Journal Article

The next generation of population-based spinal muscular atrophy carrier screening: comprehensive pan-ethnic SMN1 copy-number and sequence variant analysis by massively parallel sequencing

Beaudet, Arthur L., Tian, Xia, Yang, Yaping, Li, Jianli, Schmitt, Eric S., Chen, Zhao, Jin, Weihong, Xia, Fan, Scull, Jennifer, Cheng, Hanyin, Meng, Linyan, Eng, Christine M., Liu, Pengfei, Zhang, Tao, Wen, Shu, Liu, Xiaoming, Wong, Lee-Jun, Muzny, Donna, Mei, Hui, Li, Fangyuan, Wang, Yue, Zhang, Jinglan, Zhang, Wei V., Ge, Xiaoyan, Wang, Xia, Feng, Yanming, Tokita, Mari

2017

Overview

Purpose: 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). Methods: 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. Results: 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. Conclusion: 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

• Publisher: Nature Publishing Group US,Elsevier Limited
• Subject: 631/208/514/2254 / 692/699/375/374 / 692/700/139/1512 / 692/700/478/2772 / Biomedical and Life Sciences / Biomedicine / Gene Dosage / Genetic Carrier Screening / High-Throughput Nucleotide Sequencing - methods / Human Genetics / Humans / Laboratory Medicine / Muscular Atrophy, Spinal - ethnology / Muscular Atrophy, Spinal - genetics / Neuromuscular diseases / original-research-article / Polymorphism, Single Nucleotide / Reproducibility of Results / Sensitivity and Specificity / Survival of Motor Neuron 1 Protein - genetics / Survival of Motor Neuron 2 Protein - genetics