Proband Whole-Exome Sequencing Identified Genes Responsible for Autosomal Recessive Non-Syndromic Hearing Loss in 33 Chinese Nuclear Families

Abstract

Autosomal recessive non-syndromic hearing loss (ARNSHL) is a highly heterogeneous disease involving more than 70 pathogenic genes. However, most ARNSHL families have small-sized pedigrees with limited genetic information, rendering challenges for the molecular diagnosis of these patients. Therefore, we attempted to establish a strategy for identifying deleterious variants associated with ARNSHL by applying proband whole-exome sequencing (proband-WES). Aside from desiring to improve molecular diagnostic rates, we also aimed to search for novel deafness genes shared by patients with similar phenotype, making up for the deficiency of small ARNSHL families. In this study, 48.5% (16/33) families were detected the pathogenic variants in eight known deafness genes, including 10 novel variants identified in TMPRSS3 (MIM 605551), MYO15A (MIM 602666), TMC1 (MIM 606706), ADGRV1 (MIM 602851), and PTPRQ (MIM 603317). Apart from six novel variants with a truncating effect (nonsense, deletion, insertion, and splice-site), four novel missense variants were not found in 200 unrelated control population by using Sanger sequencing. It is important to note that none of novel genes were shared across different pedigrees, indicating that a larger sample size might be needed. Proband-WES is a cost-effective and precise way of identifying causative variants in nuclear families with ARNSHL. This economical strategy may be appropriated as a clinical application to provide molecular diagnostics, genetic counseling, and individualized health maintenance measures for patients with ARNSHL at hearing clinics.

Keywords: ARNSHL; molecular diagnosis; nuclear families; proband-WES; similar phenotype.

Figure 1

Overall workflow of the proband whole-exome sequencing (proband-WES) pipeline. O/D, Phred-like quality score divided by depth; MAF, minor allele frequency.

Figure 2

Pedigree information, variation spectrum and three-dimensional protein modeling of TMPRSS3. (A) are pedigree charts, DNA sequence chromatograms of the two families with TMPRSS3 mutations as well as the conservative prediction of the c.551T>C (p.Leu184Ser) mutation. (B) is the mutant spectrum of TMPRSS3. (C) is the 3D models showing that the p.Gln144fs mutation destroys the spatial structure of protein (yellow) and the p.Leu184Ser mutation makes Ser184 form three extra hydrogen bonds with His186 and formed an extra hydrogen bond with Ser187.

Figure 3

Pedigree information, variation spectrum, and three-dimensional protein modeling of MYO15A. (A) are pedigree charts, DNA sequence chromatograms, and the conservative prediction of four MYO15A mutations which is found in two different families. (B) is the mutant spectrum of MYO15A. (C) is the 3D models showing that the p.Gln1278Pro mutation shortens the side chain and deletes the hydrogen bonds with Gln1275 and Glu1274, which may affect the function of adjacent ATP binding pocket (red); (D) the p.Cys2154Tyr mutation lengthens the side chain and adds hydrogen bond with Pro2078 and Leu2074, and (E) the p.Trp3292Cys mutation shortens the side chain and destructs the hydrophobic core. NT, not tested.