Targeted Next-Generation Sequencing Facilitates Genetic Diagnosis and Provides Novel Pathogenetic Insights into Deafness with Enlarged Vestibular Aqueduct

Abstract

Enlarged vestibular aqueduct (EVA) is an inner-ear malformation associated with sensorineural hearing impairment. Most EVAs are associated with Pendred syndrome and nonsyndromic autosomal recessive deafnesse4 (DFNB4), two autosomal-recessive disorders caused by mutations in SLC26A4. However, many EVA patients cannot have a confirmed diagnosis by screening common SLC26A4 mutations, constituting an enigma in genetic diagnosis. To enable comprehensive genetic examination and explore the etiologies of EVA, we designed a next-generation sequencing panel targeting the entire length of 3 Pendred syndrome/ DFNB4 genes (SLC26A4, FOXI1, and KCNJ10) and exons of 10 other genes related to EVA and performed genetic testing in 50 EVA families without confirmative results on screening for SLC26A4 hotspots (c.919-2A>G and p.H723R). Bi-allelic SLC26A4 mutations were identified in 34 families and EYA1 mutations in two families, yielding a diagnostic rate of 72% (36 of 50). In addition, two variants were identified in KCNJ10 and FOXI1, but findings did not support the previous hypothesis that mutations in these two genes are probable contributors to EVA through recessive inheritance or digenic inheritance with SLC26A4. Of note, a large SLC26A4 deletion was confirmed in one step using our panel. These results show the utility of a nextgeneration sequencingebased panel to address EVA families by identifying various types of gene mutations with satisfactory diagnostic yields and provide novel insights into the pathogenesis of EVA. (J Mol Diagn 2019, 21: 138e148; https://doi.

Unique spectra of deafness-associated mutations in Mongolians provide insights into the genetic relationships among Eurasian populations

“…All the probands in the three families with mono-allelic SLC26A4 mutations showed EVA on imaging studies. According to previous reports [43–46], a second occult mutant SLC26A4 allele, which could not be detected using current sequencing techniques, might exist in these three families, and presumably SNHI in the affected members could be attributed to SLC26A4 mutations.…”

Genetic Epidemiology and Clinical Features of Hereditary Hearing Impairment in the Taiwanese Population

“…SLC26A4 mutations are distributed over all 21 exons of the gene and are mostly single nucleotide variations, yet copy number variations were occasionally reported [36,64,65,66]. As such, genetic examination using conventional sequencing strategies is highly laborious and may fail to detect the pathogenic variants.…”

“…As such, genetic examination using conventional sequencing strategies is highly laborious and may fail to detect the pathogenic variants. On the contrary, our recent study demonstrated the utility of a NGS-based panel in addressing SLC26A4 -related SNHI by identifying various types of mutations with satisfactory diagnostic yields in one step [36].…”

“…For NGS-based genetic examinations, sample preparation, DNA sequencing, and data analyses were performed as previously described [33,34,35,36]. Briefly, paired-end reads were aligned, sorted, and converted by BWA-MEM and Picard.…”

Increased diagnosis of enlarged vestibular aqueduct by multiplex PCR enrichment and next‐generation sequencing of the SLC26A4 gene

“…These methods can only be used to diagnose some of the patients with HL; for many patients only one or no mutation is detected. Recent application of next‐generation sequencing (NGS) has proven to be powerful in identifying pathogenic mutations in EVA patients (Lin et al, 2019; Liu, Wang, et al, 2016; Liu et al, 2020). Multiplex PCR can simultaneously amplify multiple regions in the same reaction tube, thus significantly saving time and reagents, and providing more accurate diagnostic information (Lin et al, 2012).…”