Flexible Real-Time Polymerase Chain Reaction-Based Platforms for Detecting Deafness Mutations in Koreans: A Proposed Guideline for the Etiologic Diagnosis of Auditory Neuropathy Spectrum Disorder

Abstract

Routine application of next-generation sequencing in clinical settings is often limited by time- and cost-prohibitive complex filtering steps. Despite the previously introduced genotyping kit that allows screening of the 11 major recurring variants of sensorineural hearing loss (SNHL) genes in the Korean population, the demand for phenotype- and variant-specific screening kits still remains. Herein, we developed a new real-time PCR-based kit (U-TOP™ HL Genotyping Kit Ver2), comprising six variants from two auditory neuropathy spectrum disorder (ANSD) genes (OTOF and ATP1A3) and five variants from three SNHL genes (MPZL2, COCH, and TMC1), with a distinct auditory phenotype, making this the first genotyping kit dedicated to ANSD. The concordance rate with Sanger sequencing, sensitivity, and specificity of this genotyping kit were all 100%, suggesting reliability. The kit not only allows timely and cost-effective identification of recurring OTOF variants, but it also allows timely detection of cochlear nerve deficiency for those without OTOF variants. Herein, we provide a clinical guideline for an efficient, rapid, and cost-effective etiologic diagnosis of prelingual ANSD. Our study provides a good example of continuing to update new key genetic variants, which will continuously be revealed through NGS, as targets for the newly developed genotyping kit.

Clinical and Genetic Characteristics of Finnish Patients with Autosomal Recessive and Dominant Non-Syndromic Hearing Loss Due to Pathogenic TMC1 Variants

“…Previous work has shown variable auditory outcome in patients with pathogenic biallelic TMC1 variants [ 19 , 21 , 22 , 23 ]. Most reports are small case series with heterogeneous samples, which makes it difficult to assess the full effect of a particular genotype.…”

Full etiologic spectrum of pediatric severe to profound hearing loss of consecutive 119 cases

“…These did not test the genes beyond m.1555A > G, GJB2 and SLC26A4, and also did not report the CNS lesions or CND in detail, leaving room for further investigations. Regardless of the necessity of exome sequencing, the first line screening for prevalent variants of GJB2 , OTOF and SLC26A4 using previously reported diagnostic kits 45 , 46 in tandem with IAC-MRI could possibly lead to better etiologic diagnosis, as high as 58.0% in pediatric SP-SNHL (Fig. 2 ).…”

Efficacy of cochlear implants in children with borderline hearing who have already achieved significant language development with hearing aids

“…According to our etiologic diagnostic pipeline for pediatric CI candidates with SNHL, all available methods were used including internal auditory canal magnetic resonance imaging (IAC-MRI) and Molecular genetic testing (MGT). Except for subjects with already known etiologies, MGT was conducted with the following process: [ 1 ] U-Top screening kit [ 5 , 6 ] or Direct Sanger sequencing in subjects with a characteristic phenotype, such as enlarged vestibular aqueduct, [ 2 ] deafness panel sequencing (TES-129) [ 7 , 8 ] or exome sequencing [ 9 , 10 ], and [ 3 ] fluorescent in situ hybridization (FISH), if necessary [ 11 ]. Panel sequencing or exome sequencing results were analyzed as previously described [ 12 , 13 ].…”