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An investigation of downstream processing methods for challenging skeletal samples 具有挑战性的骨骼样品的下游处理方法的调查。
IF 3.2 2区 医学 Q2 GENETICS & HEREDITY Pub Date : 2024-12-14 DOI: 10.1016/j.fsigen.2024.103209
Jennifer L. Snedeker , Michelle A. Peck , David A. Russell , Amy S. Holmes , Christina M. Neal , Carmen R. Reedy , Sheree R. Hughes , Rachel M. Houston
While skeletal remains are known for their resilience and often serve as the final source of information for unidentified human remains (UHRs), the traditional downstream processing of these samples is challenging due to their low template nature, DNA degradation, and the presence of PCR inhibitors, typically resulting in limited probative information. To address this issue, advanced genotyping methods can be explored to retrieve additional genetic information from these challenging samples to maximize investigative leads. Therefore, this study investigated the effectiveness of three advanced genotyping methods and assessed their suitability with compromised skeletal samples: 1) targeted next generation sequencing (NGS) of both STRs and SNPs using the ForenSeq® DNA Signature Prep chemistry, 2) targeted NGS of SNPs using the ForenSeq® Kintelligence kit, and 3) SNP genotyping using a microarray via the Infinium Global Screening Array. The genotype recovery and added investigative leads were compared across all methods. All three approaches demonstrated success with the challenging skeletal samples used in this study. Specifically, the ForenSeq® DNA Signature Prep chemistry outperformed traditional STR typing by improving the recovery of CODIS core loci. Additionally, the ForenSeq® Kintelligence kit and Infinium Global Screening Array provided eligible results for forensic investigative genetic genealogy (FIGG) searching. Based on these successes, we have developed a proposed workflow for downstream processing of challenging skeletal samples. Following the guidelines of the US Department of Justice, the recovery of the CODIS core loci should be attempted through traditional CE-based methods or a NDIS-approved NGS chemistry, such as ForenSeq® DNA Signature Prep. Alternatively, a mitochondrial DNA profile may be uploaded to CODIS for comparisons in UHR cases. However, if no probative information is developed from the forensic profile uploaded to CODIS, then FIGG methods can be implemented using the Infinium Global Screening Array for high-quality skeletal samples (DNA concentrations ≥ 0.5 ng/µL) or the ForenSeq® Kintelligence chemistry for low-template skeletal remains (DNA concentration ≤ 0.5 ng/µL). These findings provide valuable insight into the suitability and efficacy of advanced genotyping methods, offering promising opportunities for enhancing the investigation of cases involving UHRs.
虽然骨骼遗骸以其弹性而闻名,并且通常作为身份不明的人类遗骸(uhr)的最终信息来源,但由于其低模板性质,DNA降解和PCR抑制剂的存在,这些样本的传统下游处理具有挑战性,通常导致有限的证明信息。为了解决这个问题,可以探索先进的基因分型方法,从这些具有挑战性的样本中检索额外的遗传信息,以最大限度地提高调查线索。因此,本研究研究了三种先进的基因分型方法的有效性,并评估了它们对骨骼样本的适用性:1)使用ForenSeq®DNA Signature Prep化学对STRs和SNP进行靶向下一代测序(NGS), 2)使用ForenSeq®Kintelligence试剂盒对SNP进行靶向NGS,以及3)使用Infinium Global Screening Array使用微阵列进行SNP基因分型。对所有方法的基因型恢复和增加的调查线索进行比较。所有三种方法都证明了在本研究中使用的具有挑战性的骨骼样本的成功。具体来说,ForenSeq®DNA Signature Prep化学通过提高CODIS核心位点的恢复,优于传统的STR分型。此外,ForenSeq®Kintelligence试剂盒和Infinium Global Screening Array为法医调查遗传谱系(FIGG)搜索提供了合格的结果。基于这些成功,我们已经开发了一个具有挑战性的骨骼样本下游处理的工作流程。根据美国司法部的指导方针,CODIS核心基因座的恢复应该通过传统的基于ce的方法或ndis批准的NGS化学方法(如ForenSeq®DNA Signature Prep)进行。或者,可以将线粒体DNA图谱上传到CODIS进行UHR病例的比较。但是,如果没有从上传到CODIS的法医档案中开发出证据信息,则可以使用Infinium Global Screening Array对高质量骨骼样本(DNA浓度≥0.5 ng/µL)或ForenSeq®Kintelligence化学对低模板骨骼遗骸(DNA浓度≤0.5 ng/µL)实施FIGG方法。这些发现对先进基因分型方法的适用性和有效性提供了有价值的见解,为加强涉及uhr病例的调查提供了有希望的机会。
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引用次数: 0
Development and validation of a multiplex panel with 232 microhaplotypes and software for forensic kinship analysis 开发和验证包含 232 个微单倍型的多重面板和用于法医亲属关系分析的软件。
IF 3.2 2区 医学 Q2 GENETICS & HEREDITY Pub Date : 2024-12-13 DOI: 10.1016/j.fsigen.2024.103212
Shengjie Gao , Qiujuan Wang , Yunlu Gao , Xiaoxiao Feng , Kunjie Pang , Haicheng Li , Feixue Zheng , Jingwen Lu , Bowen Li , Jia Liu , Mingxia Yang , Kefeng Li , Halmurat Ismayiljan , Huanming Yang , Jiangwei Yan , Xiaosen Guo , Ye Yin
In this study, we developed and validated a novel microhaplotype (MH) panel, the FGID Microhaplotype Kit, which contains 232 loci and was specifically designed for forensic kinship analysis. The performance of the panel was evaluated through rigorous testing that included sensitivity, species specificity, inhibitor resistance, uniformity, stability, accuracy and mixture deconvolution. The results showed that the kit is capable of reliably detecting all loci with minimal DNA input. It showed high species specificity for 12 non-human DNA samples and resistance to common inhibitors. In addition, forensic statistical analysis revealed a combined discriminatory power (cDP) of 1-1.68e-223 and superior combined exclusion power for duo and trio cases compared to standard STR panels. The panel was also tested for kinship analyzes with simulated and real pedigree samples and showed significantly higher likelihood ratios (LR) for detecting relationships between parents and offspring, full siblings, half siblings and first cousins, especially for more distant kinship types where conventional STR panels have difficulties. Using the FGID kinship software with the MH panel significantly improved the accuracy of kinship analysis, allowing even closely related individuals to be effectively discriminated while reducing the number of false negatives. In addition, principal component analysis (PCA) showed that the panel can distinguish the major world populations and East Asian subpopulations. Taken together, these results suggest that the FGID Microhaplotype Kit and associated software provide an efficient and accurate solution for forensic kinship analysis that offers better discriminatory power and reliability than traditional STR-based methods.
在这项研究中,我们开发并验证了一种新的微单倍型(MH)面板,FGID微单倍型试剂盒,包含232个位点,专门用于法医亲属分析。该面板的性能通过严格的测试进行评估,包括灵敏度、物种特异性、抑制剂抗性、均匀性、稳定性、准确性和混合物反褶积。结果表明,该试剂盒能够以最小的DNA输入量可靠地检测所有基因座。对12种非人类DNA样品具有较高的物种特异性,对常见抑制剂具有耐药性。此外,法医统计分析显示,与标准STR面板相比,二人组和三人组的联合歧视力(cDP)为1-1.68e-223,联合排除力更强。该小组还对模拟和真实谱系样本进行了亲属关系分析测试,结果显示,在检测父母与子女、全兄弟姐妹、半兄弟姐妹和表亲之间的关系方面,可能性比(LR)显著提高,尤其是在传统STR小组难以发现的更遥远的亲属类型方面。将FGID亲属关系软件与MH面板结合使用,显著提高了亲属关系分析的准确性,即使是关系密切的个体也能得到有效的区分,同时减少了假阴性的数量。主成分分析(PCA)表明,该面板能够区分世界主要种群和东亚亚种群。综上所述,这些结果表明FGID Microhaplotype Kit和相关软件为法医亲属分析提供了一种高效、准确的解决方案,比传统的基于str的方法具有更好的鉴别能力和可靠性。
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引用次数: 0
Characterizing stutter in single cells and the impact on multi-cell analysis 单细胞口吃的特征及其对多细胞分析的影响。
IF 3.2 2区 医学 Q2 GENETICS & HEREDITY Pub Date : 2024-12-13 DOI: 10.1016/j.fsigen.2024.103211
Amber C.W. Vandepoele, Natalie Novotna, Dan Myers, Michael A. Marciano
Short tandem repeat analysis is a robust and reliable DNA analysis technique that aids in source identification of a biological sample. However, the interpretation, particularly when DNA mixtures are present at low levels, can be complicated by the presence of PCR artifacts most commonly referred to as stutter. The presence of stutter products can increase the difficulty of interpretation in DNA mixtures as well as low-level DNA samples down to a single cell. Stutter product formation is stochastic in nature and although methods exist that can estimate the magnitude of stutter product formation, it still is not well understood. With the increased sensitivity of forensic DNA analyses, it has become possible to obtain interpretable DNA profiles from as low as 6.6 pg of DNA, or a single human diploid cell. However, this presents an interpretational challenge because the stutter in these low-level DNA samples might stray from the expected patterns observed in high-level DNA samples. Therefore, this project focuses on characterizing stutter in single cell samples to help generate a deeper understanding of stutter and provide a guide for detecting and evaluating stutter in low-level samples. Stutter analysis was performed using data generated from 180 single cells isolated with the DEPArrayTM NxT, amplified using the PowerPlex Fusion 6 C amplification kit at 29 or 30 cycles. Stutter was successfully characterized in single cells and stutter percentages were highly elevated compared to high-level samples where the variance increased as the number of cells being analyzed decreased leading to potential high stutter at low DNA levels. Using empirical and simulated (resampled) data, this study also reinforces historically relevant patterns in stutter product formation and demonstrates the relative differences in stutter in n-1, n-2 and n + 1 stutter product formation in simple, complex and compound repeats.
短串联重复序列分析是一种可靠的DNA分析技术,有助于生物样品的来源鉴定。然而,解释,特别是当DNA混合物存在于低水平时,可能会由于PCR伪影的存在而变得复杂,最常见的是被称为口吃。在DNA混合物以及低水平DNA样本中,口吃产物的存在会增加解释的难度,直至单个细胞。口吃产物的形成在本质上是随机的,虽然有方法可以估计口吃产物形成的大小,但它仍然没有得到很好的理解。随着法医DNA分析灵敏度的提高,从低至6.6 pg的DNA或单个人类二倍体细胞中获得可解释的DNA图谱已经成为可能。然而,这提出了一个解释上的挑战,因为这些低水平DNA样本中的口吃可能偏离在高水平DNA样本中观察到的预期模式。因此,本项目将重点研究单细胞样本中的口吃特征,以加深对口吃的认识,并为低水平样本中的口吃检测和评估提供指导。使用DEPArrayTM NxT分离的180个单细胞产生的数据进行口吃分析,使用PowerPlex Fusion 6 C扩增试剂盒在29或30个周期进行扩增。与高水平样本相比,在高水平样本中,随着分析细胞数量的减少,差异会增加,从而导致在低DNA水平下潜在的高口吃。利用经验和模拟(重采样)数据,本研究还强化了口吃产物形成的历史相关模式,并证明了简单、复杂和复合重复中n-1、n-2和n + 1口吃产物形成的相对差异。
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引用次数: 0
Searching national DNA databases with complex DNA profiles: An empirical study using probabilistic genotyping 利用复杂的 DNA 图谱搜索国家 DNA 数据库:使用概率基因分型的实证研究。
IF 3.2 2区 医学 Q2 GENETICS & HEREDITY Pub Date : 2024-12-10 DOI: 10.1016/j.fsigen.2024.103208
Séverine Nozownik , Tacha Hicks , Patrick Basset , Vincent Castella
In most National DNA databases (NDNADB), only single source DNA profiles, and sometimes two-person DNA mixtures, can be searched provided a minimum number of loci (or alleles) is available. DNA profiles that do not meet these criteria (about 14 % of the traces analyzed in Western Switzerland) can be compared locally with candidates upon request from police services, used for one-off search, or remain unused. With the advent of probabilistic genotyping (PG), such complex DNA profiles can be compared to those stored in NDNADB based on likelihood ratios (LRs). In this pilot study, traces of known contributors and casework DNA profiles were used to evaluate the performance of the DBLR™ “Search database” tool in conjunction with the Swiss NDNADB. First, 40 DNA mixtures (2–5 contributors) from 15 volunteers were prepared in the wet laboratory. They were deconvoluted with STRmix™ and compared to a database containing the DNA profiles of these 15 volunteers, along with 174,493 person DNA profiles from the Swiss NDNADB (ground-truth experiments). Using LR thresholds of 103 and 106, sensitivity and specificity were respectively 90.0 %/57.1 % and 99.9 %/100.0 %. For the lower LR threshold, this resulted in 52 adventitious associations out of more than 24 million pairwise comparisons. Second, 160 DNA mixture profiles from casework (2–4 contributors) that had previously been locally compared were searched with DBLR™ using the same conditions as for phase 1. With the 103 LR threshold, 380 associations were retrieved: 194 of these corresponded to expected associations, as they were previously made through the local comparisons with known persons, and 186 were new. With the 106 LR threshold, 199 associations were recovered of which 180 were expected and 19 new. This demonstrates that even with complex DNA profiles (up to 4 contributors) all expected associations were retrieved with a limited number of candidates per trace. Database searches of complex DNA mixtures allow for the generation of leads early in an investigation for DNA profiles that might otherwise remain underutilized. Next steps for the possible integration of DBLR™ or similar software within an operational context will require discussions on legal, financial, and technical aspects among stakeholders.
在大多数国家 DNA 数据库(NDNADB)中,只有单个来源的 DNA 图谱,有时是两人的 DNA 混合物,才可以进行搜索,条件是必须有最低数量的位点(或等位基因)。不符合这些标准的DNA图谱(在瑞士西部分析的痕迹中约占14%)可根据警方要求在当地与候选图谱进行比较,或用于一次性搜索,或保持闲置。随着概率基因分型技术(PG)的出现,这种复杂的 DNA 图谱可以根据似然比(LR)与 NDNADB 中存储的 DNA 图谱进行比较。在这项试验性研究中,使用了已知贡献者的痕迹和个案DNA图谱来评估DBLR™"搜索数据库 "工具与瑞士NDNADB的结合性能。首先,在湿实验室中制备了来自 15 名志愿者的 40 份 DNA 混合物(2-5 个贡献者)。使用 STRmix™ 对这些混合物进行去卷积,并与包含这 15 名志愿者 DNA 图谱的数据库以及瑞士 NDNADB 中 174,493 人的 DNA 图谱(地面实况实验)进行比较。使用 103 和 106 的 LR 阈值,灵敏度和特异性分别为 90.0 %/57.1 % 和 99.9 %/100.0%。对于较低的 LR 阈值,在 2,400 多万次配对比较中发现了 52 个偶然关联。其次,在与第一阶段相同的条件下,使用 DBLR™ 对以前进行过局部比对的 160 份来自个案工作(2-4 个贡献者)的 DNA 混合图谱进行了搜索。在 103 LR 阈值下,共检索到 380 条关联:其中 194 条符合预期关联,因为这些关联是之前通过与已知人员进行局部比对得出的,186 条是新关联。在 106 LR 临界值下,检索到 199 个关联,其中 180 个是预期关联,19 个是新关联。这表明,即使是复杂的 DNA 图谱(多达 4 个贡献者),在每个痕量的候选者数量有限的情况下,也能检索到所有预期关联。对复杂的 DNA 混合物进行数据库搜索,可在调查初期为 DNA 图谱提供线索,否则这些线索可能仍未得到充分利用。要将 DBLR™ 或类似软件整合到业务中,还需要利益相关者就法律、财务和技术方面的问题进行讨论。
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引用次数: 0
Uncovering genetic signatures of the Walser migration in the Alps: Patterns of diversity and differentiation 揭示阿尔卑斯山瓦尔泽迁徙的遗传特征:多样性和分化模式。
IF 3.2 2区 医学 Q2 GENETICS & HEREDITY Pub Date : 2024-12-09 DOI: 10.1016/j.fsigen.2024.103206
Peter Resutik , Joëlle Schneider , Simon Aeschbacher , Magnus Dehli Vigeland , Mario Gysi , Corinne Moser , Chiara Barbieri , Paul Widmer , Mathias Currat , Adelgunde Kratzer , Michael Krützen , Cordula Haas , Natasha Arora
Since leaving Africa, human populations have gone through a series of range expansions. While the genomic signatures of these expansions are well detectable on a continental scale, the genomic consequences of small-scale expansions over shorter time spans are more challenging to disentangle. The medieval migration of the Walser people from their homeland in ssouthern Switzerland (Upper Valais) into other regions of the Alps is a good example of such a comparatively recent geographic and demographic expansion in humans. While several studies from the 1980s, based on allozyme markers, assessed levels of isolation and inbreeding in individual Walser communities, they mostly did so by focusing on a single community at a time. Here, we provide a comprehensive overview of genetic diversity and differentiation based on samples from multiple Walser, Walser-homeland, and non-Walser Alpine communities, along with an idealized (simulated) Swiss reference population (Ref-Pop). To explore genetic signals of the Walser migration in the genomes of their descendants, we use a set of forensic autosomal STRs as well as uniparental markers. Estimates of pairwise FST based on autosomal STRs reveal that the Walser-homeland and Walser communities show low to moderate genetic differentiation from the non-Walser Alpine communities and the idealized Ref-Pop. The geographically more remote and likely more isolated Walser-homeland community of Lötschental and the Walser communities of Vals and Gressoney appear genetically more strongly differentiated than other communities. Analyses of mitochondrial DNA revealed the presence of haplogroup W6 among the Walser communities, a haplogroup that is otherwise rare in central Europe. Our study contributes to the understanding of genetic diversity in the Walser-homeland and Walser people, but also highlights the need for a more comprehensive study of the population genetic structure and evolutionary history of European Alpine populations using genome-wide data.
自从离开非洲以来,人类经历了一系列的范围扩张。虽然这些扩张的基因组特征在大陆范围内可以很好地检测到,但在较短时间跨度内小规模扩张的基因组后果更难以解开。中世纪瓦尔泽人从瑞士南部(上瓦莱州)的家乡迁移到阿尔卑斯山脉的其他地区,这是人类相对较近的地理和人口扩张的一个很好的例子。虽然从20世纪80年代开始的几项研究,基于同工酶标记,评估了个体瓦尔瑟群落的隔离和近交水平,但它们大多是一次只关注一个群落。在这里,我们提供了遗传多样性和分化的综合概述,基于多个沃尔瑟人,沃尔瑟人家园,和非沃尔瑟高山群落的样本,以及一个理想的(模拟的)瑞士参考群体(Ref-Pop)。为了探索Walser迁徙在其后代基因组中的遗传信号,我们使用了一组法医常染色体str以及单亲标记。基于常染色体str的成对FST估计显示,与非Walser高山群落和理想的Ref-Pop相比,Walser-homeland和Walser群落表现出低至中等的遗传分化。地理上更偏远、可能更孤立的Lötschental Walser-homeland群落和Vals和Gressoney的Walser群落在遗传上比其他群落表现出更强的分化。对线粒体DNA的分析显示,在瓦尔泽人群落中存在W6单倍群,这是中欧罕见的单倍群。我们的研究有助于了解瓦尔瑟人故土和瓦尔瑟人的遗传多样性,但也强调了利用全基因组数据对欧洲阿尔卑斯人群遗传结构和进化史进行更全面研究的必要性。
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引用次数: 0
STRAF 2: New features and improvements of the STR population data analysis software straf2: STR人口数据分析软件的新功能和改进。
IF 3.2 2区 医学 Q2 GENETICS & HEREDITY Pub Date : 2024-12-07 DOI: 10.1016/j.fsigen.2024.103207
Alexandre Gouy , Martin Zieger
Population data in forensic genetics must be checked for a variety of statistical parameters before it can be employed for casework. Several tools exist to perform such tasks; however, it can become challenging to obtain the right results due to the number of software to use and the broad range of input formats. Furthermore, a substantial amount of experience is required to use some of these programs. To overcome these difficulties, we have developed STRAF (STR Analysis for Forensics), a convenient online tool to analyse STR data in forensic genetics. Since its first release in 2017, it has been used in many studies to report allele frequencies, forensic and population genetics parameters, and to explore genetic datasets interactively through a user-friendly interface. Herewith, we introduce the latest version of the STRAF software and the improvements we have implemented over the last years. STRAF 2 includes several new features, such as new statistical methods (multidimensional scaling, comparison to a reference population, haplotype diversities and frequencies) and file conversion utilities. Performance and user experience have also been improved and documentation has been extended. This new version is freely available as an R package (https://github.com/agouy/straf) and a web application (https://straf.fr).
法医遗传学中的人口数据必须经过各种统计参数的检查,才能用于案件工作。有几种工具可用于执行此类任务;然而,由于要使用的软件数量众多,输入格式范围广泛,要获得正确的结果可能具有挑战性。此外,使用其中一些程序还需要大量的经验。为了克服这些困难,我们开发了 STRAF(法医用 STR 分析),这是一款方便的在线工具,用于分析法医遗传学中的 STR 数据。自2017年首次发布以来,它已被许多研究用于报告等位基因频率、法医和群体遗传学参数,并通过友好的用户界面交互式地探索遗传数据集。在此,我们将介绍 STRAF 软件的最新版本以及我们在过去几年中实施的改进。STRAF 2 包含多项新功能,如新的统计方法(多维缩放、与参照群体比较、单体型多样性和频率)和文件转换工具。此外,还改进了性能和用户体验,并扩展了文档。新版本作为 R 软件包(https://github.com/agouy/straf)和网络应用程序(https://straf.fr)免费提供。
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引用次数: 0
Using an interaction timeline to investigate factors related to shedder status 使用交互时间轴调查与脱壳状态相关的因素。
IF 3.2 2区 医学 Q2 GENETICS & HEREDITY Pub Date : 2024-12-02 DOI: 10.1016/j.fsigen.2024.103205
Duncan Taylor , Amy Cahill , Roland A.H. van Oorschot , Luke Volgin , Mariya Goray
A major factor that influences DNA transfer is the propensity of individuals to ‘shed’ DNA, commonly referred to as their ‘shedder status’. In this work we provide a novel method to analyse and interrogate DNA transfer data from a largely uncontrolled study that tracks the movements and actions of a group of individuals over the course of an hour. By setting up a model that provides a simplistic description of the world, parameters within the model that represent properties of interest can be iteratively refined until the model can sufficiently describe a set of final DNA observations. Because the model describing reality can be constructed and parametrised in any desired configuration, aspects that may be difficult to traditionally test together can be investigated. To that end, we use a 60-min timeline of activity between four individuals and use DNA profiling results from objects taken at the conclusion of the hour to investigate factors that may affect shedder status. We simultaneously consider factors of: the amount of DNA transferred per contact, the rate of self-DNA regeneration, the capacity of hands to hold DNA, and the rate of non-self-DNA removal, all of which may ultimately contribute to someone’s shedder status.
影响DNA转移的一个主要因素是个体“脱落”DNA的倾向,通常被称为他们的“脱落状态”。在这项工作中,我们提供了一种新的方法来分析和询问DNA转移数据,这些数据来自一项很大程度上不受控制的研究,该研究跟踪了一组个体在一小时内的运动和行为。通过建立一个提供对世界的简单描述的模型,模型中表示感兴趣的属性的参数可以迭代地改进,直到模型能够充分描述一组最终的DNA观察结果。由于描述现实的模型可以在任何期望的配置中构造和参数化,因此可以对传统上难以一起测试的方面进行调查。为此,我们使用四个人之间的活动60分钟的时间线,并使用DNA分析结果,在一个小时的结论采取的对象,以调查可能影响脱落状态的因素。我们同时考虑了以下因素:每次接触转移的DNA量,自我DNA再生的速度,手持有DNA的能力,以及非自我DNA去除的速度,所有这些都可能最终导致某人的脱毛状态。
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引用次数: 0
XGBoost as a reliable machine learning tool for predicting ancestry using autosomal STR profiles - Proof of method XGBoost是一种可靠的机器学习工具,用于使用常染色体STR谱预测祖先-方法证明。
IF 3.2 2区 医学 Q2 GENETICS & HEREDITY Pub Date : 2024-11-29 DOI: 10.1016/j.fsigen.2024.103183
Dejan Šorgić , Aleksandra Stefanović , Dušan Keckarević , Mladen Popović
The aim of this study was to test the validity of a predictive model of ancestry affiliation based on Short Tandem Repeat (STR) profiles. Frequencies of 29 genetic markers from the Promega website for four distinct population groups (African Americans, Asians, Caucasians, Hispanic Americans) were used to generate 360,000 profiles (90000 profiles per group), which were later used to train and test a range of machine learning algorithms with the goal of establishing the most optimal model for accurate ancestry prediction. The chosen models (Decision Trees, Support Vector Machines, XGBoost, among others) were deployed in Python, and their performance was compared. The XGBoost model outperformed others, displaying significant predictive power with an accuracy rating of 94.24 % for all four classes, and an accuracy rating of 99.06 % on a differentiation task involving Asian, African American, and Caucasian subsamples and an accuracy rating of 98.57 % when differentiating between the African-American, Asian, and the mixed group combining Caucasians and Hispanics. Evaluating the impact of training set size revealed that model accuracy peaked at 94 % with 90,000 profiles per category, but decreased to 83 % as the number of profiles per category was reduced to 500, particularly affecting precision when distinguishing between Caucasian and Hispanic subgroups. The study further investigated the impact of marker quantity on model accuracy, finding that the use of 21 markers, commonly available in commercial amplification kits, resulted in an accuracy of 96.3 % for African Americans, Asians, and Caucasians, and 88.28 % for all four groups combined. These findings underscore the potential of STR-based models in forensic analysis and hint at the broader applicability of machine learning in genetic ancestry determination, with implications for enhancing the precision and reliability of forensic investigations, particularly in heterogeneous environments where ancestral background can be a crucial piece of information.
本研究的目的是检验基于短串联重复序列(STR)谱的祖先隶属关系预测模型的有效性。来自Promega网站的29个遗传标记的频率用于四个不同的人群(非洲裔美国人、亚洲人、高加索人、西班牙裔美国人),生成了36万个档案(每个群体9万个档案),这些档案后来被用于训练和测试一系列机器学习算法,目的是建立最优的模型,以准确预测祖先。选择的模型(决策树,支持向量机,XGBoost等)在Python中部署,并比较它们的性能。XGBoost模型优于其他模型,在所有四个类别中显示出显著的预测能力,准确率为94.24 %,在涉及亚洲,非洲裔美国人和高加索人子样本的区分任务中准确率为99.06 %,在区分非裔美国人,亚洲人和高加索人和西班牙人的混合组时准确率为98.57 %。评估训练集大小的影响显示,当每个类别有90,000个配置文件时,模型准确率达到94 %的峰值,但当每个类别的配置文件数量减少到500个时,模型准确率下降到83 %,特别是在区分高加索人和西班牙裔亚组时影响精度。该研究进一步调查了标记物数量对模型准确性的影响,发现使用21种标记物(通常在商业扩增试剂盒中可用)对非洲裔美国人、亚洲人和高加索人的准确率为96.3% %,对所有四种人群的准确率为88.28 %。这些发现强调了基于str的模型在法医分析中的潜力,并暗示了机器学习在遗传祖先测定中的更广泛适用性,这对提高法医调查的准确性和可靠性具有重要意义,特别是在祖先背景可能是关键信息的异质环境中。
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引用次数: 0
Improved understanding of sequence polymorphisms at 42 Y chromosome short tandem repeats for the Chinese Han population 增进对中国汉族人口 42 个 Y 染色体短串联重复序列多态性的了解
IF 3.2 2区 医学 Q2 GENETICS & HEREDITY Pub Date : 2024-11-22 DOI: 10.1016/j.fsigen.2024.103181
Lei Miao , Shuang Liu , Kun-Peng Pan , Rui-Lian Jiao , Qian Zhang , Tao-Yong Xu , Shi-Yu Tong , Ke-Lai Kang , Jie Zhao , Chi Zhang , Kai-Di Wang , An-Quan Ji , Jian Wu , Le Wang
Y-chromosome short tandem repeat (Y-STR) is an important type of genetic markers in the human genome, widely used in molecular anthropology and forensic genetics. However, most Y-STR studies has been focused on the length-based variations resulting from differences in the number of repeat units. Less attention was paid to sequence-based Y-STR variations. Consequently, sequence-based variation characteristics of Y-STRs in Chinese populations remain insufficiently studied. In this study, targeted sequencing of 42 Y-STR loci was performed for 331 Chinese Han males (with an average sequencing depth of 612 ×), unveiling a total of 387 sequence allele types and their frequencies in the population. Repeat pattern variations were observed in seven loci containing multiple repeat units. Across all sequenced repeat and flanking regions, 46 single-nucleotide substitutions and insertion/deletion variations were identified, including 13 mutations not recorded in the dbSNP database. Twenty-seven previously unreported sequence-based alleles were identified. Additionally, differences in Y-STRs between the Chinese Han population and three American populations (African Americans, Caucasians, and Hispanics) were revealed from sequence-based data analysis. In summary, this study provides a detailed summary of the sequence features of 42 Y-STRs in the Chinese Han population, improving our understanding of Y-STRs and providing basic data of sequence variations for the application of Y-STRs.
Y 染色体短串联重复(Y-STR)是人类基因组中一类重要的遗传标记,广泛应用于分子人类学和法医遗传学。然而,大多数 Y-STR 研究都集中在因重复单位数量不同而产生的基于长度的变异上。对基于序列的 Y-STR 变异关注较少。因此,对中国人群中 Y-STR 基于序列的变异特征的研究仍然不足。本研究对 331 名中国汉族男性进行了 42 个 Y-STR 位点的定向测序(平均测序深度为 612 ×),共发现了 387 个等位基因序列类型及其在人群中的频率。在 7 个含有多个重复单元的位点上观察到了重复模式的变化。在所有测序的重复区和侧翼区,共发现了 46 个单核苷酸置换和插入/缺失变异,其中包括 13 个未在 dbSNP 数据库中记录的突变。还发现了 27 个以前未报道过的基于序列的等位基因。此外,通过基于序列的数据分析,还发现了中国汉族人群与三个美国人群(非裔美国人、白种人和西班牙裔美国人)在 Y-STRs 上的差异。总之,本研究详细总结了中国汉族人群中 42 个 Y-STR 的序列特征,增进了我们对 Y-STR 的了解,并为 Y-STR 的应用提供了序列变异的基础数据。
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引用次数: 0
Illicit drug distribution: Evaluation of DNA transfer between ziplock bags and capsules 非法药物分销:对密封袋和胶囊之间 DNA 转移的评估
IF 3.2 2区 医学 Q2 GENETICS & HEREDITY Pub Date : 2024-11-21 DOI: 10.1016/j.fsigen.2024.103182
Madison Nolan , Adrian Linacre
Powders containing illicit substances are frequently poured into capsules and then distributed in small bags to users, often via intermediaries. We report on the transfer of DNA between individuals involved in making, packing, and transporting capsules within ziplock bags (ZLB) via two pathways, each using 10 ZLBs. A two-person chain was created where participant A made and packed the capsules into ZLBs and participant C then carried the bags for four days. A three-person chain was devised where participant A made the capsules, participant B placed the capsules in bags, and participant C carried the bags. The ZLBs were sampled for DNA on the inside, the inner semi-protected portion of the opening, and the outside surface. The exterior of capsules were also sampled along with a storage container. DNA profiling using Verifiler™ Plus was performed with data deconvoluted by STRmix™. Informative DNA profiles were obtained from capsules despite evidence of DNA transfer from the capsules to both storage containers and the inside of the ZLB. The outside of ZLBs yielded complex mixtures, however, the inside of the bag and the exterior of capsules, which had greater protection, yielded profiles with predominately only one to two contributors. This highlights that the inside of the bags and exterior of capsules could be targeted to identify individuals involved in the early packaging stages of the illicit drug pathway while the outside provided more information on recent handling.
含有非法物质的粉末经常被倒入胶囊中,然后装入小袋分发给使用者,通常是通过中间商进行分销。我们报告了制作、包装和运输密封袋(ZLB)中胶囊的人员之间通过两种途径进行 DNA 转移的情况,每种途径使用 10 个密封袋。在两人链中,参与者 A 制作胶囊并将其装入 ZLB,参与者 C 将胶囊袋携带四天。设计了一个三人链,参与者 A 制作胶囊,参与者 B 将胶囊装入袋子,参与者 C 搬运袋子。对 ZLB 的内部、开口的半保护部分和外表面进行 DNA 采样。此外,还对胶囊外部和储存容器进行了取样。使用 Verifiler™ Plus 进行 DNA 图谱分析,并通过 STRmix™ 对数据进行解卷积。尽管有证据表明 DNA 从胶囊转移到了储存容器和 ZLB 内部,但还是从胶囊中获得了信息丰富的 DNA 图谱。ZLB 外部产生了复杂的混合物,而保护性更强的包装袋内部和胶囊外部则产生了主要只有一到两种成分的DNA图谱。这突出表明,可以针对包装袋内部和胶囊外部来识别参与非法药物途径早期包装阶段的个人,而外部则提供了更多关于近期处理情况的信息。
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引用次数: 0
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Forensic Science International-Genetics
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