Novel compound heterozygous MYO15A splicing variants in autosomal recessive non-syndromic hearing loss

BACKGROUND

Hereditary hearing loss is a highly heterogeneous disorder. This study aimed to identify the genetic cause of a Chinese family with autosomal recessive non-syndromic sensorineural hearing loss (ARNSHL).

METHODS

Clinical information and peripheral blood samples were collected from the proband and its parents. Two-step high-throughput next-generation sequencing on the Ion Torrent platform was applied to detect variants as follows. First, long-range PCR was performed to amplify all the regions of the GJB2, GJB3, SLC26A4, and MT-RNR1 genes, followed by next-generation sequencing. If no candidate pathogenetic variants were found, the targeted exon sequencing with AmpliSeq technology was employed to examine another 64 deafness-associated genes. Sanger sequencing was used to identify variants and the lineage co-segregation. The splicing of the MYO15A gene was assessed by in silico bioinformatics prediction and minigene assays.

RESULTS

Two candidate MYO15A gene (OMIM, #602,666) heterozygous splicing variants, NG_011634.2 (NM_016239.3): c.6177 + 1G > T and c.9690 + 1G > A, were identified in the proband, and these two variants were both annotated as pathogenic according to the American College of Medical Genetics and Genomics (ACMG) guidelines. Further bioinformatic analysis predicted that the c.6177 + 1G > T variant might cause exon skipping and that the c.9690 + 1G > A variant might activate a cryptic splicing donor site in the downstream intronic region. An in vitro minigene assay confirmed the above predictions.

CONCLUSIONS

We identified a compound heterozygous splicing variant in the MYO15A gene in a Han Chinese family with ARNSHL. Our results broaden the spectrum of MYO15A variants, potentially benefiting the early diagnosis, prevention, and treatment of the disease.

Mutation analysis of GJB2, SLC26A4, GJB3 and mtDNA12SrRNA genes in 251 non-syndromic hearing loss patients in Fujian, China

OBJECTIVES

The molecular etiology of non-syndromic hearing loss (NSHL) in Southeastern China (Fujian) has not been precisely identified. our study selected patients with NSHL and analyzed their causative genes, which helped to improve the accuracy of the diagnosis of hereditary hearing loss (HHL) and its treatment.

METHODS

251 unrelated patients who attended the otolaryngology clinic of Fujian Maternal and Child Health Hospital with hearing loss were enrolled to our study. All patients had genetic tests and listening tests, of which 251 were diagnosed with NSHL. In addition, we used whole-exome sequencing (WES) in a patient who has a significant family history of HHL but negative for gene chip testing, as well as in his family members.

RESULT

Among of 251 patients, Nucleotide changes were found in 63 cases (25.09%), including 34 located in GJB2(13.5%, including 235delC and 299_300delAT), 13 located in SLC26A4(5.18%, including c.919-2G > A and 2168 A > G), 1 located in GJB3(0.4%,538C > T) and 16 located in mtDNA12SrRNA (6.37%,1555 A > G). In addition, we discuss the process of identifying novel PLS1 mutations from 251 patients.

CONCLUSION

Our results demonstrate the conventional deafness gene mutation in 251 NSHL patients in Fujian, China. Compared with the other area of China, we have a lower detection rate, but GJB2 235delC remains the most common mutation in Fujian. In addition, we discuss the process of discovering novel mutation locus for deafness, which provides an understanding for deafness diagnosis and genetic testing.

A Descriptive Observational Study of GJB2 and GJB6 Mutations in Familial Autosomal Recessive Non-syndromic Hearing Impairment

Mutations in the genes, GJB2 and GJB6 play an important role in autosomal recessive, non-syndromic hearing loss. This study is aimed to detect the association of mutations in GJB2 and GJB6 genes in familial autosomal recessive non-syndromic hearing impairment cases. We included 26 families with at least two affected individuals having congenital bilateral, non-syndromic sensorineural hearing loss. Blood samples were drawn, DNA was extracted, and sent for multiplex PCR and Sanger sequencing. Of the 26 families analyzed, GJB2 mutations were detected in 9(34.6%) and GJB6 mutations were not detected in any of the families. GJB2 mutations are a major cause of congenital, non-syndromic hearing loss in this study population. This study also suggests that GJB6 mutations do not contribute to autosomal recessive non-syndromic hearing loss in the Indian population.

Non-Syndromic Sensorineural Hearing Loss in Children

Pediatric hearing loss is common with significant consequences in terms of language, communication, social and emotional development, and academic advancement. Radiological imaging provides useful information regarding hearing loss etiology, prognosis, therapeutic options, and potential surgical pitfalls. This review provides an overview of temporal bone imaging protocols, an outline of the classification of inner ear anomalies associated with sensorineural hearing loss and illustrates some of the more frequently encountered and/or important causes of non-syndromic hearing loss.

Autosomal dominant non-syndromic hearing loss caused by a novel mutation in MYO7A: A case report and review of the literature

BACKGROUND

Variants in the MYO7A gene commonly result in Usher syndrome, and in rare cases lead to autosomal dominant non-syndromic deafness (DFNA11). Currently, only nine variants have been reported to be responsible for DFNA11 and their clinical phenotypes are not identical. Here we present a novel variant causing DFNA11 identified in a three-generation Chinese family.

CASE SUMMARY

The proband was a 53-year-old Han male who presented with post-lingual bilateral symmetrical moderate sensorineural hearing loss. We learned from the patient's medical history collection that multiple family members also had similar hearing loss, generally occurring around the age of 40. Subsequent investigation by high-throughput sequencing identified a novel MYO7A variant. To provide evidence supporting that this variant is responsible for the hearing loss in the studied family, we performed Sanger sequencing on 11 family members and found that the variant co-segregated with the deafness phenotype. In addition, the clinical manifestation of the 11 affected family members was found to be late-onset bilateral slowly progressive hearing loss, inherited in this family in an autosomal dominant manner. None of the affected family members had visual impairment or vestibular symptoms; therefore, we believe that this novel MYO7A variant is responsible for the rare DFNA11 in this family.

CONCLUSION

We report a novel variant leading to DFNA11 which further enriches the collection of MYO7A variants, and our review of the nine previous variants that have been identified to cause DFNA11 provides a reference for clinical genetic counseling.

Loss-of-function mutations in MYO15A and OTOF cause non-syndromic hearing loss in two Yemeni families

BACKGROUND

Hearing loss is a rare hereditary deficit that is rather common among consanguineous populations. Autosomal recessive non-syndromic hearing loss is the predominant form of hearing loss worldwide. Although prevalent, hearing loss is extremely heterogeneous and poses a pitfall in terms of diagnosis and screening. Using next-generation sequencing has enabled a rapid increase in the identification rate of genes and variants in heterogeneous conditions, including hearing loss. We aimed to identify the causative variants in two consanguineous Yemeni families affected with hearing loss using targeted next-generation sequencing (clinical exome sequencing). The proband of each family was presented with sensorineural hearing loss as indicated by pure-tone audiometry results.

RESULTS

We explored variants obtained from both families, and our analyses collectively revealed the presence and segregation of two novel loss-of-function variants: a frameshift variant, c.6347delA in MYO15A in Family I, and a splice site variant, c.5292-2A > C, in OTOF in Family II. Sanger sequencing and PCR-RFLP of DNA samples from 130 deaf and 50 control individuals confirmed that neither variant was present in our in-house database. In silico analyses predicted that each variant has a pathogenic effect on the corresponding protein.

CONCLUSIONS

We describe two novel loss-of-function variants in MYO15A and OTOF that cause autosomal recessive non-syndromic hearing loss in Yemeni families. Our findings are consistent with previously reported pathogenic variants in the MYO15A and OTOF genes in Middle Eastern individuals and suggest their implication in hearing loss.

Comprehensive functional network analysis and screening of deleterious pathogenic variants in non-syndromic hearing loss causative genes

Hearing loss (HL) is a significant public health problem and causes the most frequent congenital disability in developed societies. The genetic analysis of non-syndromic hearing loss (NSHL) may be considered as a complement to the existent plethora of diagnostic modalities available. The present study focuses on exploring more target genes with respective non-synonymous single nucleotide polymorphisms (nsSNPs) involved in the development of NSHL. The functional network analysis and variant study have successfully been carried out from the gene pool retrieved from reported research articles of the last decade. The analyses have been done through STRING. According to predicted biological processes, various variant analysis tools have successfully classified the NSHL causative genes and identified the deleterious nsSNPs, respectively. Among the predicted pathogenic nsSNPs with rsIDs rs80356586 (I515T), rs80356596 (L1011P), rs80356606 (P1987R) in OTOF have been reported in NSHL earlier. The rs121909642 (P722S), rs267606805 (P722H) in FGFR1, rs121918506 (E565A) and rs121918509 (A628T, A629T) in FGFR2 have not been reported in NSHL yet, which should be clinically experimented in NSHL. This also indicates this variant's novelty as its association in NSHL. The findings and the analyzed data have delivered some vibrant genetic pathogenesis of NSHL. These data might be used in the diagnostic and prognostic purposes in non-syndromic congenitally deaf children.

Whole exome sequencing, in silico and functional studies confirm the association of the GJB2 mutation p.Cys169Tyr with deafness and suggest a role for the TMEM59 gene in the hearing process

The development of next generation sequencing techniques has facilitated the detection of mutations at an unprecedented rate. These efficient tools have been particularly beneficial for extremely heterogeneous disorders such as autosomal recessive non-syndromic hearing loss, the most common form of genetic deafness. GJB2 mutations are the most common cause of hereditary hearing loss. Amongst them the NM_004004.5: c.506G > A (p.Cys169Tyr) mutation has been associated with varying severity of hearing loss with unclear segregation patterns. In this study, we report a large consanguineous Emirati family with severe to profound hearing loss fully segregating the GJB2 missense mutation p.Cys169Tyr. Whole exome sequencing (WES), in silico, splicing and expression analyses ruled out the implication of any other variants and confirmed the implication of the p.Cys169Tyr mutation in this deafness family. We also show preliminary murine expression analysis that suggests a link between the TMEM59 gene and the hearing process. The present study improves our understanding of the molecular pathogenesis of hearing loss. It also emphasizes the significance of combining next generation sequencing approaches and segregation analyses especially in the diagnosis of disorders characterized by complex genetic heterogeneity.

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.

The Mitochondrial tRNAHis G12192A Mutation May Modulate the Clinical Expression of Deafness-Associated tRNAThr G15927A Mutation in a Chinese Pedigree

BACKGROUND

Mutations in mitochondrial tRNA (mt-tRNA) genes have been found to be associated with both syndromic and non-syndromic hearing impairment. However, the pathophysiology underlying mt-tRNA mutations in clinical expression of hearing loss remains poorly understood.

OBJECTIVE

The aim of this study was to explore the potential association between mttRNA mutations and hearing loss.

METHODS AND RESULTS

We reported here the molecular features of a pedigree with maternally transmitted non-syndromic hearing loss. Among 12 matrilineal relatives, five of them suffered variable degree of hearing impairment, but none of them had any medical history of using aminoglycosides antibiotics (AmAn). Genetic screening of the complete mitochondrial genomes from the matrilineal relatives identified the coexistence of mt-tRNAHis G12192A and mt-tRNAThr G15927A mutations, together with a set of polymorphisms belonging to human mitochondrial haplogroup B5b1b. Interestingly, the G12192A mutation occurred 2-bp from the 3' end of the TψC loop of mt-tRNAHis, which was evolutionarily conserved from various species. In addition, the well-known G15927A mutation, which disrupted the highly conserved C-G base-pairing at the anticodon stem of mt-tRNAThr, may lead to the failure in mt-tRNA metabolism. Furthermore, a significant decreased in ATP production and an increased ROS generation were observed in polymononuclear leukocytes (PMNs) which were isolated from the deaf patients carrying these mt-tRNA mutations, suggested that the G12192A and G15927A mutations may cause mitochondrial dysfunction that was responsible for deafness. However, the absence of any functional mutations/variants in GJB2, GJB3, GJB6 and TRMU genes suggested that the nuclear genes may not play important roles in the clinical expression of non-syndromic hearing loss in this family.

CONCLUSION

Our data indicated that mt-tRNAHis G12192A mutation may increase the penetrance and expressivity of deafness-associated m-tRNAThr G15927A mutation in this family.

Post-lingual non-syndromic hearing loss phenotype: a polygenic case with 2 biallelic mutations in MYO15A and MITF

BACKGROUND

Hearing loss (HL) represents the most common congenital sensory impairment with an incidence of 1-5 per 1000 live births. Non-syndromic hearing loss (NSHL) is an isolated finding that is not part of any other disorder accounting for 70% of all genetic hearing loss cases.

METHODS

In the current study, we reported a polygenic mode of inheritance in an NSHL consanguineous family using exome sequencing technology and we evaluated the possible effect of the detected single nucleotide variants (SNVs) using in silico methods.

RESULTS

Two bi-allelic SNVs were detected in the affected patients; a MYO15A (. p.V485A) variant, and a novel MITF (p.P338L) variant. Along with these homozygous mutations, we detected two heterozygous variants in well described hearing loss genes (MYO7A and MYH14). The novel MITF p. Pro338Leu missense mutation was predicted to change the protein structure and function.

CONCLUSION

A novel MITF mutation along with a previously described MYO15A mutation segregate with an autosomal recessive non-syndromic HL case with a post-lingual onset. The findings highlight the importance of carrying whole exome sequencing for a comprehensive assessment of HL genetic heterogeneity.

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.

Exome-wide copy number variation analysis identifies a COL9A1 in frame deletion that is associated with hearing loss

Pathogenic variants in COL9A1 are primarily associated with autosomal recessive Stickler syndrome. Patients with COL9A1-associated Stickler syndrome (STL) present hearing loss (HL), ophthalmic manifestations and skeletal abnormalities. However, the clinical spectrum of patients with COL9A1 variants can also include multiple epiphyseal dysplasia, as well as non-syndromic HL that was observed in one previously reported proband. Exome sequencing was performed on the genomic DNA of an Iranian patient and his affected brother who both report non-syndromic HL. A 44.6 kb homozygous in-frame deletion spanning exons 6 to 33 of COL9A1 was detected via exome-based copy number variation analysis. The deleted exons were confirmed by PCR in the patient and his affected brother, who both have non-syndromic HL. Segregation analysis via qPCR confirmed the parents as heterozygous deletion carriers. Breakpoint analysis mapped the homozygous deletion spanning introns 5 to 33 (g.70,948,188_70,997,277del, NM_001851.4(COL9A1):c.697-3754_2112+769del, p.(Phe233_Ser704del), with an additional 67 bp of inserted intronic sequence that may have originated due to a fork stalling and template switching/microhomology-mediated break-induced replication (FoSTeS/MMBIR) mechanism. This mechanism has not been previously implicated in HL or STL. This is also the first reported copy number variation in COL9A1 that was identified through an exome data set in an Iranian family with apparent non-syndromic HL. The present study emphasizes the importance of exome-wide copy number variation analysis in molecular diagnosis and provides supporting evidence to associate COL9A1 with autosomal recessive non-syndromic HL.

An update of spectrum and frequency of GJB2 mutations causing hearing loss in the south of Iran: A literature review

OBJECTIVE

Mutations in the GJB2 gene are a major cause of autosomal recessive non-syndromic HL (ARNSHL) in many populations. Previous studies have estimated the average frequency of GJB2 mutations to be between 16 and 18% in Iran, but would vary among different ethnic groups. Here, we have taken together and reviewed results from our three previous publications and data from search other published mutation reports to provide a comprehensive collection of data for GJB2 mutations and HL in the south of Iran.

METHODS

In all, 447 unrelated families were included and analyzed for the prevalence and type of the GJB2 gene mutations.

RESULTS

Totally, the frequency of GJB2 mutations was found to be 11.5% in the southern provinces studied which is significantly lower than that identified in Northern populations of Iran, and also a southwest to southeast Iranian gradient in the frequency of GJB2 mutations is suggested.

CONCLUSIONS

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

The TECTA mutation R1890C is identified as one of the causes of genetic hearing loss: a case report

Background

Many mutations in the α-tectorin gene (TECTA) have been reported to cause non-syndromic hearing loss (NSHL) in either a dominant or recessive inheritance pattern. Among the identified TECTA mutations, H1400Y has been associated with NSHL in two independent studies. However, its exact role in contributing to genetic hearing loss remains elusive.

Case presentation

We herein report the whole-exome sequencing of a proband presenting with prelingual, non-progressive, mild-to-moderate hearing loss in a simplex family. By using trio-based whole-exome sequencing, we found two heterozygous mutations of R1890C and H1400Y in the ZP and ZA domains of TECTA, respectively. R1890C, previously reported as a pathogenic autosomal dominant mutation of genetic hearing loss, was found to be inherited in a de novo pattern, causing hearing loss in the proband. By contrast, H1400Y was not segregated in this family, and one family member with normal hearing also carried the H1400Y mutation.

Conclusion

According to the hearing loss-specific American College of Medical Genetics and Genomics (ACMG) guidelines, we conclude that H1400Y should be disqualified as a cause of genetic hearing loss. True pathogenic variants causing genetic hearing loss should be more deliberately reported in accordance with ACMG guidelines.

Identification of causative variants in patients with non-syndromic hearing loss in the Minnan region, China by targeted next-generation sequencing

BACKGROUND

Due to extreme genetic heterogeneity, targeted next-generation sequencing (NGS) can be an efficient tool for rapid genetic diagnosis of hereditary non-syndromic hearing loss (NSHL).

AIMS/OBJECTIVES

This study was aiming to identify causative variants in NSHL patients from the Minnan region through targeted NGS.

MATERIAL AND METHODS

Genomic DNA samples from 90 NSHL subjects were extracted and subjected to SureSelect target enrichment system to capture the entire coding exons and flanking intronic regions of gene GJB2, SLC26A4, and MT-RNR1. The captured DNA was then sequenced by Illumina HiSeq2500. The sequence data was processed and quality-checked using Burrows-Wheeler Alignment, Picard, and GATK, and annotated by SnpEff, SIFT, and GERP++.

RESULTS

Twenty-six candidate variants in GJB2, SLC26A4, and MT-RNR1 were detected in 57 of 90 NSHL patients. GJB2 c.109G > A was the most frequent variant, followed by GJB2 c.608T > C and c.235delC. Genetic diagnosis was available for 22 NSHL patients, including 19 patients associated with autosomal recessive NSHL, one patients with autosomal dominant NSHL, and two individuals with mitochondrial disorders.

CONCLUSIONS AND SIGNIFICANCE

Our targeted NGS analysis added supports for the application of NGS in routine diagnosis and provided an overview of genetic variants with allele frequencies in the deaf population from the Minnan region.

A novel mutation of the EYA4 gene associated with post-lingual hearing loss in a proband is co-segregating with a novel PAX3 mutation in two congenitally deaf family members

OBJECTIVES

This work was aimed at establishing the molecular etiology of hearing loss in a 9-year old girl with post-lingual non-syndromic mild sensorineural hearing loss with a complex family history of clinically heterogeneous deafness.

METHODS

The proband's DNA was subjected to NGS analysis of a 59-targeted gene panel, with the use of the Ion Torrent PGM platform. Conventional Sanger sequencing was used for segregation analysis in all the affected relatives. The proband and all the other hearing impaired members of the family underwent a thorough clinical and audiological evaluation.

RESULTS

A new likely pathogenic mutation in the EYA4 gene (c.1154C > T; p.Ser385Leu) was identified in the proband and in her 42-year-old father with post-lingual non-syndromic profound sensorineural hearing loss. The EYA4 mutation was also found in the proband's grandfather and uncle, both showing clinical features of Waardenburg syndrome type 1. A novel pathogenic splice-site mutation (c.321+1G > A) of the PAX3 gene was found to co-segregate with the EYA4 mutation in these two subjects.

CONCLUSION

The identified novel EYA4 mutation can be considered responsible of the hearing loss observed in the proband and her father, while a dual molecular diagnosis was reached in the relatives co-segregating the EYA4 and the PAX3 mutations. In these two subjects the DFNA10 phenotype was masked by Waardenburg syndrome. The use of NGS targeted gene-panel, in combination with an extensive clinical and audiological examination led us to identify the genetic cause of the hearing loss in members of a family in which different forms of autosomal dominant deafness segregate. These results provide precise and especially important prognostic and follow-up information for the future audiologic management in the youngest affected member.

Whole-exome sequencing to identify the cause of congenital sensorineural hearing loss in carriers of a heterozygous GJB2 mutation

Bi-allelic variations in the gap junction protein beta-2 (GJB2) gene cause up to 50% of cases of newborn hearing loss. Heterozygous pathogenic GJB2 variations are also fivefold overrepresented in idiopathic patient groups compared to the normal-hearing population. Whether hearing loss in this group is due to unidentified additional variations within GJB2 or variations in other deafness genes is unknown in most cases. Whole-exome sequencing offers an effective approach in the search for causative variations in patients with Mendelian diseases. In this prospective genetic cohort study, we initially investigated a family of Turkish origin suffering from congenital autosomal recessive hearing loss. An index patient and his normal-hearing father, both bearing a single heterozygous pathogenic c.262G>T (p.Ala88Ser) GJB2 transversion as well as the normal-hearing mother were investigated by means of whole-exome sequencing. Subsequently the genetic screening was extended to a hearing-impaired cohort of 24 families of Turkish origin. A homozygous missense c.5492G>T transversion (p.Gly1831Val) in the Myosin 15a gene, previously linked to deafness, was identified as causative in the index family. This very rare variant is not listed in any population in the Genome Aggregation Database. Subsequent screening of index patients from additional families of Turkish origin with recessive hearing loss identified the c.5492G>T variation in an additional family. Whole-exome sequencing may effectively identify the causes of idiopathic hearing loss in patients bearing heterozygous GJB2 variations.

A 7666-bp genomic deletion is frequent in Chinese Han deaf patients with non-syndromic enlarged vestibular aqueduct but without bi-allelic SLC26A4 mutations

OBJECTIVES

To investigate the genetic cause of the patients with non-syndromic enlarged vestibular aqueduct (EVA) but without bi-allelic SLC26A4 mutations.

METHODS

Presence of a homozygous genomic deletion was detected in a Chinese Han deaf patient (D1467-1) who failed to amplify the first three exons of SLC26A4. The breakpoints of the deletion were fine-mapped and revealed by PCR amplification and sequencing. This deletion was subsequently screened in 22 Chinese Han EVA probands with mono-allelic SLC26A4 mutations. The possible founder effect of the newly identified genomic deletion was evaluated by haplotype analysis.

RESULTS

A homozygous c.-2071_307+3801del7666 deletion of SLC26A4 was identified in patient D1467-1. This novel genomic deletion was subsequently identified in 18% (4/22) of the Chinese Han EVA probands with mono-allelic SLC26A4 mutations. Haplotype analysis showed that this genomic deletion is likely a founder mutation in Chinese Hans.

CONCLUSION

Our results suggested that the cryptic c.-2071_307+3801del7666 deletion of SLC26A4 is relatively frequent in Chinese Han non-syndromic EVA patients without bi-allelic SLC26A4 mutations. Screening of this genomic deletion should be incorporated into the routine DNA testing of SLC26A4 in Chinese Hans.

The controversial p.Met34Thr variant in GJB2 gene: Two siblings, one genotype, two phenotypes

INTRODUCTION

Recent advances in molecular genetics have increased the identification of genes and mutations responsible for inherited forms of hearing loss (HL), enabling early detection of these cases. Approximately, 60% of early-onset HL cases are due to genetic causes, of which 70% are non-syndromic. Of these, 75-80% are inherited in an autosomal recessive pattern (DFNB). Mutations in GJB2 gene, coding for connexin 26 (Cx26), are the major cause of autosomal recessive hereditary HL, but some GJB2 mutations are yet of unclear or controversial significance.

OBJECTIVES

The aim of the present study was to identify the etiology of hearing loss, and correlate genotype-phenotype, in two Portuguese siblings with profound and moderate non-syndromic sensorineural bilateral HL.

MATERIAL AND METHODS

The affected subjects and their parents underwent audiological and genetic study. Molecular analysis of GJB2 gene was performed, searching for mutations in the coding region and receptor splicing site by automated sequencing.

RESULTS

The onset and the degree of HL were different in the two affected subjects. However, the same GJB2 genotype [p.Met34Thr]+[p.Arg184Pro] was identified in both siblings. The c.551G>C (p.Arg184Pro) and c.101T>C (p.Met34Thr) missense variants were inherited from the father and mother, respectively, both heterozygous carriers of these variants.

CONCLUSION

The clinical and genetic data here presented suggest that the non-syndromic sensorineural HL of these two Portuguese siblings might be due to the presence of p.Met34Thr and p.Arg184Pro variants in compound heterozygosity. If so, p.Met34Thr variant could have function as a hypomorphic allele that may cause HL depending on the opposing GJB2 allele. The observed phenotypic variability may not, however, be solely explained by variable expression of this genotype. A putative modifier gene or mutations in another HL-associated gene could probably be contributing to the severe HL in one of the siblings.

A new compound heterozygous mutation in GJB2 causes nonsyndromic hearing loss in a consanguineous Iranian family

OBJECTIVE

To investigate mutations in GJB2 in a consanguineous Iranian family with multiple members affected by non-syndromic hearing loss.

METHODS

DNA was extracted from blood samples and the coding region of the conexin 26 gene was amplified using PCR. Bidirectional sequencing was carried out on PCR products.

RESULTS

Direct sequencing of the PCR products led to the identification of a novel compound heterozygous mutation of c.551G>C/c.397T>G (p.R184P/p.W133G) and a previously reported homozygous mutation c.551G>C (R184P/R184P). Compound heterozygous mutation was identified in the father and his daughter and homozygous mutation was identified in his affected son. In silico analysis of p.W133G predicted mutation has deleterious effect on protein structure.

CONCLUSION

These results show the usefulness of GJB2 mutation screening and bioinformatic analysis for genetic diagnosis and counseling of non-syndromic hearing loss.

Autosomal recessive non-syndromic hearing loss is caused by novel compound heterozygous mutations in TMC1 from a Tibetan Chinese family

OBJECTIVES

Hearing loss is the most common sensory disorder worldwide. Biallelic mutations in 42 different genes have been identified as associated with autosomal recessive non-syndromic hearing loss (ARNSHL). One of the common genes responsible for ARNSHL is TMC1. TMC1 mutations have been reported to cause non-syndromic hearing loss in a variety of populations. The current study is designed to investigate mutations prevalent among Chinese ethnic groups with ARNSHL.

METHODS

Targeted exome sequencing (TES) was employed to study the genetic causes of two siblings with ARNSHL in a Tibetan Chinese family. Variants identified by TES were further confirmed by Sanger sequencing.

RESULTS

We identified two distinct variants in the TMC1 gene in two deaf siblings of one Tibetan Chinese family using TES. Both siblings inherited a paternal allele containing a deletion of c.1396_1398AAC (p.Asn466del) and a maternal allele containing an insertion of c.2210_2211insCT (p.Glu737HisfsX2). The former disrupts a highly conserved residue in the large intracellular loop domain adjacent to the fourth transmembrane domain, and the latter causes a truncation of a portion of the C-terminal domain. These variants were compound heterzygous and segregated with the hearing impairment in this family.

CONCLUSION

The novel compound heterozygous mutant alleles of TMC1 identified in this study were responsible for the ARNSHL in this Tibetan Chinese family. Although compound heterozygous mutations in TMC1 occurring in different TMC1 domains have been previously described in Han Chinese; this result suggests that the TMC1 variants contributing to hereditary deafness in Chinese populations may be more complex than initially assumed and that sequence-based diagnostics will be required for a comprehensive evaluation of ARNSHL.

Hair phenotype in non-syndromic deafness

The GJB2 gene is located on chromosome 13q12 and it encodes the connexin 26, a transmembrane protein involved in cell-cell attachment of almost all tissues. GJB2 mutations cause autosomal recessive (DFNB1) and sometimes dominant (DFNA3) non-syndromic sensorineural hearing loss. Moreover, it has been demonstrated that connexins are involved in regulation of growth and differentiation of epidermal tissues. Hence, mutations in GJB2 gene, which is responsible for non-syndromic deafness, may be associated with an abnormal skin and hair phenotype. We analyzed hair samples from 96 subjects: a study group of 42 patients with hearing impairments of genetic origin (38 with a non-syndromic form, 4 with a syndromic form), and a control group including 54 people, i.e. 43 patients with other, non-genetic hearing impairments and 11 healthy volunteers aged up to 10 years old. The surface structure of 49 hair samples was normal, whereas in 45 cases it was altered, with a damaged appearance. Two hair samples were considered unclassifiable: one from the patient heterozygotic for the pendrin mutation (Fig. 2C), the other from a patient from Ghana with a R134W mutation (Fig. 2D). Among the 43 altered hair samples, 31 belonged to patients with connexin mutations and the other 12 came from patients without connexin mutations.

Low prevalence of GJB2 mutations in non-syndromic hearing loss in Western India

OBJECTIVES

To identify the prevalence of GJB2 (Cx 26)and GJB6 (Cx 30) mutations in hearing impaired individuals from Western and South India.

STUDY DESIGN

Cross-sectional study.

METHODS

Families with hearing impaired individuals (prelingual, non-syndromic, sensori-neural hearing loss) were enrolled and genomic DNA was extracted. Primers were designed for amplifying the coding and non-coding exons including flanking splice sites of the Cx 26 gene. Probands heterozygous or negative for Cx 26 mutations were further analyzed for the 342Kb deletion encompassing D13S1830 microsatellite marker on Cx 30.

RESULTS

Two hundred and eighty-eight patients were enrolled in the study and 116 (40.3%) were diagnosed to have mutations in the coding exon 2 of Cx 26 gene. Fifty-four (18.8%) probands were found to have mutations in both the alleles while the remaining 62 (21.5%) were heterozygous for Cx 26 mutations. W24X, and W77X were the common mutations identified. The prevalence of familial deafness was similar in both consanguineous and non-consanguineous families (33% and 34.9% respectively). Mutations in the non-coding exon 1 and intron 1 as well as the 342 kb deletion involving D13S1830 marker on Cx 30 were ruled out in two hundred and thirty-four deaf individuals carrying none or only one mutation in the exon 2 of Cx 26 gene.

CONCLUSION

Cx30 mutations do not contribute to the autosomal recessive non-syndromic hearing loss (NSHL) in the Indian population. Homozygous Cx26 mutations account only for about 1/5th (18.8%) of autosomal recessive non-syndromic hearing implying the need to explore other contributory loci.