The Application of Next-Generation Sequencing for Mutation Detection in Autosomal-Dominant Hereditary Hearing Impairment

Mutation analysis of the WFS1 gene in a Chinese family with autosomal-dominant non-syndrome deafness

To analyse the pathogenic genes and mutations of a family with hereditary deafness. We recruited a three-generation family with NSHL. A detailed medical history inquiry and related examinations were performed. Next-generation sequencing (NGS) was used to confirm the gene mutation in the proband, and Sanger sequencing was used for verification. The effect of the WFS1 mutation on the function and structure of the wolframin protein was predicted by multiple computational software. From the Gene Expression Omnibus (GEO) database, we obtained GSE40585 dataset and performed enrichment analyses. The family clinically manifested as autosomal dominant NSHL. A novel WFS1 c.2421C>G (p.Ser807Arg) mutation was identified in four affected individuals in the pedigree . The p.Ser807Arg mutation is a highly conserved residue and causes an increase in protein stability. It had an important influence on not only amino acid size, charge and hydrophobicity but also protein intermolecular hydrogen bonding and spatial structure. There were differentially expressed genes (DEGs) in GSE40585 dataset. Enrichment analysis revealed that DEGs mainly functioned in amino acid metabolism, signal transduction and dephosphorylation. We reported a novel mutation c.2421C>G (p.Ser807Arg in WFS1. This study expands the mutation spectrum of WFS1.

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.

Prevalence of TECTA mutation in patients with mid-frequency sensorineural hearing loss

BACKGROUND

To date, 102 genes have been reported as responsible for non-syndromic hearing loss, some of which are associated with specific audiogram features. Four genes have been reported as causative for mid-frequency sensorineural hearing loss (MFSNHL), among which TECTA is the most frequently reported; however, the prevalence of TECTA mutations is unknown. To elucidate the prevalence of TECTA mutation in MFSNHL and clarify genotype-phenotype correlations, we analyzed the genetic and clinical features of patients with MFSNHL.

METHODS

Subjects with bilateral non-syndromic hearing loss were prescreened for GJB2 and m.1555A > G and m.3243A > G mitochondrial DNA mutations, and patients with inner ear malformations were excluded. We selected MFSNHL patients whose audiograms met the U-shaped criterion proposed by the GENDEAF study group, along with those with shallow U-shaped audiograms, for TECTA analysis. All TECTA exons were analyzed by Sanger sequencing. Novel missense variants were classified as possibly pathogenic, non-pathogenic, and variants of uncertain significance, based on genetic data. To evaluate novel possibly pathogenic variants, we predicted changes in protein structure by molecular modeling.

RESULTS

Pathogenic and possibly pathogenic variants of TECTA were found in 4 (6.0%) of 67 patients with MFSNHL. In patients with U-shaped audiograms, none (0%) of 21 had pathogenic or possibly pathogenic variants. In patients with shallow U-shaped audiograms, four (8.7%) of 46 had pathogenic or possibly pathogenic variants. Two novel possibly pathogenic variants were identified and two previously reported mutations were considered as variant of unknown significance. The clinical features of patients with pathogenic and possibly pathogenic variants were consistent with those in previous studies. Pathogenic or possibly pathogenic variants were identified in 3 of 23 families (13.0%) which have the family histories compatible with autosomal dominant and 1 of 44 families (2.3%) which have the family histories compatible with sporadic or autosomal recessive.

CONCLUSIONS

TECTA mutations were identified in 6.0% of MFSNHL. These mutations were more frequent in patients with shallow U-shaped audiograms than those with U-shaped audiograms, and in families which have the family histories compatible with autosomal dominant than those with the family histories compatible with sporadic or autosomal recessive.