Set of 15 SNP-SNP Markers for Detection of Unbalanced Degraded DNA Mixtures and Noninvasive Prenatal Paternity Testing.
Set of 15 SNP-SNP Markers for Detection of Unbalanced Degraded DNA Mixtures and Noninvasive Prenatal Paternity Testing.
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DOI：
10.3389/fgene.2021.800598
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发表时间：
2021
影响因子：
3.7
通讯作者：
Liang W
中科院分区：
文献类型：
--
作者：
Zhang R;Tan Y;Wang L;Jian H;Zhu J;Xiao Y;Tan M;Xue J;Yang F;Liang W
不平衡和降解混合物（UDM）在法医DNA分析中非常常见。例如，犯罪嫌疑人的DNA信号被大量受害者的DNA掩盖，或者母体血浆中的无细胞胎儿DNA（cffDNA）被母体DNA的高背景掩盖。目前，检测这些混合物中的微量DNA是复杂和具有挑战性的。我们开发了一套新的SNP-SNP微单倍型与短扩增子，我们成功地进行基因分型的扩增-难治性突变系统PCR（ARMS-PCR）的新方法结合SNaPshot技术的基础上毛细管电泳（CE）平台。该基因组在中国西南地区汉族人群中具有较高的多态性，因此具有很好的混合研究潜力。我们评估了该面板用于UDM检测和无创产前亲子鉴定（NIPPT）的可行性。15个SNP-SNPs检测自制DNA混合物中的微量DNA，灵敏度为0.025-0.05 ng，特异性为1：1，000。此外，该小组成功地对来自单一和混合样品的降解DNA进行了基因分型。最后，将15个SNP-SNPs应用于26个trios。所有样品均显示具有至少一种标记物的阳性结果以检测cffDNA。此外，所有的胎儿等位基因在母体血浆中证实了基因分型胎儿基因组DNA从胎盘穿刺和父亲的基因组DNA从外周血。结果表明，基于CE平台的SNP-SNP策略可用于UDM的检测和NIPPT。
Unbalanced and degraded mixtures (UDM) are very common in forensic DNA analysis. For example, DNA signals from criminal suspects are masked by a large amount of DNA from victims, or cell-free fetal DNA (cffDNA) in maternal plasma is masked by a high background of maternal DNA. Currently, detecting minor DNA in these mixtures is complex and challenging. We developed a new set of SNP-SNP microhaplotypes with short amplicons, and we successfully genotyped them using the new method of amplification-refractory mutation system PCR (ARMS-PCR) combined with SNaPshot technology based on a capillary electrophoresis (CE) platform. This panel reflects a high polymorphism in the Southwest Chinese Han population and thus has excellent potential for mixture studies. We evaluated the feasibility of this panel for UDM detection and noninvasive prenatal paternity testing (NIPPT). Fifteen SNP-SNPs detected minor DNA of homemade DNA mixtures, with a sensitivity of 0.025–0.05 ng and a specificity of 1:1,000. In addition, the panel successfully genotyped degraded DNA from single and mixed samples. Finally, 15 SNP-SNPs were applied to 26 trios. All samples displayed positive results with at least one marker to detect cffDNA. Besides, all fetal alleles in maternal plasma were confirmed by genotyping fetal genomic DNA from amniocentesis and paternal genomic DNA from peripheral blood. The results indicated that the SNP-SNP strategy based on the CE platform was useful for UDM detection and NIPPT.
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