Department of Forensic Medicine, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea; Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea.
Department of Forensic Medicine, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea; Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea.
Leg Med (Tokyo). 2023 Jul;63:102256. doi: 10.1016/j.legalmed.2023.102256. Epub 2023 Apr 8.
Single nucleotide polymorphisms (SNPs) have become popular in forensic genetics as an alternative to short tandem repeats (STRs). The Precision ID Identity Panel (Thermo Fisher Scientific), consisting of 90 autosomal SNPs and 34 Y-chromosomal SNPs, enabled human identification studies on global populations through next-generation sequencing (NGS). However, most previous studies on the panel have used the Ion Torrent platform, and there are few reports on the Southeast Asian population. Here, a total of 96 unrelated males from Myanmar (Yangon) were analyzed with the Precision ID Identity Panel on a MiSeq (Illumina) using an in-house TruSeq compatible universal adapter and a custom variant caller, Visual SNP. The sequencing performance evaluated by locus balance and heterozygote balance was comparable to that of the Ion Torrent platform. For 90 autosomal SNPs, the combined match probability (CMP) was 6.994 × 10, lower than that of 22 PowerPlex Fusion autosomal STRs (3.130 × 10). For 34 Y-SNPs, 14 Y-haplogroups (mostly O2 and O1b) were observed. We found 51 cryptic variations (42 haplotypes) around target SNPs, of which haplotypes corresponding to 33 autosomal SNPs decreased CMP. Interpopulation analysis revealed that the Myanmar population is genetically closer to the East and Southeast Asian populations. In conclusion, the Precision ID Identity Panel can be successfully analyzed on the Illumina MiSeq and provides high discrimination power for human identification in the Myanmar population. This study broadened the accessibility of the NGS-based SNP panel by expanding the available NGS platforms and adopting a robust NGS data analysis tool.
单核苷酸多态性 (SNP) 已成为法医遗传学中的热门选择，可替代短串联重复序列 (STR)。由 90 个常染色体 SNP 和 34 个 Y 染色体 SNP 组成的 Precision ID 身份面板 (Thermo Fisher Scientific) 通过下一代测序 (NGS) 实现了对全球人群的人类识别研究。然而，该面板的大多数先前研究都使用了 Ion Torrent 平台，并且有关东南亚人群的报道很少。在这里，使用 MiSeq (Illumina) 上的 Precision ID 身份面板对来自缅甸仰光的 96 名无关男性进行了分析，使用的是内部 TruSeq 兼容通用接头和定制的变体调用器 Visual SNP。通过基因座平衡和杂合子平衡评估的测序性能与 Ion Torrent 平台相当。对于 90 个常染色体 SNP，联合匹配概率 (CMP) 为 6.994×10, 低于 22 个 PowerPlex Fusion 常染色体 STR 的 3.130×10。对于 34 个 Y-SNP，观察到 14 个 Y 单倍群 (主要是 O2 和 O1b)。我们在目标 SNP 周围发现了 51 个隐匿变异 (42 种单倍型)，其中对应于 33 个常染色体 SNP 的单倍型降低了 CMP。种群间分析表明，缅甸人群在遗传上与东亚和东南亚人群更为接近。总之，Precision ID 身份面板可以在 Illumina MiSeq 上成功分析，并为缅甸人群的身份识别提供高鉴别力。本研究通过扩展可用的 NGS 平台和采用强大的 NGS 数据分析工具，拓宽了基于 NGS 的 SNP 面板的可及性。
