Wu Xiaohui, Gao Xingqiang, Han Peng, Zhou Yulin
a Xiamen Neonatal Hearing Screening and Diagnostic Center , Xiamen Maternity and Child Health Care Hospital , Siming District , Xiamen , China.
b Department of Otolaryngology-Head and Neck Surgery , Children's Hospital of Fudan University; Xiamen Branch; Xiamen Children's Hospital , Huli District, Xiamen , China.
Acta Otolaryngol. 2019 Mar;139(3):243-250. doi: 10.1080/00016489.2018.1552015. Epub 2019 Feb 14.
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.
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++.
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.
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.
由于存在极端的基因异质性，靶向二代测序（NGS）可能是遗传性非综合征性听力损失（NSHL）快速基因诊断的有效工具。
本研究旨在通过靶向NGS鉴定闽南地区NSHL患者的致病变异。
提取90例NSHL受试者的基因组DNA样本，采用SureSelect靶向富集系统捕获基因GJB2、SLC26A4和MT-RNR1的全部编码外显子及侧翼内含子区域。然后使用Illumina HiSeq2500对捕获的DNA进行测序。使用Burrows-Wheeler比对、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。
在90例NSHL患者中的57例中检测到GJB2、SLC26A4和MT-RNR1中的26个候选变异。GJB2 c.109G＞A是最常见的变异，其次是GJB2 c.608T＞C和c.235delC。22例NSHL患者获得了基因诊断，其中19例与常染色体隐性NSHL相关，1例与常染色体显性NSHL相关，2例与线粒体疾病相关。
我们的靶向NGS分析为NGS在常规诊断中的应用提供了支持，并概述了闽南地区聋人群体中等位基因频率的基因变异情况。
