Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Central Avenue 55, Airport Business Park East Building E3, Tianjin, 300308, China.
BGI Genomics, BGI-Shenzhen, Bei Shan Industrial Zone, Yantian District, Shenzhen, 518083, Guangdong, China.
Sci Rep. 2022 Jan 7;12(1):223. doi: 10.1038/s41598-021-04325-1.
Spinal muscular atrophy (SMA) is one of the most common and severe genetic diseases. SMA carrier screening is an effective way to identify couples at risk of having affected children. Next-generation sequencing (NGS)-based expanded carrier screening could detect SMN1 gene copy number without extra experiment and with high cost performance. However, its performance has not been fully evaluated. Here we conducted a systematic comparative study to evaluate the performance of three common methods. 478 samples were analyzed with multiplex ligation probe amplification (MLPA), real-time quantitative polymerase chain reaction (qPCR) and NGS, simultaneously. Taking MLPA-based results as the reference, for 0 copy, 1 copy and ≥ 2 copy SMN1 analysis with NGS, the sensitivity, specificity and precision were all 100%. Using qPCR method, the sensitivity was 100%, 97.52% and 94.30%, respectively; 98.63%, 95.48% and 100% for specificity; and 72.72%, 88.72% and 100% for precision. NGS repeatability was higher than that of qPCR. Moreover, among three methods, NGS had the lowest retest rate. Thus, NGS is a relatively more reliable method for SMN1 gene copy number detection. In expanded carrier screening, compared with the combination of multiple methods, NGS method could reduce the test cost and simplify the screening process.
脊髓性肌萎缩症（SMA）是最常见和最严重的遗传疾病之一。SMA 携带者筛查是识别有患病子女风险的夫妇的有效方法。基于下一代测序（NGS）的扩展携带者筛查可以在不进行额外实验的情况下检测 SMN1 基因拷贝数，并且具有较高的性价比。然而，其性能尚未得到充分评估。在这里，我们进行了一项系统的比较研究，以评估三种常用方法的性能。同时使用多重连接探针扩增（MLPA）、实时定量聚合酶链反应（qPCR）和 NGS 分析了 478 个样本。以 MLPA 为参考，对于 NGS 的 0 拷贝、1 拷贝和≥2 拷贝 SMN1 分析，其敏感性、特异性和精度均为 100%。使用 qPCR 方法，其敏感性分别为 100%、97.52%和 94.30%；特异性分别为 98.63%、95.48%和 100%；精度分别为 72.72%、88.72%和 100%。NGS 的重复性高于 qPCR。此外，在这三种方法中，NGS 的复测率最低。因此，NGS 是一种用于检测 SMN1 基因拷贝数相对更可靠的方法。在扩展携带者筛查中，与多种方法的组合相比，NGS 方法可以降低检测成本并简化筛查过程。
