A New Genetic Diagnostic for Enlarged Vestibular Aqueduct Based on Next-Generation Sequencing

Yalan Liu; Lili Wang; Yong Feng; Chufeng He; Deyuan Liu; Xinzhang Cai; Lu Jiang; Hongsheng Chen; Chang Liu; Hong Wu; Lingyun Mei

doi:10.1371/journal.pone.0168508

A New Genetic Diagnostic for Enlarged Vestibular Aqueduct Based on Next-Generation Sequencing

PLoS One. 2016 Dec 20;11(12):e0168508. doi: 10.1371/journal.pone.0168508. eCollection 2016.

Authors

Yalan Liu^{1

2}, Lili Wang³, Yong Feng^{1

2

4}, Chufeng He^{1

2}, Deyuan Liu⁵, Xinzhang Cai^{1

2}, Lu Jiang^{1

2}, Hongsheng Chen^{1

2}, Chang Liu^{1

2}, Hong Wu^{1

2}, Lingyun Mei^{1

2}

Affiliations

¹ Department of Otolaryngology, Xiangya Hospital, Central South University, Changsha, Hunan, China.
² Province Key Laboratory of Otolaryngology Critical Diseases, Xiangya Hospital, Central South University, Changsha, Hunan, China.
³ Department of Otolaryngology, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China.
⁴ The State Key Laboratory of Medical Genetics, Central South University, Changsha, Hunan, China.
⁵ R&D Department, Genesky Diagnostics Inc., Suzhou, Jiangsu, China.

Abstract

Enlarged vestibular aqueduct (EVA) is one of the most common congenital inner ear malformations and accounts for 1-12% of sensorineural deafness in children and adolescents. Multiple genetic defects contribute to EVA; therefore, early molecular diagnosis is critical for EVA patients to ensure that the most effective treatment strategies are employed. This study explored a new genetic diagnosis method for EVA and applied it to clinic diagnoses of EVA patients. Using next-generation sequencing technology, we set up a multiple polymerase chain reaction enrichment system for target regions of EVA pathogenic genes (SLC26A4, FOXI1, and KCNJ10). Forty-six EVA samples were sequenced by this system. Variants were detected in 87.0% (40/46) of cases, including three novel variants (SLC26A4 c.923_929del, c.1002-8C>G, and FOXI1 c.519C>A). Biallelic potential pathogenic variants were detected in 27/46 patient samples, leading to a purported diagnostic rate of 59%. All results were verified by Sanger sequencing. Our target region capture system was validated to amplify and measure SLC26A4, FOXI1, and KCNJ10 in one reaction system. The result supplemented the mutation spectrum of EVA. Thus, this strategy is an economic, rapid, accurate, and reliable method with many useful applications in the clinical diagnosis of EVA patients.

Publication types

Clinical Trial

MeSH terms

Adolescent
Adult
Anion Transport Proteins / genetics*
Child
Child, Preschool
Female
Forkhead Transcription Factors / genetics*
Hearing Loss, Sensorineural* / diagnosis
Hearing Loss, Sensorineural* / genetics
High-Throughput Nucleotide Sequencing*
Humans
Infant
Male
Mutation*
Potassium Channels, Inwardly Rectifying / genetics*
Sulfate Transporters
Vestibular Aqueduct / abnormalities*

Substances

Anion Transport Proteins
FOXI1 protein, human
Forkhead Transcription Factors
Kcnj10 (channel)
Potassium Channels, Inwardly Rectifying
SLC26A1 protein, human
Sulfate Transporters

Supplementary concepts

Deafness, Autosomal Recessive 4

Grants and funding

This study was partly supported by the National Basic Research Program of China (973 Program) (2014CB943003), the National Nature Science Foundation of China (81470705 and 81301172), the Special Scientific Research Fund for Public Welfare Industry of the Ministry of Health in China (201302001), the Natural Science Foundation of Hunan Province, China (14JJ7009), and the Science and Technology Project of Hunan Province, China (S2012F1023). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Genesky Diagnostics Inc provided support in the form of salaries for author Deyuan Liu, but did not have any additional role in the research funding, study design, data collection and analysis, decision to publish, or preparation of the manuscript. The specific roles of Deyuan Liu are articulated in the ‘author contributions’ section.