Pilot study for forensic evaluations of the Precision ID GlobalFiler™ NGS STR Panel v2 with the Ion S5™ system
Pilot study for forensic evaluations of the Precision ID GlobalFiler™ NGS STR Panel v2 with the Ion S5™ system
复制标题
使用 Ion S5 (TM) 系统对 Precision ID GlobalFiler (TM) NGS STR Panel v2 进行法医评估的试点研究
DOI：
10.1016/j.fsigen.2019.102147
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发表时间：
2019-11-01
影响因子：
3.1
通讯作者：
Li, Chengtao
中科院分区：
文献类型：
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作者：
Tao, Ruiyang;Qi, Wenjie;Li, Chengtao
随着大规模并行测序技术的不断发展，越来越多的实验室将该方法用于法医基因组分析。在对常见的短串联重复序列(STR)进行测序时，MPS确实比使用传统毛细管电泳法(CE)的基于长度的基因分型方法有许多优势。Precision ID GlobalFeller(TM)NGS STR Panel v2最近发布，可通过Ion S5(TM)系统同时针对31个常染色体STR(20个扩展组合DNA指数系统(CODIS)核心基因座和11个非CODIS基因座)和4个性别决定基因座(釉质、DYS391、SRY和Y-indel(Rs2032678))。在目前的研究中，我们对这一新型MPS-STR面板进行了初步验证，包括以下分析：重复性、一致性、卡顿和平衡、敏感性、病例类型样本测试、稳定性、混合和总体调查。用125pg的阳性对照DNA获得完整可靠的图谱。常见的病例样本类型和比例为1：1、1：3和3：1的人工混合物也进行了完全的基因分型。在50个无关个体的样本中检测到了额外的等位基因序列变异，随后，获得了更高的辨别力和排斥力。然而，检测到五角体D基因座的平均覆盖深度(Doc)显著低于其他基因座，这导致了基因座间的不平衡；这可能是该基因座在焦点内不平衡的原因之一，在一致性研究中0.18%的结果不一致。尽管观察到了某些缺陷，但包括DOC、序列覆盖率(SCR)和杂合子平衡(H-b)在内的信息指标足以保证可靠的测序结果，这些结果与毛细管电泳法(CE)的结果有99.61%的一致性。总的来说，Precision ID GlobalFeller(TM)NGS STR Panel v2被证明是敏感、可靠和坚固的，可以成为人类身份识别和亲属关系分析的强大工具。此外，我们期待着它的更新版。
With the continuous development of massively parallel sequencing (MPS), increasing numbers of laboratories have utilized this method for forensic genomic analyses. When sequencing common short tandem repeats (STRs), MPS does have many advantages over the length-based genotyping method that uses traditional capillary electrophoresis (CE) technology. The Precision ID GlobalFiler (TM) NGS STR Panel v2 was recently released to simultaneously target 31 autosomal STRs (20 expanded Combined DNA Index System (CODIS) core loci and 11 non-CODIS loci) and 4 gender determination loci (Amelogenin, DYS391, SRY and Y-indel (rs2032678)) with the Ion S5 (TM) System. In the current study, we performed a preliminary validation for this novel MPS-STR panel that included the following analyses: repeatability, concordance, stutter and balance, sensitivity, case-type sample testing, stability, mixture and a population investigation. Complete and reliable profiles were obtained using 125 pg of positive control DNA. The commonly encountered types of case samples and artificial mixtures with ratios of 1:1, 1:3 and 3:1 were also fully genotyped. Additional allele sequence variations were detected in samples from 50 unrelated individuals, and subsequently, an increased power of discrimination and power of exclusion were achieved. However, the average depth of coverage (DoC) of the Penta D locus was detected to be dramatically lower than those of other loci, which caused an interlocus imbalance; this could be one of the reasons for the intralocus imbalance of this locus and the 0.18% inconsistent results in the concordance study. Although certain flaws were observed, the informative metrics, including the DoC, sequence coverage ratios (SCRs) and heterozygote balance (H-b), of the novel MPS multiplex in our study were sufficient for reliable sequencing results that were 99.61% in concordance with the capillary electrophoresis (CE) results. In general, the Precision ID GlobalFiler (TM) NGS STR Panel v2 was demonstrated to be sensitive, reliable and robust and could be a powerful tool for human identification and kinship analyses. Additionally, we look forward to its updated version.