype was also highly variable within the family, with thyroid sizes ranging from normal to large goiters requiring thyroidectomy, this study leads to the conclusion that other environmental and/or genetic factors have an impact on the PS phenotype.