DNA Diagnostics of Hereditary Hearing Loss: A Targeted Resequencing Approach Combined with a Mutation Classification System

Abstract

Although there are nearly 100 different causative genes identified for nonsyndromic hearing loss (NSHL), Sanger sequencing-based DNA diagnostics usually only analyses three, namely, GJB2, SLC26A4, and OTOF. As this is seen as inadequate, there is a need for high-throughput diagnostic methods to detect disease-causing variations, including single-nucleotide variations (SNVs), insertions/deletions (Indels), and copy-number variations (CNVs). In this study, a targeted resequencing panel for hearing loss was developed including 79 genes for NSHL and selected forms of syndromic hearing loss. One-hundred thirty one presumed autosomal-recessive NSHL (arNSHL) patients of Western-European ethnicity were analyzed for SNVs, Indels, and CNVs. In addition, we established a straightforward variant classification system to deal with the large number of variants encountered. We estimate that combining prescreening of GJB2 with our panel leads to a diagnosis in 25%-30% of patients. Our data show that after GJB2, the most commonly mutated genes in a Western-European population are TMC1, MYO15A, and MYO7A (3.1%). CNV analysis resulted in the identification of causative variants in two patients in OTOA and STRC. One of the major challenges for diagnostic gene panels is assigning pathogenicity for variants. A collaborative database collecting all identified variants from multiple centers could be a valuable resource for hearing loss diagnostics.

The diagnostic yield of whole-exome sequencing targeting a gene panel for hearing impairment in The Netherlands

“…[28][29][30][31][32][33][34] A relatively high frequency of STRC deletions was found in our Dutch population (2%), as has also been reported in other populations. 8,9 In one case (ISO31), we found causative variants in a gene that is associated with an identifiable phenotype and segregating with a recessive inheritance pattern.…”

“…Other studies using massively parallel sequencing have reported similar overall diagnostic rates, despite of using different technologies and testing different populations. [32][33][34]37,38 We found that causative variants in GJB2, USH2A, MYO6, STRC and MYO15A underlie HI in 14.0% of the cases in our cohort. This is in agreement with the previously published studies on the involvement of HI genes in other populations.…”

“…This is in agreement with the previously published studies on the involvement of HI genes in other populations. [6][7][8][9][32][33][34]36,[38][39][40] The diagnostic yield of WES targeting a panel of HI-related genes is generally higher than that of single gene testing. Therefore, we recommend to reduce prescreening of single genes to a minimum.…”

Advantages and pitfalls of an extended gene panel for investigating complex neurometabolic phenotypes

“…Indeed, coverage of targeted areas was similar or superior to that reported in other gene panels despite the large number of genes covered (Nemeth et al , 2013; Yohe et al , 2015). Moreover, the diagnosis rate in our study was comparable to, or higher than, that reported in similar approaches recently applied in other patient groups exhibiting phenotypic heterogeneity (Kammermeier et al , 2014; Sommen et al , 2016; Trump et al , 2016). …”

Navigating genetic diagnostics in patients with hearing loss

“…Sommen and colleagues evaluated 131 GJB2 -negative individuals with ARNSHL using a 79-gene panel that included in-house CNV detection and a variant scoring system; they estimated their positive diagnostic rate as ~30% [23*]. Bademci and colleagues investigated 160 multiplex GJB2 -negative ARNSHL families for causative variants in 58 genes and identified a genetic etiology in 90 (56%) families, who segregated likely pathogenic or pathogenic variants in 31 genes [24**].…”