Department of Biomedicine and Prevention, Tor Vergata University of Rome, 00133 Rome, Italy.
Department of Biomedicine and Prevention, Section of Legal Medicine, Social Security and Forensic Toxicology, University of Rome Tor Vergata, 00133 Rome, Italy.
Genes (Basel). 2021 Feb 3;12(2):221. doi: 10.3390/genes12020221.
A custom plate of OpenArray™ technology was evaluated to test 60 single-nucleotide polymorphisms (SNPs) validated for the prediction of eye color, hair color, and skin pigmentation, and for personal identification. The SNPs were selected from already validated subsets (Hirisplex-s, Precision ID Identity SNP Panel, and ForenSeq DNA Signature Prep Kit). The concordance rate and call rate for every SNP were calculated by analyzing 314 sequenced DNA samples. The sensitivity of the assay was assessed by preparing a dilution series of 10.0, 5.0, 1.0, and 0.5 ng. The OpenArray™ platform obtained an average call rate of 96.9% and a concordance rate near 99.8%. Sensitivity testing performed on serial dilutions demonstrated that a sample with 0.5 ng of total input DNA can be correctly typed. The profiles of the 19 SNPs selected for human identification reached a random match probability (RMP) of, on average, 10. An analysis of 21 examples of biological evidence from 8 individuals, that generated single short tandem repeat profiles during the routine workflow, demonstrated the applicability of this technology in real cases. Seventeen samples were correctly typed, revealing a call rate higher than 90%. Accordingly, the phenotype prediction revealed the same accuracy described in the corresponding validation data. Despite the reduced discrimination power of this system compared to STR based kits, the OpenArray™ System can be used to exclude suspects and prioritize samples for downstream analyses, providing well-established information about the prediction of eye color, hair color, and skin pigmentation. More studies will be needed for further validation of this technology and to consider the opportunity to implement this custom array with more SNPs to obtain a lower RMP and to include markers for studies of ancestry and lineage.
我们评估了定制的 OpenArray 技术芯片，用于测试 60 个经验证可用于预测眼睛颜色、头发颜色和皮肤色素沉着以及个人识别的单核苷酸多态性 (SNP)。这些 SNP 是从已经验证的子集中选择的（Hirisplex-s、Precision ID Identity SNP Panel 和 ForenSeq DNA Signature Prep Kit）。通过分析 314 个测序 DNA 样本，计算每个 SNP 的一致性率和可调用率。通过制备 10.0、5.0、1.0 和 0.5 ng 的稀释系列来评估测定法的灵敏度。OpenArray 平台获得了平均 96.9%的可调用率和接近 99.8%的一致性率。对连续稀释液进行的灵敏度测试表明，总输入 DNA 为 0.5 ng 的样本可以正确分型。为人类识别选择的 19 个 SNP 的图谱达到平均随机匹配概率 (RMP) 为 10。对 8 个人的 21 个生物学证据实例的分析，在常规工作流程中生成单个短串联重复序列图谱，证明了该技术在实际案例中的适用性。17 个样本得到正确分型，调用率高于 90%。因此，表型预测显示出与相应验证数据中描述的相同准确性。尽管与基于 STR 的试剂盒相比，该系统的鉴别能力降低，但 OpenArray 系统可用于排除嫌疑人并优先对下游分析进行样本分类，提供有关眼睛颜色、头发颜色和皮肤色素沉着预测的可靠信息。需要进一步验证这项技术，并考虑有机会实施包含更多 SNP 的这种定制芯片，以获得更低的 RMP，并包括用于研究祖先和血统的标记。
