Genetic background in late-onset sensorineural hearing loss patients

www.nature.com/jhg ARTICLE OPEN Genetic background in late-onset sensorineural hearing loss patients ✉ Natsumi Uehara 1 , Takeshi Fujita1, Daisuke Yamashita1, Jun Yokoi1, Sayaka Katsunuma1, Akinobu Kakigi1, Shin-ya Nishio ✉ 1 Ken-ichi Nibu and Shin-ichi Usami 2 2 , 1234567890();,: © The Author(s) 2021 Genetic testing for congenital or early-onset hearing loss patients has become a common diagnostic option in many countries. On the other hand, there are few late-onset hearing loss patients receiving genetic testing, as late-onset hearing loss is believed to be a complex disorder and the diagnostic rate for genetic testing in late-onset patients is lower than that for the congenital cases. To date, the etiology of late-onset hearing loss is largely unknown. In the present study, we recruited 48 unrelated Japanese patients with late-onset bilateral sensorineural hearing loss, and performed genetic analysis of 63 known deafness gene using massively parallel DNA sequencing. As a result, we identified 25 possibly causative variants in 29 patients (60.4%). The present results clearly indicated that various genes are involved in late-onset hearing loss and a significant portion of cases of late-onset hearing loss is due to genetic causes. In addition, we identified two interesting cases for whom we could expand the phenotypic description. One case with a novel MYO7A variant showed a milder phenotype with progressive hearing loss and late-onset retinitis pigmentosa. The other case presented with Stickler syndrome with a mild phenotype caused by a homozygous frameshift COL9A3 variant. In conclusion, comprehensive genetic testing for late-onset hearing loss patients is necessary to obtain accurate diagnosis and to provide more appropriate treatment for these patients. Journal of Human Genetics; https://doi.org/10.1038/s10038-021-00990-2 INTRODUCTION Sensorineural hearing loss (SNHL) is one of the most common sensory disorders in humans [1, 2]. The incidence of the congenital SNHL is estimated to be 1–2 in 1000 newborns, among which at least 60% are presumed to be associated with genetic causes [3]. Sloan-Heggen et al. undertook the genetic analysis of congenital deafness patients by targeted genomic enrichment with massively parallel DNA sequencing (TGE + MPS) and identified the causative gene mutations in 44% of cases [3]. In Japan, Mori et al. reported that the diagnostic rate was 41% in congenital or early-onset (<6 year) hearing loss (HL) patients based on screening for 154 mutations in 19 deafness genes using MPS combined with Invader assay and TaqMan genotyping [4]. On the other hand, these studies also reported that the diagnostic rates in late-onset hearing loss patients were lower than those in early-onset patients (28% and 16%, respectively) [3, 4]. Late-onset SNHL is believed to be a complex disorder, associated with agerelated hearing loss, idiopathic sudden SNHL, acoustic neuroma, chronic otitis media or environmental risk factors (including noise exposure and ototoxic drug exposure). However, a certain number of late-onset bilateral symmetrical HL cases are thought to involve genetic factors, particularly in those with progressive HL presenting as worse than the average hearing for age. At present, a majority of late-onset SNHL cases do not receive genetic testing; thus, the etiology of late-onset SNHL remains largely unknown. In this study we focused on late-onset bilateral SNHL patients and aimed to show the frequency of hereditary HL as well as describe the clinical features of these cases. MATERIALS AND METHODS This study was conducted with the approval of the Ethics Committee of Kobe University Graduate School of Medicine (Approval number:170081). Written informed consent was obtained from all subjects. All procedures were performed in accordance with the Guidelines for Genetic Tests and Diagnoses in Medical Practice of the Japanese Association of Medical Sciences and the tenets of the Declaration of Helsinki. Subjects Sixty-four unrelated patients with bilateral SNHL were enrolled in this study. We defined late-onset HL as the HL with an age at onset of 6 years of age and over and, based on this definition, we excluded cases with congenital or pre-lingual onset SNHL (with an age at onset of under 6 years of age). In addition, we also excluded patients aged over 60 years at SNHL onset to remove cases of presbycusis. Finally, 48 unrelated Japanese patients with late-onset bilateral SNHL who underwent clinical genetic testing between April 2012 and April 2020 at Kobe University Graduate School of Medicine participated in this study (Table 1). Clinical evaluations Hearing thresholds were evaluated using pure-tone audiometry (PTA) and classified by pure-tone average over 500, 1000, 2000, and 4000 Hz. The 1 Department of Otolaryngology-Head and Neck Surgery, Kobe University Graduate School of Medicine, Kobe, Japan. 2Department of Hearing Implant Sciences, Shinshu University School of Medicine, Matsumoto, Japan. ✉email: ; Received: 9 August 2021 Revised: 5 October 2021 Accepted: 18 October 2021 N. Uehara et al. 2 Table 1. Patients characteristics Characteristic Number % Number of subjects 48 100.0 Sex Female 25 52.1 Male 23 47.9 Family history of HL (+) 22 45.8 (−) 26 54.2 18.8 Age at onset 6–10 y.o. 9 11–20 y.o. 4 8.3 >20 y.o. 35 72.9 mild/mild 5 10.4 moderate/moderate 19 39.6 severe/severe 4 8.3 profound/profound 4 8.3 normal/mild 1 2.1 mild/moderate 3 6.3 moderate/severe 7 14.6 moderate/profound 3 6.3 profound/severe 2 4.2 Flat 15 31.3 Gently sloping 13 27.1 Steeply sloping 10 20.8 Deaf 3 6.3 U-shaped 3 6.3 Different types on each side 4 8.3 Severity Audiometric configuration y.o. years old, HL hearing loss. severity of HL was classified into mild (21–40 dB HL), moderate (41–70 dB HL), severe (71–95 dB HL), and profound (>95 dB HL). The audiometric configurations were categorized into low-frequency, mid-frequency (Ushaped), high-frequency (gently sloping type and steeply sloping type), flat type, and deaf, as reported previously [5]. The data for age at onset of HL, the progressiveness of HL and family history were obtained from medical charts. Amplicon resequencing and variant annotation Amplicon libraries were prepared using an Ion AmpliSeq™ Custom Panel for 68 genes reported to cause non-syndromic hereditary HL (ThermoFisher Scientific, MA, USA), in accordance with the manufacturer’s instructions. The detailed protocol has been described elsewhere [6]. MPS was performed with an Ion Proton system using an Ion HiQ Chef Kit and an Ion P1 Chip (ThermoFisher Scientific). The sequence data were mapped against the human genome sequence (build GRCh37/hg19) with a Torrent Mapping Alignment Program. After sequence mapping, the DNA variant regions were piled up with Torrent Variant Caller plug-in software. After variant detection, their effects were analyzed using ANNOVAR software [7, 8]. T (...truncated)