Mutation screening in non-syndromic hearing loss patients with cochlear implantation by massive parallel sequencing in Taiwan

RESEARCH ARTICLE Mutation screening in non-syndromic hearing loss patients with cochlear implantation by massive parallel sequencing in Taiwan Wei-Hsiu Liu1,2☯, Pi-Yueh Chang3,4☯, Shih-Cheng Chang3,4, Jang-Jih Lu3,4*, CheMing Wu ID2* a1111111111 a1111111111 a1111111111 a1111111111 a1111111111 OPEN ACCESS Citation: Liu W-H, Chang P-Y, Chang S-C, Lu J-J, Wu C-M (2019) Mutation screening in nonsyndromic hearing loss patients with cochlear implantation by massive parallel sequencing in Taiwan. PLoS ONE 14(1): e0211261. https://doi. org/10.1371/journal.pone.0211261 Editor: Namik Kaya, King Faisal Specialist Hospital and Research Center, SAUDI ARABIA Received: May 6, 2018 Accepted: January 10, 2019 Published: January 25, 2019 Copyright: © 2019 Liu et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Data Availability Statement: All relevant data are within the paper and its Supporting Information files. Funding: This study was supported by the ChangGung Memorial Hospital Research Program CMRPG3C1403 to CMW. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing interests: The authors have declared that no competing interests exist. 1 Department of Laboratory Medicine, Chang-Gung Memorial Hospital, Linkou Branch, College of Medicine, Chang-Gung University, Taoyuan, Taiwan, 2 Department of Otolaryngology—Head and Neck Surgery, Chang-Gung Memorial Hospital, Linkou Branch, College of Medicine, Chang-Gung University, Taoyuan, Taiwan, 3 Department of Medical Biotechnology and Laboratory Science, Chang-Gung University, Taoyuan, Taiwan, 4 Department of Medical Research, Chang-Gung Memorial Hospital and Graduate of Institute of Clinical Medical Science, Chang Gung University, Taoyuan, Taiwan ☯ These authors contributed equally to this work. * (CMW); (J-JL) Abstract Objectives To explore the molecular epidemiology of rare deafness genes in Taiwanese sensorineural hearing impairment (SNHI) patients with cochlear implantation (CI) by performing massive parallel sequencing (MPS) and correlating genetic factors and CI outcomes. Methods We enrolled 41 Taiwanese non-syndromic deafness patients with CI that lacked known mutations in common deafness genes. All probands were screened by a targeted exon amplification method that used massively parallel sequencing to screen a customized panel that included 40 relatively rare non-syndromic deafness genes. Results Thirteen candidate variants in nine relatively rare deafness genes (MYO15A, TMC1, MYH14, MYO3A, ACTG1, COL11A2, DSPP, GRHL2, and WFS1) were identified in 24.4% (10/41) of the non-syndromic deafness probands with CI. According to the ACMG Standards and Guidelines, five variants in MYO15A and ACTG1 were classified as likely pathogenic variants. Two of three multi-generational pedigrees exhibiting deafness were analyzed for the segregation of the disorder with the possible disease-causing variants. Patients with variants detected in most of the identified variant-bearing genes showed relatively good CI outcomes. Conclusions We successfully identified candidate variants in partially deaf Taiwanese probands who lacked the known mutations in common deafness genes. Comparing the progress of hearing rehabilitation in CI patients with their apparent causative variants and the expression PLOS ONE | https://doi.org/10.1371/journal.pone.0211261 January 25, 2019 1 / 15 Genetic deafness and post-implant outcomes profiles of their altered genes allowed us to speculate on how alterations in specific gene sets may influence outcomes in hearing rehabilitation after CI. Introduction Sensorineural hearing impairment (SNHI) is a common clinical disorder that severely to profoundly affects at least 1 in 1000 children of developed countries [1]. Cochlear implantation (CI) is currently regarded as the standard treatment for severe to profound SNHI in children. CI has well-documented benefits for spoken language, reading skills, and cognitive development [2], but the outcomes after CI can vary among individuals. Age at implantation [3, 4], residual hearing [5], the presence of inner ear malformations [6], the presence of cochlear nerve deficiency [7], parent-child interactions [2], and socioeconomic status [2] have all been shown to affect the outcomes. Genetic factors contribute to SNHI in more than 50% of these patients [8]. To date, more than 100 genes and loci have been associated with deafness, and approximately 50 genes have been shown to cause non-syndromic hereditary hearing impairment (The Hereditary Hearing Loss Homepage, http://hereditaryhearingloss.org/) [9]. Due to limitations in mutation detection methodologies, most of the existing studies have focused on the three most common deafness genes, GJB2 (or Cx26), SLC26A4 (or PDS), and MT-RNR1 [10], in the context of epidemiological studies or examining the correlation between CI outcomes and genotypes [11–14]. Only 1/3 of SNHI patients and 1/4 patients with CI can be identified as having known mutations in common deafness genes [10, 14]. The development of massively parallel sequencing (MPS), also known as next-generation sequencing, has allowed researchers and clinicians to more easily address such extraordinarily heterogenetic disorders [15–20]. The powerful strategy of simultaneously obtaining high-throughput reads from multiple targeted genes in numerous samples has reduced the sequencing cost and turnaround time of genetic examination. In recent years, MPS technology has been widely used to examine the prevalence of relatively rare deafness genes and the correlations between various genotypes and the outcomes of CI rehabilitation [15, 19–24]. The auditory performance in patients with CIs can be predicted according to the pathologies that are associated with mutations in different genes [14, 20–22, 24, 25]. When the function of the mutated gene is confined to the intra-cochlear etiology, good post-CI auditory performance is possible [14]. Conversely, poor CI performance can be predicted when the causative mutation occurs in a gene that is expressed in the spiral ganglion neurons (SGNs), brainstem auditory nuclei, or hair cell synapses. Genetic information about predicted good or poor CI outcomes could allow clinicians to counsel patients on whether to undergo an operation and/or decide on a rehabilitation program [24, 26]. Therefore, it is beneficial to identify the causative gene mutation prior to CI intervention. A greater knowledge of the genetic backgrounds of deafness patients with CI will enable clinicians to offer a more precise, genetically based prediction of CI outcome. In this study, we sought to unveil the prevalence rate of rare deafness-associated variants in 41 Taiwanese SNHI patients with CIs, using (...truncated)