Identification of causative variants in patients with non-syndromic hearing loss in the Minnan region, China by targeted next-generation sequencing

Abstract

Background: Due to extreme genetic heterogeneity, targeted next-generation sequencing (NGS) can be an efficient tool for rapid genetic diagnosis of hereditary non-syndromic hearing loss (NSHL).

Aims/Objectives: This study was aiming to identify causative variants in NSHL patients from the Minnan region through targeted NGS.

Material and methods: Genomic DNA samples from 90 NSHL subjects were extracted and subjected to SureSelect target enrichment system to capture the entire coding exons and flanking intronic regions of gene GJB2, SLC26A4, and MT-RNR1. The captured DNA was then sequenced by Illumina HiSeq2500. The sequence data was processed and quality-checked using Burrows-Wheeler Alignment, Picard, and GATK, and annotated by SnpEff, SIFT, and GERP++.

Results: Twenty-six candidate variants in GJB2, SLC26A4, and MT-RNR1 were detected in 57 of 90 NSHL patients. GJB2 c.109G > A was the most frequent variant, followed by GJB2 c.608T > C and c.235delC. Genetic diagnosis was available for 22 NSHL patients, including 19 patients associated with autosomal recessive NSHL, one patients with autosomal dominant NSHL, and two individuals with mitochondrial disorders.

Conclusions and significance: Our targeted NGS analysis added supports for the application of NGS in routine diagnosis and provided an overview of genetic variants with allele frequencies in the deaf population from the Minnan region.

Chinese abstract

背景：由于极端的遗传异质性, 靶向新测序（NGS）可以成为遗传性非综合征性听力损失（NSHL）的快速遗传性诊断的有效工具。

目标/目的：本研究旨在通过靶向NGS鉴定闽南地区NSHL患者的致病变体。

材料和方法：提取来自90个NSHL受试者的基因组DNA样品, 并对此进行SureSelect靶标富集系统检测, 以获得基因GJB2、SLC26A4和MT-RNR1的整个编码外显子和侧翼内含子区域。然后通过Illumina HiSeq2500对捕获的DNA进行测序。使用Burrows-Wheeler Alignment、Picard和GATK对序列数据进行处理和质量检查, 并通过SnpEff、SIFT和GERP ++ 进行注释。

结果：在90名NSHL患者中, 57名中检测到GJB2、SLC26A4和MT-RNR1中的26种候选变体。 GJB2 c.109G> A是最常见的变体, 其次是GJB2 c.608T> C和c.235delC。对22名NSHL患者进行基因诊断, 包括19名与常染色体隐性遗传性NSHL相关的患者, 其中1名患有常染色体显性NSHL, 两名患有线粒体疾病。

结论和意义：我们的靶向NGS分析支持NGS在常规诊断中的应用, 并提供了闽南地区耳聋人群中具有等位基因频率的遗传变异的概况。

Keywords:

• Non-syndromic hearing loss
• targeted next-generation sequencing
• GJB2
• SLC26A4
• MT-RNR1
• genetic diagnosis

Acknowledgments

We are grateful to the patients and families included in this study. We thank all the physicians and genetic counselors involved in this study for their tremendous supports.

Disclosure statement

The authors report no conflict of interest.

Additional information

Funding

This work was supported by Xiamen Science and Technology Bureau [grant number 3502Z20134033].