Homozygosity for the V37I GJB2 mutation in fifteen probands with mild to moderate sensorineural hearing impairment: further confirmation of pathogenicity and haplotype analysis in Asian populations

The GJB2 (Cx26) Gene Variants in Patients with Hearing Impairment in the Baikal Lake Region (Russia)

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.

Evolutionary origin of pathogenic GJB2 alleles in China

The frequency of the pathogenic allele of the autosomal recessive deafness gene GJB2 varies among different populations in the world, and accumulates to a sufficiently high frequency in certain population. The purpose of this study is to investigate the origin and evolution of GJB2 pathogenic alleles in Chinese deaf patients. Children with non-syndromic hearing loss, and their parents, from 295 families were recruited. Customized capture probes targeted at 943 SNPs related to GJB2 gene were designed for sequencing of genomic DNA in blood samples. Haplotypes carrying pathogenic allele were analyzed through linkage disequilibrium block building, ancestry tracing, and extended haplotype heterozygosity calculation. Two pathogenic GJB2 alleles, c.235delC (18.41%) and c.109G>A (15.57%), were observed in 867 donors. For c.235delC allele, 3 different core haplotypes with one major haplotype (97.32%) were found, and their core SNPs were 100% conserved. For c.109G>A allele, 6 different haplotypes with one major haplotype (93.28%) were found and the major c.109G>A allele evolved from a specific ancestral haplotype. Geographical origins of donors carrying GJB2 c.109G>A and c.235delC core haplotypes centered between Qinghai and Neimenggu. GJB2 c.235delC has long-range linkage disequilibrium. No positive selection signature was found for GJB2 c.235delC or c.109G>A in the studied population. In conclusion, we discovered a single origin of GJB2 c.235delC allele and multiple independent origins of GJB2 c.109G>A allele. Alternative to positive selection or multiple independent recurrent mutation event, population bottleneck effect might account for the observed high population frequency of these pathogenic alleles.

A common founder effect of the splice site variant c.-23 + 1G > A in GJB2 gene causing autosomal recessive deafness 1A (DFNB1A) in Eurasia

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.

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

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.

Association of Racial/Ethnic Categories With the Ability of Genetic Tests to Detect a Cause of Cardiomyopathy

Importance

Individuals of all races/ethnicities have a fundamental right to access health care and benefit from advances in science and medicine, including genetic testing.

Objective

To determine whether detection rates for cardiomyopathy genetic testing differed between white people, Asian people, and underrepresented minorities (individuals of black, Hispanic, Native American, Alaskan Native, or Pacific Islander descent).

Design, Setting, and Participants

We conducted a cross-sectional analysis of the genetic panel test results of 5729 probands who had a suspected diagnosis or family history of cardiomyopathy and who had been referred for testing between October 2003 and December 2017. Testing was performed at the Laboratory for Molecular Medicine at Partners Personalized Medicine in Cambridge, Massachusetts. Results were stratified into 3 categories of self-reported race/ethnicity: white, Asian, and underrepresented minorities.

Main Outcomes and Measures

The primary outcome was whether a pathogenic or likely pathogenic variant was identified that explained the features or family history of cardiomyopathy. A secondary outcome was the number of test results that were inconclusive because of the presence of 1 or more variants of uncertain significance in the absence of an explanation for cardiomyopathy features or family history.

Results

A total of 5729 probands were studied (of whom 3523 [61.5%] were male). Of these, 4539 (79.2%) were white, 348 (6.1%) were Asian individuals, and 842 (14.7%) were underrepresented minorities. Positive detection occurred in 1314 white individuals (29.0%) compared with 155 underrepresented minorities (18.4%; χ21 = 39.8; P < .001) and 87 Asian individuals (25.0%; χ21 = 2.5; P = .12). Inconclusive results were found in 1115 white individuals (24.6%) compared with 335 underrepresented minorities (39.8%; χ21 = 83.6; P < .001) and 136 Asian individuals (39.2%; χ21 = 35.8; P < .001).

Conclusions and Relevance

These results show a significantly higher positive detection rate and a significantly lower rate of inconclusive results in white individuals in comparison with underrepresented minorities. This suggests greater clinical usefulness of genetic testing for cardiomyopathy in white persons in comparison with people of other racial/ethnic groups. This clear disparity warrants further study to understand the gaps in usefulness, which may derive from a lack of clinical testing and research in underrepresented minority populations, in the hopes of improving genetic testing outcomes for cardiomyopathy in nonwhite groups.

Analysis of mutation spectrum of common deafness-causing genes in Hakka newborns in southern China by semiconductor sequencing

Hearing loss is a common neurosensory disorder, approximately half of the cases are caused by genetic factors, and approximately 70% of hereditary hearing impairments are nonsyndromic hearing loss (NSHL). The mutations of GJB2 (gap junction beta-2 protein), GJB3 (gap junction beta-3 protein), SLC26A4 (solute carrier family 26 member 4), and MT-RNR1 (mitochondrially encoded 12S RNA) are the most common inherited causes of NSHL. Because of different genetic backgrounds, the mutation spectrum of these common deafness-causing genes varies among different regions in China. Because no data are known on these mutations among the Hakka population of Southern China, we aim to investigate the mutation spectrum to add these to neonatal screening and genetic counseling. A total of 1252 blood samples from newborns have been detected by semiconductor sequencing for 100 mutations loci of 18 deafness-causing genes. Of the participants, 95 subjects carried deafness-causing genes mutations with the carrier rate of 7.59%. The mutation frequencies of GJB2, SLC26A4, GJB3, and mitochondrial genes were 3.04%, 3.51%, 0.16%, and 0.88%, respectively. We followed up subjects with single-gene homozygous or compound heterozygous mutations. Our study firstly analyzed deafness-causing genes mutation spectrum in Hakka population, providing evidence for future neonatal screening and genetic counseling in this area.

Genetic Aetiology of Nonsyndromic Hearing Loss in Moravia-Silesia

BACKGROUND AND OBJECTIVE

Hearing loss is the most common sensory deficit in humans. The aim of this study was to clarify the genetic aetiology of nonsyndromic hearing loss in the Moravian-Silesian population of the Czech Republic.

PATIENTS AND METHODS

This study included 200 patients (93 males, 107 females, mean age 16.9 years, ranging from 4 months to 62 years) with nonsyndromic sensorineural hearing loss. We screened all patients for mutations in GJB2 and the large deletion del(GJB6-D13S1830). We performed further screening for additional genes (SERPINB6, TMIE, COCH, ESPN, ACTG1, KCNQ4, and GJB3) with Sanger sequencing on a subset of patients that were negative for GJB2 mutations.

RESULTS

We detected biallelic GJB2 mutations in 44 patients (22%). Among these patients, 63.6%, 9.1% and 2.3% exhibited homozygous c.35delG, p.Trp24*, and p.Met34Thr mutations, respectively. The remaining 25% of these patients exhibited compound heterozygous c.35delG, c.-23+1G>A, p.Trp24*, p.Val37Ile, p.Met34Thr, p.Leu90Pro, c.235delC, c.313_326del14, p.Ser139Asn, and p.Gly147Leu mutations. We found a monoallelic GJB2 mutation in 12 patients (6.6%). We found no pathogenic mutations in the other tested genes. Conclusions: One fifth of our cohort had deafness related to GJB2 mutations. The del(GJB6-D13S1830), SERPINB6, TMIE, COCH, ESPN, ACTG1, GJB3, and KCNQ4 mutations were infrequently associated with deafness in the Moravian-Silesian population. Therefore, we suggest that del(GJB6-D13S1830) testing should be performed only when patients with deafness carry the monoallelic GJB2 mutation.

Simultaneous multi‑gene mutation screening using SNPscan in patients from ethnic minorities with nonsyndromic hearing‑impairment in Northwest China

The present study aimed to investigate the molecular etiology of nonsyndromic hearing impairment (HI) in hearing impaired populations of Hui, Tibetan, and Tu ethnicities in northwest China. A total of 283 unrelated subjects with HI who attended special education schools in northwest China were enrolled in the present study. Single-nucleotide polymorphisms (SNPs) in three common deafness-related genes, gap junction protein β2 (GJB2), solute carrier family 26 member 4 (SLC26A4) and mitochondrially encoded 12S RNA (mtDNA12SrRNA), were detected using a SNPscan technique. GJB2 mutations were detected in 14.89% of Hui patients, 9.37% of Tibetan patients and 11.83% of Tu patients. The most prevalent GJB2 mutation in the Hui and Tu patients was c.235delC. In the Tibetan patients, the c.109G>A SNP exhibited the highest allele frequency. SLC26A4 mutations were detected in 10.64% of Hui patients, 6.25% of Tibetan patients, and 8.6% of Tu patients. The most common SLC26A4 mutation was c.919-2A>Gin the Hui, Tibetan, and Tu patients, and the second most common SLC26A4 mutations in these patients were c.1517T>G, c.1226G>A andc.2168A>G, respectively. The mutation rates ofmtDNA12SrRNA in the Hui, Tibetan, and Tu patients were 1.06, 5.21, and 5.38%, respectively. These findings demonstrate that the mutation spectra of these deafness-related genes are unique amongst these three ethnic groups. This information will be helpful in designing a protocol for genetic testing for deafness and for achieving accurate molecular diagnoses in northwest China.

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)

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.

Phenotypic Heterogeneity in a DFNA20/26 family segregating a novel ACTG1 mutation

BACKGROUND

Genetic factors play an important role in hearing loss, contributing to approximately 60% of cases of congenital hearing loss. Autosomal dominant deafness accounts for approximately 20% of cases of hereditary hearing loss. Diseases with autosomal dominant inheritance often show pleiotropy, different degrees of penetrance, and variable expressivity.

METHODS

A three-generation Chinese family with autosomal dominant nonsyndromic hearing impairment (ADNSHI) was enrolled in this study. Audiometric data and blood samples were collected from the family. In total, 129 known human deafness genes were sequenced using next-generation sequencing (NGS) to identify the responsible gene mutation in the family. Whole Exome Sequencing (WES) was performed to exclude any other variant that cosegregated with the phenotype.

RESULTS

The age of onset of the affected family members was the second decade of life. The condition began with high-frequency hearing impairment in all family members excluding III:2. The novel ACTG1 c.638A > G (p.K213R) mutation was found in all affected family members and was not found in the unaffected family members. A heterozygous c.638A > G mutation in ACTG1 and homozygous c.109G > A (p.V37I) mutation in GJB2 were found in III:2, who was born with hearing loss. The WES result concurred with that of targeted sequencing of known deafness genes.

CONCLUSIONS

The novel mutation p.K213R in ACTG1 was found to be co-segregated with hearing loss and the genetic cause of ADNSHI in this family. A homozygous mutation associated with recessive inheritance only rarely co-acts with a dominant mutation to result in hearing loss in a dominant family. In such cases, the mutations in the two genes, as in ACTG1 and GJB2 in the present study, may result in a more severe phenotype. Targeted sequencing of known deafness genes is one of the best choices to identify the genetic cause in hereditary hearing loss families.

Mutation Spectrum of Common Deafness-Causing Genes in Patients with Non-Syndromic Deafness in the Xiamen Area, China

In China, approximately 30,000 babies are born with hearing impairment each year. However, the molecular factors causing congenital hearing impairment in the Xiamen area of Fujian province have not been evaluated. To provide accurate genetic testing and counseling in the Xiamen area, we investigated the molecular etiology of non-syndromic deafness in a deaf population from Xiamen. Unrelated students with hearing impairment (n = 155) who attended Xiamen Special Education School in Fujian Province were recruited for this study. Three common deafness-related genes, GJB2, SLC26A4, and mtDNA12SrRNA, were analyzed using all-exon sequencing. GJB2 mutations were detected in 27.1% (42/155) of the entire cohort. The non-syndromic hearing loss (NSHL) hotspot mutations c.109G>A (p.V37I) and c.235delC were found in this population, whereas the Caucasian hotspot mutation c.35delG was not. The allelic frequency of the c.109G>A mutation was 9.03% (28/310), slightly higher than that of c.235delC (8.39%, 26/310), which is the most common GJB2 mutation in most areas of China. The allelic frequency of the c.109G>A mutation was significantly higher in this Xiamen's deaf population than that in previously reported cohorts (P = 0.00). The SLC26A4 mutations were found in 16.77% (26/155) of this cohort. The most common pathogenic allele was c.IVS7-2A>G (6.13%, 19/310), and the second most common was the c.1079C>T (p.A360V) mutation (1.94%, 6/310) which has rarely been reported as a hotspot mutation in other studies. The mutation rate of mtDNA12SrRNA in this group was 3.87% (6/155), all being the m.A1555G mutation. These findings show the specificity of the common deaf gene-mutation spectrum in this area. According to this study, there were specific hotspot mutations in Xiamen deaf patients. Comprehensive sequencing analysis of the three common deaf genes can help portray the mutation spectrum and develop optimal testing strategies for deaf patients in this area.

Common molecular etiology of nonsyndromic hearing loss in 484 patients of 3 ethnicities in northwest China

CONCLUSIONS

In the study population in northwest China, a total of 33.06% of deaf patients have inherited hearing impairment caused by GJB2, SLC26A4, and mtDNA 1555A>G mutations. The mutation frequencies of GJB2, SLC26A4, and mtDNA 1555A>G genes were 16.12%, 10.54%, and 6.4%, respectively, in our study cohort. Thus, screening is conventionally performed for GJB2, SLC26A4, and mtDNA 1555A>G in these populations.

OBJECTIVE

This study aimed to investigate the mutations of GJB2, mitochondrial DNA 12S rRNA1555A>G, and SLC26A4 genes in Han Chinese, Hui people, and Tibetan ethnicities in patients with nonsyndromic hearing loss (NSHL) in northwest China.

METHODS

A total of 484 unrelated subjects with hearing loss who attended special education schools in northwest China were enrolled in this study. Three prominent deafness-related genes, GJB2, SLC26A4, and mtDNA 1555A>G, were screened for mutations in our study cohort.

RESULTS

The mutation frequencies of GJB2, SLC26A4, and mtDNA 1555A>G genes were 16.12%, 10.54%, and 6.4%, respectively. The prevalence of GJB2 mutations was 17.52%, 15.35%, and 11.43% in Han Chinese, Hui people, and Tibetan participants, respectively. c.235delC was the most prevalent mutation, accounting for 65.71% of all GJB2 mutant alleles. The prevalence of SLC26A4 mutations was 12.39%, 8.84%, and 8.57% in Han Chinese, Hui people, and Tibetan participants, respectively. The c.919-2 A>G mutation was the most common form, accounting for 60.47% of all SLC26A4 mutant alleles. The prevalence of the homoplasmic mtDNA 1555A>G mutation was 8.97%, 3.72%, and 5.71% in Han Chinese, Hui people, and Tibetan participants, respectively, which represents a statistically significant difference between the Han Chinese and Hui people (χ(2) = 5.118, p < 0.05).