(The) efficacy of targeted resequencing of deafness genes and its application in the field of hereditary deafness

Abstract

Sensorineural hearing loss (SNHL) is the most common congenital sensorineural disorder affecting 1 of 500 live births, and at least 50% of congenital hearing impairment has a genetic origin. As most genetic hearing loss has a monogenic Mendelian etiology, molecular genetic testing is useful for identifying individuals with hereditary SNHL. Owing to its easy applicability, the phenotype-driven candidate gene approach has been used widely, especially in molecular diagnosis of deafness in small to mid-sized families with no available linkage data. However, phenocopies and variable phenotypes can result from changes in a same deafness gene, depending upon the domain/location of the change. In addition, phenotyping may not always be comprehensive and robust in the clinic, making the phenotype-driven candidate gene approach unsuccessful in many cases. The recent advent of next-generation sequencing (NGS) has rapidly expanded the possibilities of massive genomic analyses, and we established targeted resequencing of 80 deafness genes (TRS-80) to identify candidate gene in SNHL cases without phenotypic markers. In this study, we performed TRS-80 in cases that showed negative results after candidate gene screening despite the presence of a characteristic phenotypic marker to demonstrate the efficacy and advantages of TRS (Part 1). Then we applied TRS-129 or 200 to identify the genotype-phenotype correlation in COCH gene related hearing loss (DFNA9) (Part 2) and reveal the significant role of CDH23 to progressive postlingual-onset SNHL in Koreans using a genetic epidemiologic tool (Part 3). Among six probands without detection of a causative variant through a phenotype-driven candidate gene approach, TRS-80 revealed a convincing causative gene in the three probands (SB82-147, SB86-154, and SB128-220), yielding a 50% molecular diagnosis solve rate in cases that remained undiagnosed after auditory phenotype-driven candidate gene screening, leaving another 50% in need of whole exome sequencing (WES) (Part 1). TRS-129 revealed the overall frequency of DFNA9 among autosomal dominant multiplex hearing loss families as 5/39 (12.8 %) in our Korean cohorts. Also, distinct vestibular phenotypes depending on the location of COCH mutations were demonstrated, correlating a genotype of p.G38D in COCH to the phenotype of bilateral total vestibular loss (Part 2). Among 32 Korean adult probands with postlingual non-syndromic SNHL sporadically or in autosomal recessive fashion, the allele frequency of these CDH23 variants in our postlingual cohort was 12.5%, which was significantly higher than that of the 2040 control chromosomes (5.53%), confirming the contribution of these rare CDH23 variants to postlingual non-syndromic SNHL (Part 3). Taken together, we demonstrated the advantages of TRS, which had been previously proposed as the strategic pipeline to make a molecular genetic diagnosis of deafness, over the phenotype-driven candidate gene screening. Using TRS, we showed the distinct vestibular phenotypes of DFNA9 depending on the location of COCH mutations, and we also demonstrated an important contribution of CDH23 mutations to poslingual-onset non-syndromic SNHL, widening phenotypic spectrum of DFNB12. With the rapid development of diagnostic tools for hereditary deafness, therapeutic approaches based on stem cell and gene therapy will be mainstream treatments for the genetic hearing loss.