Performance and characterization of 94 identity-informative SNPs in Northern Han Chinese using ForenSeq ™ DNA signature prep kit

IF 1.2 4区 医学 Q3 MEDICINE, LEGAL
Fei Guo , Ze Liu , Guannan Long , Biao Zhang , Dahua Liu , Shaobo Yu
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引用次数: 0

Abstract

Target and flanking region (FR) variation at 94 identity-informative SNPs (iSNPs) are investigated in 635 Northern Han Chinese using the ForenSeq DNA Signature Prep Kit on the MiSeq FGx Forensic Genomics System. The dataset presents the following performance characteristics (average values): ≥60% bases with a quality score of 20 or higher (%≥ Q20); >700 × of depth of coverage (DoC) from both Sample Details Reports and Flanking Region Reports; >80% of effective reads; ≥60% of allele coverage ratio (ACR); and ≥70% of inter-locus balance, while some stable low-performance characteristics are also observed: low DoC at rs1736442, rs1031825, rs7041158, rs338882, rs2920816, rs1493232, rs719366, and rs2342747; high noise at rs891700; and imbalanced ACR at rs6955448 and rs338882. The average amplicon length is 69 bp, suitable for detecting degraded samples. Bioinformatic concordance achieves 99.99% between the ForenSeq Universal Analysis Software (UAS) and the Integrative Genomic Viewer (IGV) inspection. Discordance results from flanking region deletions of rs10776839, rs8078417, rs2831700, and rs1454361. Due to FR variants within amplicons detected by massively parallel sequencing (MPS), the increases in the number of unique alleles, effective alleles (Ae), and observed heterozygosity (Hobs) are 46.81%, 4.51%, and 3.29%, respectively. Twelve FR variants are first reported to dbSNP, such as rs1252699848, rs1665500714, rs1771121532, rs2097285015, rs1851671415, rs2045669877, rs2046758811, rs2044248635, rs1251308240, rs1968822112, rs1981638299, and rs1341756746. All 94 iSNPs from target and amplicon data are in Hardy-Weinberg equilibrium (HWE) and independent within autosomes. As expected, forensic parameters from the amplicon data increase significantly on the combined power of discrimination (CPD = 1 – 3.9876 × 10−38) and the combined power of exclusion (CPE = 1 – 6.6690 × 10−8). Additionally, the power of the system effectiveness (CPD = 1 − 6.7054 × 10−72 and CPE = 1 − 4.4719 × 10−20) with sequence-based 27 autosomal STRs and 94 iSNP amplicons in combination is substantially improved compared to one type of marker alone. In conclusion, we have established a traditional length-based and current sequence-based reference database with 58 STRs and 94 iSNPs in the Northern Han Chinese population. We hope these data can serve as a solid reference and foundation for forensic practice.

Abstract Image

使用 ForenSeq ™ DNA 特征预处理试剂盒分析中国北方汉族 94 个身份信息 SNPs 的性能和特征
在 MiSeq FGx 法医基因组学系统上使用 ForenSeq DNA Signature Prep 套件对 635 名北方汉族人的 94 个身份信息 SNPs (iSNPs) 的目标和侧翼区 (FR) 变异进行了研究。该数据集具有以下性能特征(平均值):质量分数在 20 分以上的碱基≥60%(%≥ Q20);样本详情报告和侧翼区报告的覆盖深度(DoC)均为 700×;有效读数为 80%;等位基因覆盖率(ACR)≥60%;病灶间平衡率≥70%,同时也观察到一些稳定的低性能特征:rs1736442、rs1031825、rs7041158、rs338882、rs2920816、rs1493232、rs719366 和 rs2342747 的 DoC 较低;rs891700 的噪声较高;rs6955448 和 rs338882 的 ACR 不平衡。平均扩增子长度为 69 bp,适合检测降解样本。ForenSeq 通用分析软件(UAS)和整合基因组查看器(IGV)检测的生物信息学一致性达到 99.99%。rs10776839、rs8078417、rs2831700和rs1454361的侧翼区缺失导致了不一致。由于大规模平行测序(MPS)检测到扩增子中的 FR 变异,独特等位基因、有效等位基因(Ae)和观察到的杂合度(Hobs)分别增加了 46.81%、4.51% 和 3.29%。有 12 个 FR 变异首次被报告到 dbSNP,如 rs1252699848、rs1665500714、rs1771121532、rs2097285015、rs1851671415、rs2045669877、rs2046758811、rs2044248635、rs1251308240、rs1968822112、rs1981638299 和 rs1341756746。目标数据和扩增子数据中的所有 94 个 iSNPs 都处于哈代-温伯格平衡(HWE)状态,并且在常染色体内是独立的。正如预期的那样,来自扩增子数据的法证参数在综合辨别力(CPD = 1 - 3.9876 × 10-38)和综合排除力(CPE = 1 - 6.6690 × 10-8)方面显著增加。此外,基于序列的 27 个常染色体 STR 和 94 个 iSNP 扩增子组合的系统有效性(CPD = 1 - 6.7054 × 10-72 和 CPE = 1 - 4.4719 × 10-20)也比单独使用一种标记大大提高。总之,我们在中国北方汉族人群中建立了一个包含 58 个 STR 和 94 个 iSNP 的基于传统长度和当前序列的参考数据库。我们希望这些数据能为法医实践提供可靠的参考和依据。
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来源期刊
CiteScore
2.70
自引率
6.70%
发文量
106
审稿时长
57 days
期刊介绍: The Journal of Forensic and Legal Medicine publishes topical articles on aspects of forensic and legal medicine. Specifically the Journal supports research that explores the medical principles of care and forensic assessment of individuals, whether adult or child, in contact with the judicial system. It is a fully peer-review hybrid journal with a broad international perspective. The Journal accepts submissions of original research, review articles, and pertinent case studies, editorials, and commentaries in relevant areas of Forensic and Legal Medicine, Context of Practice, and Education and Training. The Journal adheres to strict publication ethical guidelines, and actively supports a culture of inclusive and representative publication.
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