Association between the p.V37I variant of GJB2 and hearing loss: a pedigree and meta-analysis

Comparative genetic analysis of blood and semen samples in sperm donors from Hunan, China

OBJECTIVES

At present, most genetic tests or carrier screening are performed with blood samples, and the known carrier rate of disease-causing variants is also derived from blood. For semen donors, what is really passed on to offspring is the pathogenic variant in their sperm. This study aimed to determine whether pathogenic variants identified in the sperm of young semen donors are also present in their blood, and whether matching results for blood are consistent with results for sperm.

METHODS

We included 40 paired sperm and blood samples from 40 qualified semen donors at the Hunan Province Human Sperm Bank of China. All samples underwent exome sequencing (ES) analysis, and the pathogenicity was assessed according to the American College of Medical Genetics (ACMG) guidelines. Scoring for sperm donation matching, which was based on gene scoring and variant scoring, was also used to assess the consistency of sperm and blood genetic test results.

RESULTS

A total of 108 pathogenic (P)/likely pathogenic (LP) variants in 82 genes were identified. The highest carrier had 7 variants, and there was also one donor did not carry any P/LP variant. On average, each donor carried 2.7 P/LP variants. Among all the P/LP variants, missense mutation was the dominant type and most of them were located in exonic regions. Chromosome 1 harboured the largest number of variants and no pathogenic copy number variants (CNV) was identified in semen donors. The P/LP variant of all the 40 semen donors was consistent by comparing sperm and blood. Except for one case that was slightly different, the rest simulated matching results for blood were all consistent with results for sperm.

CONCLUSIONS

It is reasonable to choose either blood or sperm for genetic screening in semen donors.

Spectrum and Frequencies of Genes for Inherited Hearing Loss in Southwestern Chinese Families

Background: Inherited hearing loss is an extremely heterogeneous and often ethnicity-specific disorder, with more than 150 genes identified to date. Thus, clinical diagnosis is challenging, particularly because of the thousands of different severe causal mutations between populations. Materials and methods: In this study, we aimed to identify the mutational spectra associated with hearing loss in 89 Southwestern Chinese families. We used a hearing loss-targeted panel to sequence 163 genes known to cause or be candidate genes for hearing loss. The targeted panel was implemented to 89 families with syndromic or nonsyndromic hearing loss. Results: Of the total 89 patients, 55 patients carried 101 pathogenic/likely pathogenic alleles, providing a genetic diagnosis in 61.80%. GJB2 variants were predominant, with a frequency of 43.6% among all variants, followed by variants of SLC26A4 (31.7%), MYO15A (5.9%), and MT-RNR1 (5%). These 4 genes accounted for 80.56% (87/108) of all identified alleles. Furthermore, 3 of the 89 patients carried 7 alleles of unknown significance. In total, 45 variants were identified, including 35 variants reported in the Human Gene Mutation Database Professional and 10 novel variants that had not been previously reported. Conclusion: Our findings provide a survey of the mutation spectrum in patients with hearing loss from Southwestern Chinese families. This highlights the fact that genomic sequencing with a selected gene panel specific to hearing loss is effective for its genetic diagnosis.

Systematic review and meta-analysis of pathogenic GJB2 variants in the Asian population

OBJECTIVES

Define the extent to which pathogenic GJB2 (gap junction beta-2) variants are responsible for non-syndromic hearing loss (NSHL) in the Asian population.

METHODS

Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) guidelines were followed. CINAHL, Embase, and PubMed's MEDLINE were accessed from 1997 to 2023 using permutations of the MeSH terms: "Asian," ''Southeast Asian,'' "South Asian," "East Asian," "Southeastern Asian," and "GJB2." Additionally, all countries within the Indian subcontinent, Far East, and Southeast Asia, were included as key terms. Exclusion criteria included non-English publications, a non-Asian study population (per US Office of Management and Budget), and literature not investigating GJB2. An allele frequency analysis of pathogenic GJB2 variants in the Asian population was performed and stratified by country of origin.

RESULTS

One thousand one hundred and forty-one unique studies were identified, of which 420 met our inclusion criteria during the abstract screen. One hundred and ninety-five studies were included in the systematic review after full-text screen. Over 45 pathogenic variants were identified across 11 countries within the Indian subcontinent, Far East, and Southeast Asia. A total of 4,220,591 people from over 30 ethnic groups were included with ages ranging from 0 to 97 years. Of those with reported demographic information, 50 % (221,336/445,813) were female and 50 % (224,477/445,813) were male. The prevalence of pathogenic GJB2 variants varied by country, with common variants including c.235del; p.Leu79Cysfs∗3, c.109G > A; p.Val37Ile, and c.299_300del; p.His100Argfs∗14.

CONCLUSION

Variation in the prevalence of pathogenic GJB2 variants is likely due to the wide diversity of ancestral contributions in the Asian population. There are limited studies on the prevalence of GJB2 variants particularly for countries within the Indian subcontinent and Southeast Asia. Additional studies on the prevalence of GJB2 variants in these countries as well as ethnic sub-groups may be helpful in the development of assays for high throughput diagnosis for patients with hereditary hearing loss.

Genotype-phenotype analysis of hearing function in patients with DFNB1A caused by the c.-23+1G>A splice site variant of the GJB2 gene (Cx26)

The audiological features of hearing loss (HL) in patients with autosomal recessive deafness type 1A (DFNB1A) caused by splice site variants of the GJB2 gene are less studied than those of patients with other variants of this gene. In this study, we present the audiological features of DFNB1A in a large cohort of 134 patients with the homozygous splice site variant c.-23+1G>A and 34 patients with other biallelic GJB2 genotypes (n = 168 patients with DFNB1A). We found that the preservation of hearing thresholds in the speech frequency range (PTA0.5,1.0,2.0,4.0 kHz) in patients with the c.[-23+1G>A];[-23+1G>A] genotype is significantly better than in patients with the "severe" c.[35delG];[35delG] genotype (p = 0.005) and significantly worse than in patients with the "mild" c.[109G>A];[109G>A] genotype (p = 0.041). This finding indicates a "medium" pathological effect of this splice site variant on hearing function. A detailed clinical and audiological analysis showed that in patients with the c.[-23+1G>A];[-23+1G>A] genotype, HL is characterized as congenital or early onset (57.5% onset before 12 months), sensorineural (97.8%), bilateral, symmetrical (82.8%), variable in severity (from mild to profound HL, median hearing threshold in PTA0.5,1.0,2.0,4.0 kHz is 86.73±21.98 dB), with an extremely "flat" audioprofile, and with a tendency toward slow progression (a positive correlation of hearing thresholds with age, r = 0.144, p = 0.041). In addition, we found that the hearing thresholds in PTA0.5,1.0,2.0,4.0 kHz were significantly better preserved in females (82.34 dB) than in males (90.62 dB) (p = 0.001). We can conclude that in patients with DFNB1A caused by the c.-23+1G>A variant, male sex is associated with deteriorating auditory function; in contrast, female sex is a protective factor.

Large language models streamline automated machine learning for clinical studies

A knowledge gap persists between machine learning (ML) developers (e.g., data scientists) and practitioners (e.g., clinicians), hampering the full utilization of ML for clinical data analysis. We investigated the potential of the ChatGPT Advanced Data Analysis (ADA), an extension of GPT-4, to bridge this gap and perform ML analyses efficiently. Real-world clinical datasets and study details from large trials across various medical specialties were presented to ChatGPT ADA without specific guidance. ChatGPT ADA autonomously developed state-of-the-art ML models based on the original study's training data to predict clinical outcomes such as cancer development, cancer progression, disease complications, or biomarkers such as pathogenic gene sequences. Following the re-implementation and optimization of the published models, the head-to-head comparison of the ChatGPT ADA-crafted ML models and their respective manually crafted counterparts revealed no significant differences in traditional performance metrics (p ≥ 0.072). Strikingly, the ChatGPT ADA-crafted ML models often outperformed their counterparts. In conclusion, ChatGPT ADA offers a promising avenue to democratize ML in medicine by simplifying complex data analyses, yet should enhance, not replace, specialized training and resources, to promote broader applications in medical research and practice.

Degradation of cochlear Connexin26 accelerate the development of age-related hearing loss

The GJB2 gene, encoding Connexin26 (Cx26), is one of the most common causes of inherited deafness. Clinically, mutations in GJB2 cause congenital deafness or late-onset progressive hearing loss. Recently, it has been reported that Cx26 haploid deficiency accelerates the development of age-related hearing loss (ARHL). However, the roles of cochlear Cx26 in the hearing function of aged animals remain unclear. In this study, we revealed that the Cx26 expression was significantly reduced in the cochleae of aged mice, and further explored the underlying molecular mechanism for Cx26 degradation. Immunofluorescence co-localization results showed that Cx26 was internalized and degraded by lysosomes, which might be one of the important ways for Cx26 degradation in the cochlea of aged mice. Currently, whether the degradation of Cx26 in the cochlea leads directly to ARHL, as well as the mechanism of Cx26 degradation-related hearing loss are still unclear. To address these questions, we generated mice with Cx26 knockout in the adult cochlea as a model for the natural degradation of Cx26. Auditory brainstem response (ABR) results showed that Cx26 knockout mice exhibited high-frequency hearing loss, which gradually progressed over time. Pathological examination also revealed the degeneration of hair cells and spiral ganglions, which is similar to the phenotype of ARHL. In summary, our findings suggest that degradation of Cx26 in the cochlea accelerates the occurrence of ARHL, which may be a novel mechanism of ARHL.

Analysis of GJB2 gene mutations spectrum and the characteristics of individuals with c.109G>A in Western Guangdong

BACKGROUND

GJB2 mutations are among the most important causes of deafness, and their prevalence varies greatly among different countries and ethnic groups. This study aimed to determine the pathogenic mutation spectrum of GJB2 in patients with nonsyndromic hearing loss (NSHL) in Western Guangdong and to explore the pathogenic characteristics of the c.109G>A locus.

METHODS

In total, 97 NSHL patients and 212 normal controls (NC) were included in this study. Genetic sequencing analyses were performed on GJB2.

RESULTS

In the NSHL group, the main pathogenic mutations in GJB2 were as follows: c.109G>A, c.235delC, and c.299_300delAT with allele frequencies of 9.28%, 4.12%, and 2.06%, respectively. c.109G>A was the most frequently detected pathogenic mutation in this region. In the NC group, the allele frequency of c.109G>A among 30-50 years old subjects was markedly lower than that among 0-30 years old subjects (5.31% vs. 11.11%, p < 0.05).

CONCLUSION

We found the pathogenic mutation spectrum of GJB2 in this region and showed that c.109G>A was the most common GJB2 mutation with unique characteristics, such as clinical phenotypic heterogeneity and delayed onset. Therefore, the c.109G>A mutation should be considered as an essential marker for routine genetic assessment of deafness, which can also be beneficial for preventing deafness.

Genetic testing of sperm donors in China: a survey of current practices

Background

The National Health and Family Planning Commission of China (NHFPCC) issued the "Measures for the Management of Human Sperm Banks," which was revised in 2003 and is still in effect today. One of the standard guidelines is that potential donors undergo laboratory testing to exclude infectious and genetic diseases and karyotype analysis. However, patient demands for donor genetic testing have also increased, and only karyotype analysis to exclude genetic diseases is not sufficient to meet these demands.

Objective

To examine donor genetic screening practices at sperm banks in China and to evaluate the qualifications and skills of genetic counselors at the banks.

Materials and methods

An electronic survey was distributed to twenty-seven sperm banks to examine donor genetic screening practices at sperm banks in China and to evaluate the qualifications and skills of genetic counselors at the banks. Twenty-six human sperm banks responded to a 32-question survey about their current practices related to genetic testing of sperm donors.

Results

The 26 sperm banks reported that all qualified sperm donors undergo karyotype analysis; 22 banks (84.6%) collected three generations of family history from each qualified sperm donor; 10 (38.5%) reported that they attempted to accommodate special requests from donor semen recipients for particular genetic tests. Only 2 of the 26 (7.7%) sperm banks reported that they performed whole-exome sequencing. At all the sperm banks, consent for genetic testing was obtained as part of the overall contract for sperm donors. Nineteen (73.1%) sperm banks had genetic counselors on their staff, while six (23.1%) had no genetic counselors on their staff but had access to genetic counselors at the hospital. Only one (3.8%) sperm bank had no genetic counselors on their staff or at the hospital.

Conclusions

The need for larger scale genetic testing of donors and recipients and an extensive panel of genetic tests specific to the Chinese population. Additionally, professionally trained geneticists must be employed as genetic counsellors so that the results of genetic tests and their implications can be explained to donors.

Genetic testing of sperm donors at a human sperm bank in China

Background

In China, numerous human sperm banks only perform three-generation family history evaluation to exclude genetic diseases with clinical symptoms; therefore, many inherited risks cannot be detected before donor qualification even when a thorough genetic family history evaluation has been performed. Hence, the risk of recessive disease inheritance persists with the current eligibility guidelines in China regarding the donor selection process.

Methods

Retrospective study that reviewed the genetic test analyses and clinical outcomes of young adult men who were qualified sperm donors at the Hunan Province Human Sperm Bank of China from January 1, 2018, to May 1, 2021. We included a total of 3231 qualified sperm donors: all donors underwent primary screening for thalassemia and glucose-6-phosphate dehydrogenase (G6PD) deficiency. Whereafter, 278 of donors underwent genetic testing for specific genes, and 43 donors underwent whole exome sequencing.

Results

2.4% of 3231 qualified sperm donors might have thalassemia and 1.4% might have G6PD deficiency. Sperm donors with thalassemia and G6PD deficiency would be eliminated. Specific gene testing identified 7 of the 278 donors (2.5%) as carriers of at least one pathogenic or likely pathogenic variant in a gene, including 1.9% of 154 donors (3/154) as carrier variants in α-Like or β-Like globin genes, 17.6% of 17 donors (3/17) as carrier variants in GJB2, 12.5% of 8 donors (1/8) as carrier variants in SMN1. In addition, among the 43 sperm donors carrying the 111 pathogenic/likely pathogenic variants, eight (18.6%) were carriers of pathogenic variants of the GJB2 gene. The frequency, therefore, was approximately 1 in 5.

Conclusions

The data suggest that used blood routine and RDT can make a preliminary screening of sperm donors, and special gene testing should be performed for sperm donors according to the regional incidence of specific genetic diseases. Meanwhile, whole exome sequencing can be used as a supplementary application in sperm donor genetic testing, and aid a successful and healthy pregnancy. However, industry guidelines must be modified to incorporate its use.

Genetic profiles of non-syndromic severe-profound hearing loss in Chinese Hans by whole-exome sequencing

Hereditary hearing loss is highly heterogeneous. Despite over 120 non-syndromic deafness genes have been identified, there are still some of novel genes and variants being explored. In the study, we investigated 105 Chinese Han children with non-syndromic, prelingual, severe-profound hearing loss by whole-exome sequencing on DNA samples. The most common deafness gene was GJB2, mainly in variant c.235delC (p.Leu79CysfsTer3). 14 children were identified with pathogenic mutations in three genes, GJB2, SLC26A4, and OTOF. Two mutations have been identified to be pathogenic and not recorded previously, including c.4691G > A (p.Trp1564Ter) and c.3928_3930dup (p.Lys1310dup) in OTOF. The rare variants c.1349G > A (p.Arg450His) and c.456 T > G (p.Asn152Lys) in GSDME, and c.1595G > T (p.Ser532Ile) in SLC26A4 were detected. The frequency of nonsense variant c.2359G > T (p.Glu787Ter) in OTOA was very high in 17 cases. Four of them were identified to be digenic inheritance, including GJB2 and COL4A4, GJB2 and EYA1, GJB2 and COL4A5, and GJB2 and DFNA5. The findings showed that a novel pathogenic variant and rare variants may be associated with severe and profound hearing loss.

Comprehensive analysis of recessive carrier status using exome and genome sequencing data in 1543 Southern Chinese

Traditional carrier screening has been utilized for the detection of carriers of genetic disorders. Since a comprehensive assessment of the carrier frequencies of recessive conditions in the Southern Chinese population is not yet available, we performed a secondary analysis on the spectrum and carrier status for 315 genes causing autosomal recessive disorders in 1543 Southern Chinese individuals with next-generation sequencing data, 1116 with exome sequencing and 427 with genome sequencing data. Our data revealed that 1 in 2 people (47.8% of the population) was a carrier for one or more recessive conditions, and 1 in 12 individuals (8.30% of the population) was a carrier for treatable inherited conditions. In alignment with current American College of Obstetricians and Gynecologists (ACOG) pan-ethnic carrier recommendations, 1 in 26 individuals were identified as carriers of cystic fibrosis, thalassemia, and spinal muscular atrophy in the Southern Chinese population. When the >1% expanded carrier screening rate recommendation by ACOG was used, 11 diseases were found to meet the criteria in the Southern Chinese population. Approximately 1 in 3 individuals (35.5% of the population) were carriers of these 11 conditions. If the 1 in 200 carrier frequency threshold is used, and additional seven genes would meet the criteria, and 2 in 5 individuals (38.7% of the population) would be detected as a carrier. This study provides a comprehensive catalogue of the carrier spectrum and frequency in the Southern Chinese population and can serve as a reference for careful evaluation of the conditions to be included in expanded carrier screening for Southern Chinese people.

Identification and Computational Analysis of Rare Variants of Known Hearing Loss Genes Present in Five Deaf Members of a Pakistani Kindred

Hearing loss (HL) is the most common neurosensory defect in humans that affects the normal communication. Disease is clinically and genetically heterogeneous, rendering challenges for the molecular diagnosis of affected subjects. This study highlights the phenotypic and genetic complexity of inherited HL in a large consanguineous Pakistan kindred. Audiological evaluation of all affected individuals revealed varying degree of mild to profound sensorineural HL. Whole exome (WES) of four family members followed by Sanger sequencing revealed candidate disease-associated variants in five known deafness genes: GJB2 (c.231G>A; p.(Trp77 *)), SLC26A4 (c.1337A>G; p.(Gln446Arg)), CDH23 (c.2789C>T; p.(Pro930Leu)), KCNQ4 (c.1672G>A; p.(Val558Met)) and MPDZ (c.4124T>C; p.(Val1375Ala)). All identified variants replaced evolutionary conserved residues, were either absent or had low frequencies in the control databases. Our in silico and 3-Dimensional (3D) protein topology analyses support the damaging impact of identified variants on the encoded proteins. However, except for the previously established “pathogenic” and “likely pathogenic” categories for the c.231G>A (p.(Trp77 *)) allele of GJB2 and c.1377A>G (p.(Gln446Arg)) of SLC26A4, respectively, all the remaining identified variants were classified as “uncertain significance” based on the American College of Medical Genetics and Genomics/Association for Molecular Pathology (ACMG/AMP) variant pathogenicity guidelines. Our study highlights the complexity of genetic traits in consanguineous families, and the need of combining the functional studies even with the comprehensive profiling of multiple family members to improve the genetic diagnosis in complex inbred families.

Evaluation of the GJB2 and GJB6 Polymorphisms with Autosomal Recessive Nonsyndromic Hearing Loss in Iranian Population

INTRODUCTION

Hearing loss (HL), with more than 100 gene loci, is the most common sensorineural defects in humans. The mutations in two GJB2 and GJB6 (Gap Junction Protein Beta 2, 6) genes are responsible for nearly 50% of autosomal recessive nonsyndromic hearing loss. The aim of the present study was to evaluate polymorphisms of 111C>T (rs7329857) and 337G>T (rs7333214) in GJB2 (encoding connexin 26) and GJB6 (encoding connexin 32) genes, respectively.

MATERIALS AND METHODS

In this study, 32 blood samples were obtained from Iranian patients with HL defect and 32 normal blood samples were prepared. After genomic deoxyribonucleic acid extraction, genotyping in rs7333214 and rs7329857 polymorphisms was conducted using tetra-amplification refractory mutation system-polymerase chain reaction and the obtained data were analyzed.

RESULTS

In this study, the prevalence rates of CC, CT, and TT genotypes in GJB2 gene were reported as 84.4%, 68.7%, and 0% in the affected subjects and 0%, 15.6%, and 31.3% in the control samples, respectively, which were statistically significant (P=0.004). In relation to GJB6 gene, the prevalence rates of GG, GT, and TT genotypes were 65.2%, 78.1%, and 25% in the control subjects and 21.9%, 9.4%, and 0% in the affected samples, respectively, which were not statistically significant (P>0.05).

CONCLUSION

The results of this study revealed that 111C>T polymorphism in GJB2 gene was involved in the incidence of HL in the studied population and could be suggested as a prognostic factor in genetic counseling before marriage and pregnancy.

Natural Course of Residual Hearing with Reference to GJB2 and SLC26A4 Genotypes: Clinical Implications for Hearing Rehabilitation

BACKGROUND

Understanding the characteristics of residual hearing at low frequencies and its natural course in relation to molecular genetic etiology may be important in developing rehabilitation strategies. Thus, we aimed to explore the characteristics and natural course of residual hearing at low frequencies associated with the two most frequent deafness genes: GJB2 and SLC26A4.

METHODS

Initially, 53 GJB2 and 65 SLC26A4 subjects were enrolled, respectively. Only those whose audiograms exhibited hearing thresholds ≤70 dB at 250 and 500 Hz, and who had at least 1-year follow-up period between the first and last audiograms, were included. Collectively, the clinical characteristics of 14 ears from eight subjects with GJB2 variants, and 31 ears from 22 subjects with SLC26A4 variants fulfilled the strict criteria. In this study, a dropout rate refers to an incidence of dropping out of the cohort by cochlear implant surgery due to severe hearing deterioration.

RESULTS

Among the ears with complete serial audiogram data set, significant residual hearing at low frequencies at the time of inclusion was observed in 18.8% of those with GJB2 variants (15 out of 80 ears) and 42.6% of those with SLC26A4 variants (46 out of 108 ears), revealing a difference between two deafness genes. Subsequently, ears with SLC26A4 variants (11 of 46 ears, 23.9%) turned out to have a higher dropout rate for cochlear implantation due to hearing deterioration within the first year than those with GJB2 variants (1 of 15, 6.7%), albeit with no statistical significance. Throughout the follow-up period (mean: 37.2 ± 6.8, range: 12 to 80 months), deterioration of residual hearing at low frequencies at 250 Hz (dB HL/y) and 500 Hz (dB HL/y) of those with GJB2 variants exhibited 3.1 ± 1.3 (range: 0 to 15) and 5.2 ± 1.6 (range: 0 to 20), respectively, suggesting the deterioration of residual hearing in GJB2 variants was rather slow and gradual. Specifically, GJB2 p.Leu79Cysfs*3 show less remarkable residual hearing at low frequencies, but then a relatively stable nature. In contrast, SLC26A4 variants demonstrated a significantly higher dropout rate due to severe hearing deterioration requiring cochlear implantation compared with the GJB2 variants. This trend was observed not only in the first-year follow-up period but also in the follow-up periods thereafter. The p.His723Arg;c.919-2A>G genotype of SLC26A4, in particular, was associated with a high propensity for sudden hearing deterioration, as indicated by the dropout rate, which was as high as 46.2% for cochlear implantation due to hearing deterioration during the first year follow-up period. Furthermore, the dropout rate for cochlear implantation was observed in 7.1% of those with GJB2 variants (one out of 14 ears) and 30.3% of those with SLC26A4 variants (10 out of 33 ears) throughout the entire follow-up period.

CONCLUSIONS

Our results suggest that there is a difference with respect to the progressive nature of residual hearing at low frequencies between the two most common genes responsible for hearing loss, which may provide clinical implications of having individualized rehabilitation and timely intervention.

Next-generation sequencing identifies rare pathogenic and novel candidate variants in a cohort of Chinese patients with syndromic or nonsyndromic hearing loss

Background

Hearing loss (HL) is a common sensory disorder in humans characterized by extreme clinical and genetic heterogeneity. In recent years, next‐generation sequencing (NGS) technologies have proven to be highly effective and powerful tools for population genetic studies of HL. Here, we analyzed clinical and molecular data from 21 Chinese deaf families who did not have hotspot mutations in the common deafness genes GJB2, SLC26A4, GJB3, and MT‐RNR1.

Method

Targeted next‐generation sequencing (TGS) of 127 known deafness genes was performed in probands of 12 families, while whole‐exome sequencing (WES) or trio‐WES was used for the remaining nine families.

Results

Potential pathogenic mutations in a total of 12 deafness genes were identified in 13 probands; the mutations were observed in GJB2, CDH23, EDNRB, MYO15A, OTOA, OTOF, TBC1D24, SALL1, TMC1, TWNK, USH1C, and USH1G, with eight of the identified mutations being novel. Further, a copy number variant (CNV) was detected in one proband with heterozygous deletion of chromosome 4p16.3‐4p15.32. Thus, the total diagnostic rate using NGS in our deafness patients reached 66.67% (14/21).

Conclusions

These results expand the mutation spectrum of deafness‐causing genes and provide support for the use of NGS detection technologies for routine molecular diagnosis in Chinese deaf populations.

Identification of novel variants in MYO15A, OTOF, and RDX with hearing loss by next-generation sequencing

BACKGROUND

Nonsyndromic hearing loss (NSHL) is the most common sensorineural disorder and one of the most common human defects. Autosomal recessive inheritance accounts for a huge percentage of familial cases. Next-generation sequencing (NGS) is a powerful molecular diagnostic strategy for NSHL. The combination of a microarray gene chip and NGS can better delineate the etiology and genetic cause of deafness in many cases.

METHODS

One hundred and thirty-one unrelated students with NSHL who attend a special education school in Yunnan Province were recruited. Firstly, four common deafness-related genes (GJB2, GJB3, SLC26A4, and mtDNA 12S rRNA) were evaluated for mutations using a microarray kit. Furthermore, 227 known human deafness genes were sequenced to identify the responsible genetic variant of the proband in three Chinese families with autosomal recessive hearing loss. The mutational status of family members of the probands was validated by Sanger sequencing.

RESULTS

Five novel variants were found in three families using NGS. In family 1, we identified compound heterozygosity at the MYO15A (OMIM, #600316), including an duplication variant c.3866dupC, p.His1290Alafs*25 and a 3-bp deletion (c.10251_10253del, p.Phe3420del), resulting in protein length changes and premature protein truncation, respectively. In family 2, two affected siblings from a consanguineous Chinese Dai family harbored an c.1274G>C, p.Arg425Pro missense variant in the OTOF (OMIM, #601071). In family 3, we identified compound heterozygosity for c.129_130del, p.His43Glnfs*28 and c.76_79del, p.Lys26* in the RDX gene (OMIM, #611022).

CONCLUSION

Five novel variants were found in three families with NSHL. Our findings extend the mutational spectrum in deafness-related genes and will help physicians in better understanding the etiology of hearing loss.

Systematic evaluation of gene variants linked to hearing loss based on allele frequency threshold and filtering allele frequency

As the number of genes identified for linkage to hearing loss has been increasing and more public databases have become available, we aimed to systematically evaluate all variants reported for nonsyndromic hearing loss (NSHL) based on their allele frequencies (AFs) in the general population. Among the 3,549 variants in 97 NSHL genes reported as pathogenic/likely pathogenic in ClinVar and HGMD, 1,618 were found in public databases (gnomAD, ExAC, EVS, and 1000G). To evaluate the pathogenicity of these variants, we employed AF thresholds and NSHL-optimized ACMG guidelines. AF thresholds were determined using a high-resolution variant frequency framework and Hardy-Weinberg equilibrium calculation: 0.6% and 0.1% for recessive and dominant genes, respectively. Filtering AFs of variants linked to NSHL were obtained based on AFs reported in gnomAD and ExAC. We found that 48 variants in 23 genes had filtering AFs above the suggested thresholds and assumed that these variants might be benign based on their filtering AFs. 47 variants, except for one notorious high-frequency GJB2 mutation (c.109G > A; p.Val37Ile), were confirmed to be benign/likely benign by the NSHL-optimized ACMG guidelines. The proposed systematic approach will aid in precise evaluation of NSHL variant pathogenicity in the context of filtering AFs, AF thresholds, and NSHL-specific ACMG guidelines, thus improving NSHL diagnostics.

Whole-exome sequencing identifies a novel missense variant within LOXHD1 causing rare hearing loss in a Chinese family

Background

Deafness, autosomal recessive 77 (DFNB77) is a rare non-syndromic hearing loss (NSHL) worldwide, which is caused by deleterious variants within lipoxygenase homology domains 1 (LOXHD1). Here we identified that a novel missense variant of LOXHD1 was associated with NSHL in a Chinese family under consanguineous marriage.

Case presentation

A 28-year-old woman suffered a bilateral profound NSHL. Impedance audiometry, temporal bone computerized tomography (TBCT) scans and magnetic resonance imaging-inner ear hydrography (MRI-IEH) did not find any obvious abnormality of middle or inner ear. Routine genetic detection did not find pathogenic variants in common HL-associated genes. Therefore, we performed a whole-exome sequencing (WES) in this family. By trio-WES, co-segregation validation and bioinformatics analysis, we revealed that a novel homozygous variant in this patient, LOXHD1: c.5948C > T (p.S1983F), might be the pathogenic factor. Her parents (heterozygotes) and brother (wild-type) were asymptomatic.

Conclusions

We successfully identified a novel variant of LOXHD1 associated with a rare NSHL from a Chinese family. Our finds highlight the effectiveness of trio-WES for molecular diagnosis of rare NHSL, and expand the genotypic spectrum of DFNB77.

Electronic supplementary material

The online version of this article (10.1186/s12881-019-0758-2) contains supplementary material, which is available to authorized users.

Genetic screening involving 101 hot spots for neonates not passing newborn hearing screening and those random recruited in Dongguan

In order to investigate essential molecular causes for hearing loss and mutation frequency of deafness-related genes, 1315 newborns who did not pass the Newborn Hearing Screening (NHS) (audio-no-pass) and 1000 random-selected infants were subjected to detection for 101 hotspot mutations in 18 common deafness-related genes. Totally, 23 alleles of 7 deafness genes were detected out. Significant difference (χ² = 25.320, p = 0.000) existed in causative mutation frequency between audio-no-pass group (81/1315, 6.160%) and random-selected cohort (18/1000, 1.80%). Of the genes detected out, GJB2 gene mutation was with significant difference (χ² = 75.132, p = 0.000) between audio-no-pass group (417/1315, 31.711%) and random-selected cohort (159/1000, 15.900%); c.109G > A was the most common allele, as well as the only one with significantly different allele frequency (χ² = 79.327, p = 0.000) between audio-no-pass group (392/1315, 16.84%) and random-selected cohort (140/1000, 7.55%), which suggested c.109G > A mutation was critical for newborns' hearing loss. This study performed detection for such a large scale of deafness-associated genes and for the first time compared mutations between audio-no-pass and random-recruited neonates, which not only provided more reliable DNA diagnosis result for medical practioners and enhanced clinical care for the newborns, but gave more accurate estimation for mutation frequency.