A novel nonsense mutation in MYO15A is associated with non-syndromic hearing loss: a case report.
ABSTRACT: BACKGROUND:Hearing loss is genetically heterogeneous and is one of the most common human defects. Here we screened the underlying mutations that caused autosomal recessive non-syndromic hearing loss in a Chinese family. CASE PRESENTATION:The proband with profound hearing loss had received audiometric assessments. We performed target region capture and next generation sequencing of 127 known deafness-related genes because the individual tested negative for hotspot variants in the GJB2, GJB3, SLC26A4, and MTRNR1 genes. We identified a novel c.6892C > T (p.R2298*) nonsense mutation and a c.10251_10253delCTT (p.F3420del) deletion in MYO15A. Sanger sequencing confirmed that both mutations were co-segregated with hearing loss in this family and were absent in 200 ethnically matched controls. Bioinformatics analysis and protein modeling indicated the deleterious effects of both mutations. The p.R2298* mutation leads to a truncated protein and a loss of the functional domains. CONCLUSIONS:Our results demonstrated that the hearing loss in this case was caused by novel, compound heterozygous mutations in MYO15A. The p.R2298* mutation in MYO15A was reported for the first time, which has implications for genetic counseling and provides insight into the functional roles of MYO15A mutations.
Project description:Molecular diagnostic testing of individuals with congenital sensorineural hearing loss typically begins with DNA sequencing of the GJB2 gene. If the cause of the hearing loss is not identified in GJB2, additional testing can be ordered. However, the step-wise analysis of several genes often results in a protracted diagnostic process. The more comprehensive Hereditary Hearing Loss Arrayed Primer Extension microarray enables analysis of 198 mutations across eight genes (GJB2, GJB6, GJB3, GJA1, SLC26A4, SLC26A5, MTRNR1 and MTTS1) in a single test. To evaluate the added diagnostic value of this microarray for our ethnically diverse patient population, we tested 144 individuals with congenital sensorineural hearing loss who were negative for biallelic GJB2 or GJB6 mutations. The array successfully detected all GJB2 changes previously identified in the study group, confirming excellent assay performance. Additional mutations were identified in the SLC26A4, SLC26A5 and MTRNR1 genes of 12/144 individuals (8.3%), four of whom (2.8%) had genotypes consistent with pathogenicity. These results suggest that the current format of this microarray falls short of adding diagnostic value beyond the customary testing of GJB2, perhaps reflecting the array's limitations on the number of mutations included for each gene, but more likely resulting from unknown genetic contributors to this phenotype. We conclude that mutations in other hearing loss associated genes should be incorporated in the array as knowledge of the etiology of hearing loss evolves. Such future modification of the flexible configuration of the Hereditary Hearing Loss Arrayed Primer Extension microarray would improve its impact as a diagnostic tool.
Project description:Hearing impairment is one of the most common sensory disease, of which more than 50% is attributed to a genetic etiology. The goal of this research is to explore the genetic cause of a Chinese deafness pedigree who was excluded of GJB2, SLC26A4, or MtDNA12SrRNA variants. Three variants, c.3971C>A (p.A1324D), c.4011insA (p.Q1337Qfs?22), and c.9690+1G>A, in the MYO15A gene were identified by targeted capture sequencing and Sanger sequencing, and the first two of them were novel. These variants were cosegregated with the disease in this family and absent in 200 normal hearing persons. They were concluded to be pathogenic mutations by phylogenetic analysis and structure modeling. Thus, the combined use of SNPScan assay and targeted capture sequencing is a high-efficiency and cost-effective screening procedure for hereditary hearing loss. Genetic counseling would be important for this family, and our finding would be a great supplement to the mutation spectrum of MYO15A.
Project description:BACKGROUND:The genetic heterogeneity of hearing loss makes genetic diagnosis expensive and time consuming using available methods. Whole-exome sequencing has recently been introduced as an alternative approach to identifying causative mutations in Mendelian disorders. METHODS:To identify the hidden mutations that cause autosomal recessive nonsyndromic hearing loss (ARNSHL), we performed whole-exome sequencing of 13 unrelated Korean small families with ARNSHL who were negative for GJB2 or SLC26A4 mutations. RESULTS:We found two novel compound heterozygous mutations, IVS11?+?1 and p.R2146Q, of MYO15A in one (SR903 family) of the 13 families with ARNSHL. In addition to these causative mutations, 13 nonsynonymous variants, including variants with uncertain pathogenicity (SR285 family), were identified in the coding exons of MYO15A from Korean exomes. CONCLUSION:This is the first report of MYO15A mutations in an East Asian population. We suggest that close attention should be paid to this gene when performing genetic testing of patients with hearing loss in East Asia. The present results also indicate that whole-exome sequencing is a valuable method for comprehensive medical diagnosis of a genetically heterogeneous recessive disease, especially in small-sized families.
Project description: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.
Project description:BACKGROUND:Recessive mutations in GJB2 is the most common cause of genetic hearing loss worldwide. The aim of this study is to determine the spectrum and frequency of GJB2 variants in Chinese Han deaf patients and to investigate the underlying causative genes in patients with mono-allelic GJB2 mutations. METHODS:We analyzed the mutation screening results of GJB2 in 1852 Chinese Han probands with apparently autosomal-recessive hearing loss in our laboratory. Targeted next-generation sequencing of 139 known deafness-related genes were performed in 44 probands with mono-allelic GJB2 mutations. RESULTS:Bi-allelic GJB2 mutations was identified in 25.65% of patients, in which the c.235delC (p.L79Cfs*3) mutation is the most frequent cause for both severe-to-profound (84.93%) and mild-to-moderate hearing loss (54.05%), while the c.109G?>?A (p.V37I) mutation is another frequent cause for mild-to-moderate hearing loss (40.54%). In 3.89% of patients only one mutant allele can be identified in GJB2. Targeted next generation sequencing in 44 such probands revealed digenic heterozygous mutations in GJB2/GJB6 and GJB2/GJB3 as the likely pathogenic mechanism in three probands. In 13 probands, on the other hand, pathogenic mutations in other deafness-associated genes (STRC, EYA1, MITF, PCDH15, USH2A, MYO15A, CDH23, OTOF, SLC26A4, SMPX, and TIMM8A) can be identified as the independent genetic cause, suggesting that the mono-allelic GJB2 mutations in those probands is likely co-incidental. CONCLUSIONS:Our results demonstrated that GJB2 should be a primary target for mutation screening in Chinese Han deaf patients, and those with mono-allelic GJB2 mutations should be further screened by next generation sequencing.
Project description:The aim of this study was to determine the clinical significance of the results of screening of newborn hearing and the incidence of deafness-susceptibility genes. One thousand newborn babies in the Handan Center Hospital (Handan, China) underwent screening of hearing and deafness-susceptibility genes. The first screening test was carried out using otoacoustic emissions (OAEs). Babies with hearing loss who failed to pass the initial screening were scheduled for rescreening at 42 days after birth. Cord blood was used for the screening of deafness-susceptibility genes, namely the GJB2, SLC26A4 and mitochondrial 12S rRNA (MTRNR1) genes. Among the 1,000 neonates that underwent the first hearing screening, 25 exhibited left-sided hearing loss, 21 exhibited right-sided hearing loss and 15 cases had binaural hearing loss. After rescreening 42 days later, only one of the initial 61 cases exhibited hearing loss under OAE testing. The neonatal deafness gene tests showed two cases with 1555A>G mutation and two cases with 1494C>T mutation of the MTRNR1 gene. In the SLC26A4 gene screening, four cases exhibited the heterozygous IVS7-2A>G mutation and one case exhibited heterozygous 1226G>A mutation. In the GJB2 gene screening, two cases exhibited the homozygous 427C>T mutation and 10 exhibited the heterozygous 235delC mutation. The genetic screening revealed 21 newborns with mutations in the three deafness-susceptibility genes. The overall carrier rate was 2.1% (21/1,000). The association of hearing and gene screening may be the promising screening strategy for the diagnosis of hearing loss.
Project description: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.
Project description:Hearing loss is a common neurosensory disorder, approximately half of the cases are caused by genetic factors, and approximately 70% of hereditary hearing impairments are nonsyndromic hearing loss (NSHL). The mutations of GJB2 (gap junction beta-2 protein), GJB3 (gap junction beta-3 protein), SLC26A4 (solute carrier family 26 member 4), and MT-RNR1 (mitochondrially encoded 12S RNA) are the most common inherited causes of NSHL. Because of different genetic backgrounds, the mutation spectrum of these common deafness-causing genes varies among different regions in China. Because no data are known on these mutations among the Hakka population of Southern China, we aim to investigate the mutation spectrum to add these to neonatal screening and genetic counseling. A total of 1252 blood samples from newborns have been detected by semiconductor sequencing for 100 mutations loci of 18 deafness-causing genes. Of the participants, 95 subjects carried deafness-causing genes mutations with the carrier rate of 7.59%. The mutation frequencies of GJB2, SLC26A4, GJB3, and mitochondrial genes were 3.04%, 3.51%, 0.16%, and 0.88%, respectively. We followed up subjects with single-gene homozygous or compound heterozygous mutations. Our study firstly analyzed deafness-causing genes mutation spectrum in Hakka population, providing evidence for future neonatal screening and genetic counseling in this area.
Project description:We demonstrate a new method, using a universal array approach termed multiplex allele-specific PCR-based universal array (ASPUA), and applied it to the mutation detection of hereditary hearing loss. Mutations in many different genes may be the cause of hereditary hearing loss, a sensory defect disorder. Effective methods for genetic diagnosis are clearly needed to provide clinical management. Owing to the broad genetic basis of this condition, clinical assay of such a highly heterogeneous disorder is expensive and time consuming. In ASPUA, the allele discrimination reaction is carried out in solution by multiplex allele-specific PCR and a universal solid phase array with different tag probes is used to display the PCR result. The purpose of developing the ASPUA platform was to utilize the rapidity and simplicity of the amplification refractory mutation system (ARMS) with the detection power of microarray hybridization. This is the first report of the combination of these two technologies, which allow for the completion of allele-specific detection of 11 of the most frequent mutations causing hereditary hearing loss in under 5 hr. The ASPUA platform was validated by accurately analyzing 141 patient samples that had been previously genotyped for GJB2, GJB3, SLC26A4, and MTRNR1. In addition, we also developed a simplified assay by using streptavidin-coated magnetic beads instead of fluorescence for signal display that can be assessed through a conventional light microscope. We demonstrate that the ASPUA platform is rapid, cost-effective, and easily-used, and is especially appropriate for mutation detection in clinical genetic diagnostics.
Project description:Introduction:Autosomal recessive non-syndromic hearing loss (ARNSHL) is a genetically heterogeneous sensorineural disorder with an approximate incidence of 1.4:1000 in neonates. Mutations in more than 60 genes including the MYO15A gene has been reported in patients affected with ARNSHL. In the present study, we report a novel MYO15A mutation identified by clinical exome sequencing and confirmed by Sanger sequencing in a consanguineous Iranian family with ARNSHL. Case presentation:A 22-year-old woman with congenital non-syndromic sensorineural hearing loss referred to our medical genetic center. Her parents were consanguineous with F?=?1/16 (first cousin), and clinical examination of the patient exclude dysmorphic features. Sanger sequencing of GJB2 and GJB6 genes, which are the most common causes of ARNSHL, was negative. Then she underwent clinical exome sequencing. Outcome:We found a novel homozygote variant (c.9611_9612+8delTGGTGAGCAT) in the MYO15A gene which creates a shift in the reading frame starting at codon 3204. This variant was confirmed by Sanger sequencing in the patient and also in her parents who were heterozygous. Discussion:The present results suggest that the homozygous MYO15A (c.9611_9612+8delTGGTGAGCAT) variant is a pathogenic mutation and to the best of our knowledge, this mutation has not been reported in any database.