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

Abstract

Background The enlarged vestibular aqueduct (EVA) is the commonest malformation of inner ear accompanied by sensorineural hearing loss in children. Three genes SLC26A4, FOXI1, and KCNJ10 have been associated with EVA, among them SLC26A4 being the most common. Yet, hotspot mutation screening can only diagnose a small number of patients. Methods Thus, in this study, we designed a new molecular diagnosis panel for EVA based on multiplex PCR enrichment and next‐generation sequencing of the exon and flanking regions of SLC26A4. A total of 112 hearing loss families with EVA were enrolled and the pathogenicity of the rare variants detected was interpreted according to the American College of Medical Genetics and Genomics (ACMG) guidelines. Results Our results showed that 107/112 (95.54%) families carried SLC26A4 biallelic mutations, 4/112 (3.57%) carried monoallelic variants, and 1/112 (0.89%) had none variant, resulting in a diagnostic rate of 95.54%. A total of 49 different variants were detected in those patients and we classified 30 rare variants as pathogenic/likely pathogenic, of which 13 were not included in the Clinvar database. Conclusion Our diagnostic panel has an increased diagnostic yield with less cost, and the curated list of pathogenic variants in the SLC26A4 gene can be directly used to aid the genetic counseling to patients.

Different Rates of the SLC26A4-Related Hearing Loss in Two Indigenous Peoples of Southern Siberia (Russia)

“…Different proportions of patients having biallelic SLC26A4 mutations were revealed in a relatively limited number of large NSHL studies performed without preselection of patients with EVA or Pendred syndrome: 3.5% of sib pairs from the UK Caucasian child population [ 24 ], 0.9% of Czech patients [ 25 ], 2.9% of Brazilian patients [ 26 ], 6.3% (0–8.3%) of patients from different regions of Iran [ 27 ], 7.2% of patients from Pakistan [ 28 ], 3.5% of patients from southern India [ 29 ], 1.1% of Korean patients [ 6 ], 4.6% of the Vietnamese pediatric population [ 30 ], 1–1.5% of Mongolian patients [ 6 , 12 ], up to 15.3% of patients from different regions of mainland China [ 31 , 32 , 33 , 34 ], and 5.8% of Taiwanese patients [ 13 ]. A significantly higher proportion of biallelic SLC26A4 mutations was found in the studies on cohorts of patients who were pre-screened for EVA, reaching 65–95% in Asian cohorts and approximately one-fourth of patients with nonsyndromic EVA in Caucasian cohorts, which is probably influenced by the different ethnicities of patients and an increased sensitivity of sequencing techniques [ 7 , 10 , 22 , 35 , 36 , 37 ].…”

Increased diagnostic yield in a cohort of hearing loss families using a comprehensive stepwise strategy of molecular testing

“…NanoDrop One (Thermo Fisher Scientific, Waltham, MA, United States) was used to measure DNA concentration and purity. A multiplex PCR kit was designed to cover the entire coding region of GJB2 , SLC26A4 , and MT-RNR1 , as an updated version of the kit developed in a previous study ( Tian et al, 2021 ). Multiplex PCR assay does not include detection of the GBJ2 exon 1.…”

Genetics of Inner Ear Malformations: A Review

“…According to the recent literature, the prevalence of SLC26A4 mutations in patients with enlarged vestibular aqueducts is variable among different ethnic groups. Biallelic mutations in SLC26A4 were found to range from the 57% to the 95% in Asian groups [33][34][35][36][37][38][39][40]. In Caucasian cohorts it is estimated that only 25% of patients with enlarged vestibular aqueducts present biallelic mutations [41], while another 25% present with monoallelic mutations [42,43], thus leaving one half of the patients without known genetic etiology of their anomaly.…”