Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Key Laboratory of Forensic Science, Ministry of Justice, Academy of Forensic Sciences, Shanghai, 200063, China.
Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China.
BMC Genomics. 2024 Sep 7;25(1):841. doi: 10.1186/s12864-024-10762-9.
In forensic genetics, utilizing massively parallel sequencing (MPS) to analyze short tandem repeats (STRs) has demonstrated several advantages compared to conventional capillary electrophoresis (CE). Due to the current technical limitations, although flanking region polymorphisms had been mentioned in several previous studies, most studies focused on the core repeat regions of STRs or the variations in the adjacent flanking regions. In this study, we developed an MPS system consisting of two sets of multiplex PCR systems to detect not only the STR core repeat regions but also to observe variants located at relatively distant positions in the flanking regions. The system contained 42 commonly used forensic STRs, including 21 autosomal STRs (A-STRs) and 21 Y-chromosomal STRs (Y-STRs), and a total of 350 male individuals from a Chinese Han population were genotyped. The length and sequence variants per locus were tallied and categorized based on length (length-based, LB), sequence without flanking region (core repeat regions sequence-based, RSB), and sequence with flanking region (core repeat and flanking regions sequence-based, FSB), respectively. Allele frequencies, Y-haplotype frequencies, and forensic parameters were calculated based on LB, RSB, and FSB, respectively, to evaluate the improvement in discrimination power, heterozygosity, and effectiveness of forensic systems. The results suggested the sequence variations have more influence on A-STRs and could improve the identification ability of MPS-STR genotyping. Concordance between MPS and CE methods was confirmed by using commercial CE-based STR kits. The impact of flanking region variations on STR genotype analysis and potential factors contributing to discordances were discussed. A total of 58 variations in the flanking regions (53 SNPs/SNVs and 5 InDels) were observed and most variations (48/58) were distributed in A-STRs. In summary, this study delved deeper into the genetic information of forensic commonly used STR and advanced the application of massively parallel sequencing in forensic genetics.
在法医遗传学中，与传统的毛细管电泳（CE）相比，利用大规模平行测序（MPS）分析短串联重复序列（STR）具有多项优势。由于当前的技术限制，尽管在之前的几项研究中已经提到侧翼区多态性，但大多数研究都集中在 STR 的核心重复区或相邻侧翼区的变异上。在这项研究中，我们开发了一种由两套多重 PCR 系统组成的 MPS 系统，不仅可以检测 STR 核心重复区，还可以观察侧翼区相对较远位置的变异。该系统包含 42 个常用的法医 STR，包括 21 个常染色体 STR（A-STRs）和 21 个 Y 染色体 STR（Y-STRs），并对来自中国汉族人群的 350 名男性个体进行了基因分型。根据长度（基于长度，LB）、无侧翼区的序列（核心重复区序列，RSB）和带侧翼区的序列（核心重复区和侧翼区序列，FSB）分别对每个基因座的长度和序列变异进行计数和分类。基于 LB、RSB 和 FSB 分别计算等位基因频率、Y 单倍型频率和法医参数，以评估鉴别能力、杂合度和法医系统的有效性的提高。结果表明，序列变异对 A-STRs 的影响更大，并能提高 MPS-STR 基因分型的识别能力。通过使用商业 CE 基于 STR 试剂盒，确认了 MPS 和 CE 方法之间的一致性。讨论了侧翼区变异对 STR 基因型分析的影响以及导致不一致的潜在因素。共观察到侧翼区 58 个变异（53 个 SNP/SNV 和 5 个插入缺失），其中大多数变异（48/58）分布在 A-STRs 中。总之，本研究深入探讨了法医常用 STR 的遗传信息，并推进了大规模平行测序在法医遗传学中的应用。
