Null alleles and sequence variations at primer binding sites of STR loci within multiplex typing systems
Null alleles and sequence variations at primer binding sites of STR loci within multiplex typing systems
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多重分型系统中 STR 基因座引物结合位点的空等位基因和序列变异
DOI：
10.1016/j.legalmed.2017.10.007
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发表时间：
2018-01-01
期刊：
影响因子：
1.5
通讯作者：
Xie, Jianhui
中科院分区：
文献类型：
--
作者：
Yao, Yining;Yang, Qinrui;Xie, Jianhui
人类基因组中广泛观察到罕见变异，引物结合位点的序列变异可能会损害 PCR 扩增过程，导致等位基因丢失，称为无效等位基因。在本研究中，使用 PowerPlex (R) 21 系统进行 STR 基因分型的常规亲子鉴定中的 5 个病例被认为分别在 TH01、FGA、D5S818、D8S1179 和 D16S539 处含有无效等位基因。通过使用替代商业试剂盒 AGCU Expressmarker 22 PCR 扩增试剂盒和 AmpFlSTR (R) 确认等位基因的缺失。 Identifiler (R) Plus Kit 和测序结果显示每个 STR 基因座的引物结合位点存在单碱基变异。之前报告收集的结果表明，D5S818 的无效等位基因在两个 PowerPlex (R) 分型系统检测到的人群中经常观察到，而 D195433 的无效等位基因主要在两个 AmpFlSTR (R) 分型系统检测到的日本人群中观察到。此外，最流行的突变类型是从C到T，G到A的转变，这可能与DNA甲基化有潜在的关系。总而言之，这些结果可以为法医实践中消除基因分型差异和开发引物组提供有用的信息。
Rare variants are widely observed in human genome and sequence variations at primer binding sites might impair the process of PCR amplification resulting in dropouts of alleles, named as null alleles. In this study, 5 cases from routine paternity testing using PowerPlex (R) 21 System for STR genotyping were considered to harbor null alleles at TH01, FGA, D5S818, D8S1179, and D16S539, respectively. The dropout of alleles was confirmed by using alternative commercial kits AGCU Expressmarker 22 PCR amplification kit and AmpFlSTR (R). Identifiler (R) Plus Kit, and sequencing results revealed a single base variation at the primer binding site of each STR locus. Results from the collection of previous reports show that null alleles at D5S818 were frequently observed in population detected by two PowerPlex (R) typing systems and null alleles at D195433 were mostly observed in Japanese population detected by two AmpFlSTR (R) typing systems. Furthermore, the most popular mutation type appeared the transition from C to T with G to A, which might have a potential relationship with DNA methylation. Altogether, these results can provide helpful information in forensic practice to the elimination of genotyping discrepancy and the development of primer sets.