Exome sequencing identifies novel variants associated with non-syndromic hearing loss in the Iranian population

Autosomal recessive non-syndromic hearing loss (ARNSHL) is a public health concern in the Iranian population, with an incidence of 1 in 166 live births. In the present study, the whole exome sequencing (WES) method was applied to identify the mutation spectrum of NSHL patients negative for GJB2 gene mutations. First, using ARMS PCR followed by Sanger sequencing of the GJB2 gene, 63.15% of mutations in patients with NSHL were identified. Among the identified mutations in GJB2:p.Val43Met and p.Gly21Arg were novel. The remaining patients were subjected to WES, which identified novel mutations including MYO15A:p.Gly39LeufsTer188, ADGRV1:p.Ser5918ValfsTer23, MYO7A: c.5856+2T>c (splicing mutation), FGF3:p.Ser156Cys. The present study emphasized the application of WES as an effective method for molecular diagnosis of NSHL patients negative for GJB2 gene mutations in the Iranian population.

Whole-Exome Sequencing Identifies a Recurrent Small In-Frame Deletion in MYO15A Causing Autosomal Recessive Nonsyndromic Hearing Loss in 3 Iranian Pedigrees

BACKGROUND

Hearing loss (HL) is the most prevalent and genetically heterogeneous sensory disabilities in humans throughout the world.

METHODS

In this study, we used whole-exome sequencing (WES) to determine the variant causing autosomal recessive nonsyndromic hearing loss (ARNSHL) segregating in 3 separate Iranian consanguineous families (with 3 different ethnicities: Azeri, Persian, and Lur), followed by cosegregation analysis, computational analysis, and structural modeling using the I-TASSER (Iterative Threading ASSEmbly Refinement) server. Also, we used speech-perception tests to measure cochlear implant (CI) performance in patients.

RESULTS

One small in-frame deletion variant (MYO15A c.8309_8311del (p.Glu2770del)), resulting in deletion of a single amino-acid residue was identified. We found it to be cosegregating with the disease in the studied families. We provide some evidence suggesting the pathogenesis of this variant in HL based on the American College of Medical Genetics (ACMG) and Genomics guidelines. Evaluation of auditory and speech performance indicated favorable outcome after cochlear implantation in our patients.

CONCLUSIONS

The findings of this study demonstrate the utility of WES in genetic diagnostics of HL.

Heterogeneity of MYO15A variants significantly determine the feasibility of acoustic stimulation with hearing aid and cochlear implant

Autosomal recessive nonsyndromic hearing loss 3 (DFNB3) mainly leads to congenital and severe-to-profound hearing impairment, which is caused by variants in MYO15A. However, audiological heterogeneity in patients with DFNB3 hinders precision medicine in hearing rehabilitation. Here, we aimed to elucidate the heterogeneity of the auditory phenotypes of MYO15A variants according to the affected domain and the feasibilities for acoustic stimulation. We conducted whole-exome sequencing for 10 unrelated individuals from seven multiplex families with DFNB3; 11 MYO15A variants, including the novel frameshift c.900delT (p.Pro301Argfs*143) and nonsense c.4879G > T (p.Glu1627*) variants, were identified. In seven probands, residual hearing at low frequencies was significantly higher in the groups with one or two N-terminal frameshift variants in trans conformation compared to that in the group without these variants. This is consistent with the 56 individuals from the previously published reports that carried a varying number of N-terminal truncating variants in MYO15A. In addition, patients with missense variants in the second FERM domain had better hearing at low frequencies than patients without these variants. Subsequently, acoustic stimulation provided by devices such as hearing aids or cochlear implants was feasible in patients with one or two N-terminal truncating variants or a second FERM missense variant. In conclusion, N-terminal or second FERM variants in MYO15A allow the practical use of acoustic stimulation through hearing aids or electroacoustic stimulation for aural rehabilitation.

Molecular diagnosis of SLC26A4-related hereditary hearing loss in a group of patients from two provinces of Iran

The SLC26A4 gene has been described as the second gene involved in most cases of autosomal recessive non-syndromic hearing loss (ARNSHL), after GJB2. Over 500 different SLC26A4 mutations have been reported, with each ethnic population having its own distinctive mutations. Here, we aimed to determine the frequency and mutation profile of the SLC26A4 gene from two different provinces (center and west) of Iran. This study included 50 nuclear families with two or more siblings segregating presumed ARNSHL. All affected tested negative for mutations in GJB2 at the DFNB1 locus and were therefore screened for autozygosity by descent using short tandem repeat polymorphisms (STRPs) of DFNB4. Sanger sequencing was performed to screen the 20 exons of the SLC26A4 gene for the families linked to this locus. In silico analyses were also performed using available software tools. Four out of 25 (16%) and 3 of 25 (12%) studied families of Isfahan and Hamedan provinces, respectively. were linked to DFNB4. Sanger sequencing led to the identification of six different mutations, one of which (c.919-2A>G) was recurrent and accounted for 31% of all mutant alleles. One out of 7 (14.3%) families with mutations were confirmed to be Pendred syndrome (PS). The SLC26A4 mutations have a high carrying rate in ARNSHL Iranian patients. The identification of a disease causing mutation can be used to establish a genotypic diagnosis and provide important information to the patients and their families.

Targeted Next-Generation Sequencing Identified Compound Heterozygous Mutations in MYO15A as the Probable Cause of Nonsyndromic Deafness in a Chinese Han Family

Hearing loss is a highly heterogeneous disorder, with more than 60% of congenital cases caused by genetic factors. This study is aimed at identifying the genetic cause of congenital hearing loss in a Chinese Han family. Auditory evaluation before and after cochlear implantation and targeted next-generation sequencing of 140 deafness-related genes were performed for the deaf proband. Compound heterozygous mutations c.3658_3662del (p. E1221Wfs∗23) and c.6177+1G>T were identified in MYO15A as the only candidate pathogenic mutations cosegregated with the hearing loss in this family. These two variants were absent in 200 normal-hearing Chinese Hans and were classified as likely pathogenic and pathogenic, respectively, based on the ACMG guideline. Our study further expanded the mutation spectrum of MYO15A as the c.3658_3662del mutation is novel and confirmed that deaf patients with recessive MYO15A mutations have a good outcome for cochlear implantation.

A Novel Cadherin 23 Variant for Hereditary Hearing Loss Reveals Additional Support for a DFNB12 Nonsyndromic Phenotype of CDH23

BACKGROUND AND OBJECTIVES

Identification of the pathogenic mutations underlying hereditary hearing loss (HL) is difficult, since causative mutations in 60 different genes have so far been reported.

METHODS

A comprehensive clinical and pedigree examination was performed on a multiplex family suffering from HL. Direct sequencing of GJB2 and genetic linkage analysis of 5 other most common recessive nonsyndromic HL (ARNSHL) genes were accomplished. Next-generation sequencing (NGS) was utilized to reveal the possible genetic etiology of the disease.

RESULTS

NGS results showed a novel rare variant c.2977G>A (p.Asp993Asn) in the CDH23 gene. The variant, which is a missense in exon 26 of the CDH23 gene, fulfills the criteria of being categorized as pathogenic according to the American College of Medical Genetics and Genomics (ACMG) guideline. Electroretinography rejects the Usher syndrome in the family.

CONCLUSIONS

The present study shows that an accurate molecular diagnosis based on NGS technologies largely improves molecular-diagnostic outcome and thus genetic counseling, and helps to clarify the recurrence risk in deaf families.

Identification and clinical implications of a novel pathogenic variant in the GJB2 gene causes autosomal recessive non-syndromic hearing loss in a consanguineous Iranian family

Mutations in the GJB2 gene, which encodes the connexin26 protein and is involved in inner ear homeostasis, are the most common cause of autosomal recessive non-syndromic hearing loss (ARNSHL) in many populations. This study was aimed to determine the molecular etiology in a consanguineous Iranian family affected by profound ARNSHL. A comprehensive family history was obtained, and clinical evaluations and pedigree analysis were performed in the family with 4 affected members. After extraction of genomic DNA, the entire coding region of GJB2 was directly sequenced in all family members. In silico analyses were also performed using available software tools. Sanger sequencing results showed a novel rare homozygous variant (c.109_110insG) in the GJB2 gene. This frameshift variant in exon 2 of the GJB2 gene fulfills the criteria of being categorized as pathogenic according to the American College of Medical Genetics and Genomics (ACMG) guideline. Confirmation was done with the co-segregation study and checking the frequency of the novel variant in 100 ethnically matched normal control subjects. The present study suggests that investigation of GJB2 mutations may still be useful to determine the etiology of HL in Iran.

Next generation sequencing and genetics of hereditary hearing loss in the iranian population: New insights from a systematic review

BACKGROUND

Hereditary hearing loss (HL) as a common disorder is genetically heterogeneous, which poses a challenge for clinical and molecular diagnosis. Next-generation sequencing (NGS) technologies have proven to be the best solution for mutational screening, even though it is not always conclusive. Here, we have reviewed the results of previously published data on HL mutations identified with NGS, as well as the efficiency of this technology in detecting HL in Iran.

METHODS

A systematic literature review of the PubMed, Google Scholar, Web of Science, and Science Direct databases were conducted for articles published before May 2019. The primary data of these studies, including the number of samples, mutation frequency and so on were extracted.

RESULTS

Seventy-five articles were reviewed, and 10 met our inclusion criteria. Totally 432 unrelated families were included and analyzed for the type and prevalence of the gene mutations and pathogenic variants were discovered in 34 non-syndromic HL (NSHL) genes. Altogether 237 different genetic mutations were detected. However, p. Gln1576Stop in PCDH15 was the most common mutation accounting for 1% of the populations studied. NGS platforms have yielded only a 47.1% molecular diagnosis rate for NSHL etiologies in the Iranian population, which is significantly lower than that identified in the other part of the Middle East.

CONCLUSION

The results showed that NGS platforms can greatly assist and enhance HL diagnosis and improve molecular diagnostic outcome. However, researchers were unable to provide 53% of their Iranian cohort with a molecular diagnosis for their HL. It seems that many rare genes are responsible for the majority of HL in the Iranian cohort. Future explorative investigations utilizing NGS technologies, such as WES, into the Iranian population are warranted.

A Novel Pathogenic Variant in the CABP2 Gene Causes Severe Nonsyndromic Hearing Loss in a Consanguineous Iranian Family

BACKGROUND AND OBJECTIVES

Hereditary hearing loss (HL) can originate from mutations in one of many genes involved in the complex process of hearing. CABP2 mutations have been reported to cause moderate HL. Here, we report the whole exome sequencing (WES) of a proband presenting with prelingual, severe HL in an Iranian family.

METHODS

A comprehensive family history was obtained, and clinical evaluations and pedigree analysis were performed in the family with 2 affected members. After excluding mutations in the GJB2 gene and 7 other most common autosomal recessive nonsyndromic HL (ARNSHL) genes via Sanger sequencing and genetic linkage analysis in the family, WES was utilized to find the possible etiology of the disease.

RESULTS

WES results showed a novel rare variant (c.311G>A) in the CABP2gene.This missense variant in the exon 4 of the CABP2gene meets the criteria of being pathogenic according to the American College of Medical Genetics and Genomics (ACMG) interpretation guidelines.

CONCLUSIONS

Up to now, 3 mutations have been reported for the CABP2gene to cause moderate ARNSHL in different populations. Our results show that CABP2variantsalso cause severe ARNSHL, adding CABP2to the growing list of genes that exhibit phenotypic heterogeneity. Expanding our understanding of the mutational spectrum of HL genes is an important step in providing the correct clinical molecular interpretation and diagnosis for patients.

A systematic review of SLC26A4 mutations causing hearing loss in the Iranian population

OBJECTIVES

The genetics of sensorineural hearing loss is characterized by a high degree of heterogeneity. In spite of this, mutations in the SLC26A4 gene, have been reported to be the second most common contributor after those of GJB2 in many populations. However, different results have been reported for the frequency of SLC26A4 mutations in Iran, which varies between 0 and 12.3%. Here, we have taken together and reviewed the spectrum and frequency of the reported SLC26A4 mutations to provide a comprehensive collection of data for SLC26A4 mutations and HL in the Iranian population and considered founder mutations.

METHODS

A systematic literature review of the PubMed, Google Scholar, Web of Science, and Science Direct databases was conducted for articles published before March 2019. The primary data of these studies including the number of samples, mutation frequency and so on were extracted.

RESULTS

Nine studies involved 827 unrelated families were included and analyzed for the type and prevalence of the SLC26A4 gene mutations. Altogether 39 different genetic mutations were detected. SLC26A4 mutations were found to be 6.39% in the population studied which is significantly lower than that identified in the east Asia. However, c.1334T > G was the most common mutation accounting for 10% of the populations studied.

CONCLUSIONS

This data gives an overview of the SLC26A4 mutations in Iran, which could be used for screening, diagnostic programs of live births and genetic counseling.

GJB2-related hearing loss in central Iran: Review of the spectrum and frequency of gene mutations

Mutations in the GJB2 gene are a main cause of autosomal-recessive nonsyndromic hearing loss (ARNSHL) in many populations. Previous studies have estimated the average frequency of GJB2 mutations to be ∼16% in Iran, but would vary among different ethnic groups. Here, we have taken together and reviewed results from our two previous publications and data from searching other published mutation reports to provide a comprehensive collection of data for GJB2 mutations and HL in central Iran. In all, 332 unrelated families were included and analyzed for the prevalence and type of the GJB2 gene mutations. In total, the frequency of GJB2 mutations was found to be 16% in the central provinces, which is significantly higher than those identified in southern populations of Iran. Also, c.35delG was the most frequent mutation in the related population. The present study suggests that mutations in the GJB2 gene, especially c.35delG, are important causes of HL in central Iran and can be used as a basis of genetic counseling and clinical guidelines in this region.

Genetics of Hereditary Hearing Loss in the Middle East: A Systematic Review of the Carrier Frequency of the GJB2 Mutation (35delG)

BACKGROUND AND OBJECTIVES

Mutations in the GJB2 gene are a major cause of hearing loss in many populations. A single mutation of this gene (c.35delG) accounts for approximately 70% of mutations in Caucasians with a carrier frequency of 2-4% in Europe. This study aims to determine the rate of c.35delG carrier frequency in the Middle East.

METHOD

A systematic literature review of the PubMed, Google Scholar, Web of Science, and Science Direct databases was conducted for articles published before March 2019. The primary data of eligible studies including the number of samples, carrier frequency and so on were extracted.

RESULTS

Fourteen studies that involved 5,200 random controls from 15 populations of the Middle East were included and analyzed for the carrier frequency. The overall c.35delG carrier frequency was found to be 1.38% in the studied populations which is significantly lower than that identified in European populations, and also a west-to-east Middle Eastern gradient in the carrier frequency of c.35delG is suggested.

CONCLUSION

This study shows the importance of establishing prevalence, based on the local population, for screening and diagnostic programs of live births.

Genetics of hereditary hearing loss in east Iran population: A systematic review of GJB2 mutations

Mutations in the GJB2 gene are the most common cause of pre-lingual hearing loss (HL) worldwide. Previous studies have shown the frequency of GJB2 mutations to be 16% in Iran, but varies among different ethnic groups. Here, we have reviewed results from previous published mutation reports to provide a comprehensive collection of data for GJB2 mutations and HL in eastern Iran. We conducted a systematic literature review of PubMed, Google Scholar, Web of Science, and Science Direct databases for articles published before March, 2019. The literature search was performed by 2 independent researchers. The primary data of these studies including the number of samples, allelic frequency, and so on were extracted. Six studies involving 812 unrelated families from four different eastern provinces were included and analyzed for the type and prevalence of GJB2 mutations. A total of 19 different genetic variants were detected. GJB2 mutations were 8.8% in the studied eastern provinces, which was lower than that reported in northern populations of Iran. Moreover, a gradient in the frequency of GJB2 mutations from north to south Iran was observed. c.35delG was the most frequent mutation, accounting for 48.5% % of the populations studied. However, this mutation was absent in the Baluchi population. This review shows that particular rare mutations are frequent in some Iranian ethnic groups, and should be considered for genetic counselling.

Genetics of Hearing Loss in North Iran Population: An Update of Spectrum and Frequency of GJB2 Mutations

Diagnosis of pre-lingual hearing loss (HL) is difficult owing to the high number of genes responsible. The most frequent cause of HL is DFNB1 due to mutations in the GJB2 gene. It represents up to 40% of HL cases in some populations. In Iran, it has previously been shown that DFNB1 accounts for 16-18% of cases but varies among different ethnic groups. Here, we reviewed results from our three previous publications and data from other published mutation reports to provide a comprehensive collection of data for GJB2 mutations and HL in northern Iran. In total, 903 unrelated families from six different provinces, viz., Gilan, Mazandaran, Golestan, Ghazvin, Semnan, and Tehran, were included and analyzed for the type and prevalence of GJB2 mutations. A total of 23 different genetic variants were detected from which 18 GJB2 mutations were identified. GJB2 mutations were 20.7% in the studied northern provinces, which was significantly higher than that reported in southern populations of Iran. Moreover, a gradient in the frequency of GJB2 mutations from north to south Iran was observed. c.35delG was the most common mutation, accounting for 58.4% of the cases studied. This study suggests that c.35delG mutation in GJB2 is the most important cause of HL in northern Iran.