Targeted capture and sequencing of 1245 SNPs for forensic applications
Targeted capture and sequencing of 1245 SNPs for forensic applications
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用于法医应用的 1245 个 SNP 的靶向捕获和测序
DOI：
10.1016/j.fsigen.2019.07.006
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发表时间：
2019
影响因子：
3.1
通讯作者：
Xiong Bo
中科院分区：
文献类型：
--
作者：
Wu Liangjun;Chu Xufeng;Zheng Jing;Xiao Chao;Zhang Zhe;Huang Guiyang;Li Dan;Zhan Jinbang;Huang Daixin;Hu Ping;Xiong Bo
下一代测序（NGS）技术使得能够在单个实验中同时分析来自多个样品的大量SNP，以补充基于STR的方法的缺点。为了有效地对所需的SNP进行基因分型，优化文库构建程序至关重要。在这项研究中，我们制定了一个战略相结合的分子倒置探针（MIP）为基础的目标区域捕获方法和NGS的基因分型1245 SNPs。根据1000个基因组数据，我们选择的所有SNPs都表现出高杂合性（次要等位基因频率（MAF）> 0.3）。我们应用该方法对来自中国湖北省的210个无关个体进行了基因分型，并评估了等位基因频率、Hardy-Weinberg平衡和连锁不平衡。超过95%的SNPs的MAF ≥0.2，98%的SNPs未观察到显著偏离或强连锁。数据表明，即使在相对有限的区域内，我们的SNP面板也适合于个体鉴定。此外，我们使用低质量的DNA样本对7个三人家庭进行了亲子鉴定。的结论是在总协议与STR为基础的分析，具有较高的置信指数。最后，我们用模拟降解的DNA样品评估了MIP-NGS方法的性能。即使基因组DNA被超声处理到100 bp范围，我们也能够对大多数SNP进行基因分型。总之，我们建立了一个高度准确和成本效益的SNP基因分型方法，这是潜在的能够解决法医实践中遇到的复杂问题。
Next generation sequencing (NGS) technologies have enabled the possibility of analyzing a large number of SNPs simultaneously from multiple samples in a single experiment, for complementing the shortcomings of STR based methods. To efficiently genotype the desired SNPs, it is critical to optimize the library construction procedures. In this study, we formulated a strategy combining the molecular inversion probe (MIP) based target region capture method and NGS for genotyping 1245 SNPs. All the SNPs we selected exhibited high heterozygosity (minor allele frequency (MAF) > 0.3) according to 1000 genomes data. We applied the method to genotype a population of 210 unrelated individuals from the Hubei province of China and assessed the allele frequencies, Hardy-Weinberg equilibrium and linkage disequilibrium. The MAFs of more than 95% of the SNPs were ≥0.2, and no significant deviation or strong linkage was observed for 98% of the SNPs. The data indicated that, even within a relatively confined region, our SNP panel is suitable for individual identifications. Furthermore, we performed paternity test for 7 trio families using low quality DNA samples. The conclusions are in total agreement with these of STR-based analyses, with higher confidence indexes. Finally, we evaluated the performance of the MIP-NGS method with mock degraded DNA samples. We were able to genotype most of the SNPs even when the genomic DNA was sonicated to ˜100 bp range. In summary, we established a highly accurate and cost-effective method of SNP genotyping, which is potentially capable of solving complex issues encountered in forensic practices.