Feng Yanming, Ge Xiaoyan, Meng Linyan, Scull Jennifer, Li Jianli, Tian Xia, Zhang Tao, Jin Weihong, Cheng Hanyin, Wang Xia, Tokita Mari, Liu Pengfei, Mei Hui, Wang Yue, Li Fangyuan, Schmitt Eric S, Zhang Wei V, Muzny Donna, Wen Shu, Chen Zhao, Yang Yaping, Beaudet Arthur L, Liu Xiaoming, Eng Christine M, Xia Fan, Wong Lee-Jun, Zhang Jinglan
Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.
Baylor Genetics Laboratories, Houston, Texas, USA.
Genet Med. 2017 Aug;19(8):936-944. doi: 10.1038/gim.2016.215. Epub 2017 Jan 26.
To investigate pan-ethnic SMN1 copy-number and sequence variation by hybridization-based target enrichment coupled with massively parallel sequencing or next-generation sequencing (NGS).
NGS reads aligned to SMN1 and SMN2 exon 7 were quantified to determine the total combined copy number of SMN1 and SMN2. The ratio of SMN1 to SMN2 was calculated based on a single-nucleotide difference that distinguishes the two genes. SMN1 copy-number results were compared between the NGS and quantitative polymerase chain reaction and/or multiplex ligation-dependent probe amplification. The NGS data set was also queried for the g.27134T>G single-nucleotide polymorphism (SNP) and other SMN1 sequence pathogenic variants.
The sensitivity of the test to detect spinal muscular atrophy (SMA) carriers with one copy of SMN1 was 100% (95% confidence interval (CI): 95.9-100%; n = 90) and specificity was 99.6% (95% CI: 99.4-99.7%; n = 6,648). Detection of the g.27134T>G SNP by NGS was 100% concordant with an restriction fragment-length polymorphism method (n = 493). Ten single-nucleotide variants in SMN1 were detectable by NGS and confirmed by gene-specific amplicon-based sequencing. This comprehensive approach yielded SMA carrier detection rates of 90.3-95.0% in five ethnic groups studied.
We have developed a novel, comprehensive SMN1 copy-number and sequence variant analysis method by NGS that demonstrated improved SMA carrier detection rates across the entire population examined.Genet Med advance online publication 19 January 2017.
通过基于杂交的目标富集结合大规模平行测序或下一代测序（NGS）来研究泛种族的生存运动神经元1（SMN1）拷贝数及序列变异。
对与SMN1和SMN2外显子7比对的NGS读数进行定量，以确定SMN1和SMN2的总拷贝数。基于区分这两个基因的单核苷酸差异计算SMN1与SMN2的比率。将NGS的SMN1拷贝数结果与定量聚合酶链反应和/或多重连接依赖探针扩增结果进行比较。还在NGS数据集中查询g.27134T>G单核苷酸多态性（SNP）和其他SMN1序列致病性变异。
检测携带一个SMN1拷贝的脊髓性肌萎缩症（SMA）携带者的测试灵敏度为100%（95%置信区间（CI）：95.9 - 100%；n = 90），特异性为99.6%（95%CI：99.4 - 99.7%；n = 6648）。通过NGS检测g.27134T>G SNP与限制性片段长度多态性方法的一致性为100%（n = 493）。通过NGS可检测到SMN1中的10个单核苷酸变异，并通过基于基因特异性扩增子的测序得到证实。在研究的五个种族群体中，这种综合方法产生的SMA携带者检测率为90.3 - 95.0%。
我们通过NGS开发了一种新颖、全面的SMN1拷贝数和序列变异分析方法，该方法在整个检测人群中显示出提高的SMA携带者检测率。《遗传医学》于201
