A new approach to detect a set of SNP-SNP markers: Combining ARMS-PCR with SNaPshot technology
A new approach to detect a set of SNP-SNP markers: Combining ARMS-PCR with SNaPshot technology
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检测一组 SNP-SNP 标记的新方法：ARMS-PCR 与 SNaPshot 技术相结合
DOI：
10.1002/elps.202000009
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发表时间：
2020-05-11
期刊：
影响因子：
2.9
通讯作者：
Liang, Weibo
中科院分区：
文献类型：
--
作者：
Zhang, Ranran;Tan, Yu;Liang, Weibo
微单倍型是一种很有前途的新型法医遗传标记。由两个SNP组成的微单倍型（SNP-SNP）具有较单一SNP短的扩增长度和较高的多态性程度，没有STRs的口吃干扰和高突变率，具有较强的应用潜力。目前，检测微单倍型最常用的方法是大规模平行测序。然而，仪器的成本和广泛使用限制了其在法医实验室的广泛应用。在本研究中，我们筛选了23个新的SNP-SNP位点，并将基于多重扩增的难突变系统的PCR （ARMS-PCR）与基于CE的SNaPshot技术相结合，建立了新的检测方法。首先，我们在设计针对SNP 1 （SNP-SNP的第一个SNP）的ARMS-PCR时，在引物的3 '端引入了额外的故意错配。然后，在SNP 2（第二个SNP）位置旁设计用于SNaPshot检测的单碱基延伸引物。最终，15个基因座被成功构建到4个基因板中，这些基因座在中国西南汉族人群中表现出较高的多态性水平。所有位点的信息基因型平均概率（I值）为0.319，综合判别能力为0.999999999。因此，这种新的检测系统将为现有的检测方法提供有价值的补充。
Microhaplotypes are a new promising type of forensic genetic marker. Without the interference of stutter and high mutation rates as for STRs, and with short amplification lengths and a higher degree of polymorphism than single SNP, microhaplotypes composed of two SNPs, SNP-SNP, have a strong application potential. Currently, the most common method to detect microhaplotypes is massive parallel sequencing. However, the cost and extensive use of instruments limit its wide application in forensic laboratories. In this study, we screened 23 new SNP-SNP loci and established a new detection method by combining a multiplex amplification refractory mutation system-based PCR (ARMS-PCR) and SNaPshot technology based on CE. First, we introduced an additional deliberate mismatch at the antepenultimate base from the 3 ' end of primers when designing ARMS-PCR for SNP 1 (the first SNP of the SNP-SNP). Then, single base extension primers for SNaPshot assay were designed next to the position of SNP 2 (the second SNP). Finally, 15 loci were successfully built into four panels and these loci showed a relatively high level of polymorphism in the Southwest Chinese Han population. All the loci had an average probability of informative genotypes (I value) of 0.319 and a combined discrimination power of 0.999999999. Therefore, this new detection system will provide a valuable supplement to current methods.