Evaluating the clinical efficacy of a long-read sequencing-based approach for carrier screening of spinal muscular atrophy.

IF 3.8 3区 医学 Q2 GENETICS & HEREDITY
Ju Long, Di Cui, Chunhui Yu, Wanli Meng
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引用次数: 0

Abstract

Spinal muscular atrophy (SMA) is the second most common fatal genetic disease in infancy. It is caused by deletion or intragenic pathogenic variants of the causative gene SMN1, which degenerates anterior horn motor neurons and leads to progressive myasthenia and muscle atrophy. Early treatment improves motor function and prognosis in patients with SMA, but drugs are expensive and do not cure the disease. Therefore, carrier screening seems to be the most effective way to prevent SMA birth defects. In this study, we genetically analyzed 1400 samples using multiplex ligation-dependent probe amplification (MLPA) and quantitative polymerase chain reaction (qPCR), and compared the consistency of the results. We randomly selected 44 samples with consistent MLPA and qPCR results for comprehensive SMA analysis (CASMA) using a long-read sequencing (LRS)-based approach. CASMA results showed 100% consistency, visually and intuitively explained the inconsistency between exons 7 and 8 copy numbers detected by MLPA in 13 samples. A total of 16 samples showed inconsistent MLPA and qPCR results for SMN1 exon 7. CASMA was performed on all samples and the results were consistent with those of resampling for MLPA and qPCR detection. CASMA also detected an additional intragenic variant c.-39A>G in a sample with two copies of SMN1 (RT02). Finally, we detected 23 SMA carriers, with an estimated carrier rate of 1/61 in this cohort. In addition, CASMA identified the "2 + 0" carrier status of SMN1 and SMN2 in a family by analyzing the genotypes of only three samples (parents and one sibling). CASMA has great advantages over MLPA and qPCR assays, and could become a powerful technical support for large-scale screening of SMA.

评估基于长读数测序的脊髓性肌萎缩症携带者筛查方法的临床疗效。
脊髓性肌萎缩症(SMA)是婴儿期第二大最常见的致命遗传病。它是由致病基因 SMN1 的缺失或基因内致病变异引起的,会使前角运动神经元变性,导致进行性肌无力和肌肉萎缩。早期治疗可改善 SMA 患者的运动功能和预后,但药物昂贵且不能治愈疾病。因此,携带者筛查似乎是预防 SMA 出生缺陷的最有效方法。在本研究中,我们使用多重连接依赖性探针扩增(MLPA)和定量聚合酶链反应(qPCR)对 1400 个样本进行了基因分析,并比较了结果的一致性。我们随机选取了 44 个 MLPA 和 qPCR 结果一致的样本,采用基于长序列测序(LRS)的方法进行 SMA 综合分析(CASMA)。CASMA 结果显示出 100% 的一致性,直观地解释了 13 个样本中 MLPA 检测到的第 7 和第 8 外显子拷贝数不一致的情况。共有 16 个样本的 SMN1 第 7 号外显子的 MLPA 和 qPCR 结果不一致。对所有样本都进行了 CASMA 检测,结果与重新取样进行 MLPA 和 qPCR 检测的结果一致。CASMA 还在一个有两个 SMN1(RT02)拷贝的样本中检测到了一个额外的基因内变异 c.-39A>G。最后,我们检测到 23 个 SMA 携带者,估计该队列中的携带率为 1/61。此外,CASMA 只分析了三个样本(父母和一个兄弟姐妹)的基因型,就确定了一个家族中 SMN1 和 SMN2 的 "2 + 0 "携带者状态。与 MLPA 和 qPCR 方法相比,CASMA 具有很大的优势,可以成为大规模筛查 SMA 的有力技术支持。
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来源期刊
Human Genomics
Human Genomics GENETICS & HEREDITY-
CiteScore
6.00
自引率
2.20%
发文量
55
审稿时长
11 weeks
期刊介绍: Human Genomics is a peer-reviewed, open access, online journal that focuses on the application of genomic analysis in all aspects of human health and disease, as well as genomic analysis of drug efficacy and safety, and comparative genomics. Topics covered by the journal include, but are not limited to: pharmacogenomics, genome-wide association studies, genome-wide sequencing, exome sequencing, next-generation deep-sequencing, functional genomics, epigenomics, translational genomics, expression profiling, proteomics, bioinformatics, animal models, statistical genetics, genetic epidemiology, human population genetics and comparative genomics.
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