Developmental validation of a custom panel including 273 SNPs for forensic application using Ion Torrent PGM
Developmental validation of a custom panel including 273 SNPs for forensic application using Ion Torrent PGM
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使用 Ion Torrent PGM 对包含 273 个 SNP 的定制面板进行开发验证，用于法医应用
DOI：
10.1016/j.fsigen.2016.12.003
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发表时间：
2017
影响因子：
3.1
通讯作者：
Li Chengtao
中科院分区：
文献类型：
--
作者：
Zhang Suhua;Bian Yingnan;Chen Anqi;Zheng Hancheng;Gao Yuzhen;Hou Yiping;Li Chengtao
利用大规模平行测序（MPS）技术进行SNP检测在法医遗传学中正变得越来越有吸引力，因为STR标记物的缺点，例如它们的高突变率和与当前PCR-CE方法相关的缺点以及其关于多重能力的限制。MPS提供了在单个实验运行中对来自多个样品的数百至数千个SNP进行基因分型的潜力。在这项研究中，我们设计了一个定制的SNP面板，其中包括273个法医学相关的身份SNP，这些SNP选自SNPforID、IISNP和HapMap数据库以及先前的相关研究，并使用Ion Torrent PGM评估了基因分型精度、序列覆盖率、灵敏度和SNP性能。在定制MPS-SNP组的一致性研究中，由于覆盖读数太低（<20），只有四个MPS调用缺失，而其他的与两个对照样品（即9947 A和9948）的桑格测序结果完全一致。分析表明，除了用于检测来自中国汉族人群和上述对照的50个受试个体中不一致的等位基因平衡和/或较低覆盖度读数的16个SNP之外，所包括的基因座之间的覆盖度平衡。除了16个表现不佳的SNP外，获得的大部分SNP的序列覆盖率是广泛的，只有三个Y-SNP（rs 16980601、rs 11096432、rs3900）显示平均覆盖率低于1000。对照DNA 9948稀释系列的分析产生了可重现的结果，低至1 ng DNA输入。此外，我们提供了一个分析工具，自动数据质量控制和基因分型检查，我们得出的结论是，SNP目标是多态性和独立的中国汉族人群。总之，对灵敏度、准确度和基因分型性能的评估为MPS技术在法医SNP分析中的应用提供了强有力的支持，并且该测定提供了简单的样品到基因型工作流程，这对于个体识别和复杂亲属关系问题的法医案例工作可能是有益的。
Utilizing massively parallel sequencing (MPS) technology for SNP testing in forensic genetics is becoming attractive because of the shortcomings of STR markers, such as their high mutation rates and disadvantages associated with the current PCR-CE method as well as its limitations regarding multiplex capabilities. MPS offers the potential to genotype hundreds to thousands of SNPs from multiple samples in a single experimental run. In this study, we designed a customized SNP panel that includes 273 forensically relevant identity SNPs chosen from SNPforID, IISNP, and the HapMap database as well as previously related studies and evaluated the levels of genotyping precision, sequence coverage, sensitivity and SNP performance using the Ion Torrent PGM. In a concordant study of the custom MPS-SNP panel, only four MPS callings were missing due to coverage reads that were too low (<20), whereas the others were fully concordant with Sanger's sequencing results across the two control samples, that is, 9947A and 9948. The analyses indicated a balanced coverage among the included loci, with the exception of the 16 SNPs that were used to detect an inconsistent allele balance and/or lower coverage reads among 50 tested individuals from the Chinese HAN population and the above controls. With the exception of the 16 poorly performing SNPs, the sequence coverage obtained was extensive for the bulk of the SNPs, and only three Y-SNPs (rs16980601, rs11096432, rs3900) showed a mean coverage below 1000. Analyses of the dilution series of control DNA 9948 yielded reproducible results down to 1 ng of DNA input. In addition, we provide an analysis tool for automated data quality control and genotyping checks, and we conclude that the SNP targets are polymorphic and independent in the Chinese HAN population. In summary, the evaluation of the sensitivity, accuracy and genotyping performance provides strong support for the application of MPS technology in forensic SNP analysis, and the assay offers a straightforward sample-to-genotype workflow that could be beneficial in forensic casework with respect to both individual identification and complex kinship issues.