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MixDeR: A SNP mixture deconvolution workflow for forensic genetic genealogy
IF 3.2 2区 医学 Q2 GENETICS & HEREDITY Pub Date : 2025-01-20 DOI: 10.1016/j.fsigen.2025.103224
Rebecca Mitchell , Michelle Peck , Erin Gorden , Rebecca Just
The generation of forensic DNA profiles consisting of single nucleotide polymorphisms (SNPs) is now being facilitated by wider adoption of next-generation sequencing (NGS) methods in casework laboratories. At the same time, and in part because of this advance, there is an intense focus on the generation of SNP profiles from evidentiary specimens for so-called forensic or investigative genetic genealogy (FGG or IGG) applications. However, FGG methods are constrained by the algorithms for genealogical database searches, which were designed for use with single-source profiles, and the fact that many forensic samples are mixtures. To enable the use of two-person mixtures for FGG, we developed a workflow, MixDeR, for the deconvolution of mixed SNP profiles. MixDeR, a flexible and easy to use R package and Shiny app, processes ForenSeq Kintelligence® (QIAGEN, Inc.) SNP genotyping results and directs deconvolution of the profiles in EuroForMix (EFM). MixDeR then filters the EFM outputs to produce inferred single-source genotypes in reports formatted for use with GEDmatch® PRO. An optional MixDeR output includes metrics that assist with testing and validation of the workflow. As the Shiny app provides a graphical user interface and the software is designed to be run offline, MixDeR should be suitable for use by any laboratory developing FGG capabilities, no matter their bioinformatic resources or expertise.
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引用次数: 0
Developmental validation of the IDseek® OmniSTR™ global autosomal STR profiling kit. IDseek®OmniSTR™全球常染色体STR分析试剂盒的发展验证
IF 3.2 2区 医学 Q2 GENETICS & HEREDITY Pub Date : 2025-01-16 DOI: 10.1016/j.fsigen.2025.103226
Erik A.C. de Jong , Melanie H.J. Arts , Kristiaan J. van der Gaag , Pieter A.M. van Oers , Joop P.G. Theelen
Forensic science takes advantage of population variability in autosomal Short Tandem Repeat (STR) lengths to establish human identification. The most common method for DNA profiling by STR is based on PCR, where the highly polymorphic STR regions are amplified and analysed using Capillary Electrophoresis (CE) or Massively Parallel Sequencing (MPS). MPS determines not only the repeat length, but also the repeat structure and variations in the flanking regions, making this method superior in discriminatory power compared to CE. Reverse Complement PCR (RC-PCR) is a novel, more sophisticated PCR based MPS library preparation method combining indexing and PCR amplification in a single closed-tube reaction. In this document we describe the complete developmental validation of the IDseek® OmniSTR™ kit, an RC-PCR based MPS library preparation kit. The developed IDseek® OmniSTR™ kit contains 28 autosomal STR targets, one Y-chromosomal STR and the Amelogenin gene covering all relevant STR core loci from the USA, EU, UK and Interpol.
法医科学利用常染色体短串联重复序列(STR)长度的人口变异性来建立人类鉴定。通过STR进行DNA分析的最常见方法是基于PCR,其中高度多态性的STR区域被扩增并使用毛细管电泳(CE)或大规模平行测序(MPS)进行分析。MPS不仅决定了重复序列的长度,而且还决定了重复序列的结构和侧翼区域的变化,使得该方法的鉴别能力优于CE。反向补体PCR (RC-PCR)是一种新颖的、更复杂的基于PCR的MPS文库制备方法,将标引和PCR扩增在单管封闭反应中结合起来。在本文中,我们描述了IDseek®OmniSTR™试剂盒的完整开发验证,这是一种基于RC-PCR的MPS文库制备试剂盒。开发的IDseek®OmniSTR™试剂盒包含28个常染色体STR靶点,1个y染色体STR和Amelogenin基因,涵盖来自美国,欧盟,英国和国际刑警组织的所有相关STR核心位点。
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引用次数: 0
The ReAct project: Analysis of data from 23 different laboratories to characterise DNA recovery given two sets of activity level propositions
IF 3.2 2区 医学 Q2 GENETICS & HEREDITY Pub Date : 2025-01-13 DOI: 10.1016/j.fsigen.2025.103222
Peter Gill , Ane Elida Fonneløp , Tacha Hicks , Stavroulla Xenophontos , Marios Cariolou , Roland van Oorschot , Iris Buckel , Viktorija Sukser , Sunčica Papić , Siniša Merkaš , Ana Kostic , Angela Marques Pereira , Christina Teutsch , Christina Forsberg , Cordula Haas , Elizabet Petkovski , Fabian Hass , Jan Masek , Jelena Stosic , Yong Sheng Lee , Ingo Bastisch
The ReAct (Recovery, Activity) project is an ENFSI (European Network of Forensic Science Institutes) supported initiative comprising a large consortium of laboratories. Here, the results from more than 23 laboratories are presented. The primary purpose was to design experiments simulating typical casework circumstances; collect data and to implement Bayesian networks to assess the value (i.e., likelihood ratio) of DNA results given activity level propositions. Two different experimental designs were used to simulate a robbery, where a screwdriver was used to force a door or window. Propositions and case information were chosen following laboratory feedback listing typical casework circumstances (included in the paper). In a direct transfer experiment, the defendant owned and used the screwdriver, but he did not force the door/window in question. An unknown person used the defendant’s stolen screwdriver. In an indirect transfer experiment, the defendant neither owned, saw, nor used the screwdriver, nor did they force the door or window. For the second experiment, given the defence view, the defendant never held the screwdriver. We envisaged the situation where an object manipulated by the defendant (or the defendant himself/herself) would be touched by the unknown offender who would then force the window. It was found for the direct transfer experiment that unless a single contributor profile aligning with the known person’s of interest profile was retrieved, the results did not allow to discriminate between propositions. On the other hand, for the indirect transfer experiment, both single and major contributor profiles that aligned with the person of interest (POI) supported the proposition that the person used the tool rather than an unknown person who had touched an object, when indeed the former was true. There was considerable variation in median recoveries of DNA between laboratories (between 200pg–5ng) for a given experiment if quantities are taken into account. These differences affect the likelihood ratios given activity level propositions. More than 2700 samples were analysed in the course of this study. Two different Bayesian Networks are made available via an open source application written in Shiny R: Shiny_React(). For comparison, all datasets were analysed using a qualitative method categorised into absent, single, major or other given contributors. The importance of standardising methods is emphasised, alongside the necessity of developing new approaches to assign the probability of laboratory-dependent DNA recovery. Freely accessible open databases play a crucial role in supporting these efforts.
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引用次数: 0
Evaluation of RMplex system for differentiating father–son pairs using Y-STRs in a Korean population 用y - str评价RMplex系统在韩国人群中区分父子对的作用。
IF 3.2 2区 医学 Q2 GENETICS & HEREDITY Pub Date : 2025-01-06 DOI: 10.1016/j.fsigen.2025.103221
Ju Yeon Jung , Eunhye Kim , Yeon Woo Song , Dong Gyu Lee , Myung Jin Park , Hwan Young Lee , Manfred Kayser , Arwin Ralf , Eungsoo Kim
Y-chromosomal short tandem repeats (Y-STRs) at rapidly mutating (RM) loci have been suggested as tools for differentiating paternally related males. RMplex is a recently developed system that incorporates 26 RM loci and four fast-mutating (FM) loci, targeting 44 male-specific loci. Here, we evaluated the RMplex by estimating Y-STR mutation rates and the overall differentiation rates for 542 Korean father–son pairs, as well as the genetic population values for 409 unrelated males. RMplex performed well, distinguishing 50.7 % of the father–son pairs by at least one mutation, a value 10 times higher than the previously reported differentiation rate achieved using the PowerPlex® Y23 System. Of the 369 mutations, 361 (97.8 %) were single-step mutations, with locus-specific mutation rates varying from 1.8 × 10−3 to 1.1 × 10−1 mutations per generation, and an average mutation rate of 2.3 × 10−2. Gene diversity values ranged from 0.5696 for DYS442 to 0.9970 for DYF1000, and the haplotype discrimination capacity of unrelated males was 100 %. Among the loci studied, DYS712 exhibited the highest mutation rate in this study of the Korean population. Similarly, the mutation rate of this locus is reported to be substantially higher for the Japanese and Chinese populations than for European populations. These findings suggest that DYS712 mutations are relatively frequent in East Asian populations. Although we did not detect significant relationships among the Y-chromosome single nucleotide polymorphism-based haplogroups, allele length was strongly correlated with the mutation rate at DYS712, which is consistent with previous studies. Although the incorporation of multi-copy loci into RMplex contributed significantly to the high mutation rates detected and to its discrimination capacity, this requires careful interpretation, owing to the potential for duplications. Nonetheless, these findings provide evidence regarding the suitability of the RMplex for distinguishing paternally related males in the Korean population.
快速突变(RM)位点上的y染色体短串联重复序列(Y-STRs)被认为是区分父系相关男性的工具。RMplex是最近开发的一种系统,包含26个RM位点和4个快速突变(FM)位点,靶向44个男性特异性位点。在这里,我们通过估算542对韩国父子对的Y-STR突变率和总体分化率,以及409对无亲缘关系男性的遗传群体值来评估RMplex。RMplex表现良好,通过至少一个突变区分50.7% %的父子对,比先前报道的使用PowerPlex®Y23系统实现的分化率高10倍。在369个突变中,361个(97.8 %)为单步突变,位点特异性突变率为每代1.8 × 10-3 ~ 1.1 × 10-1,平均突变率为2.3 × 10-2。DYS442的基因多样性值为0.5696 ~ 0.9970,无亲缘关系雄性的单倍型辨别能力为100 %。在研究的位点中,DYS712在韩国人群中表现出最高的突变率。同样,据报道,该位点的突变率在日本和中国人群中比在欧洲人群中高得多。这些发现表明DYS712突变在东亚人群中相对常见。虽然我们没有发现基于y染色体单核苷酸多态性的单倍群之间的显著关系,但等位基因长度与DYS712的突变率密切相关,这与以往的研究一致。尽管将多拷贝基因座整合到RMplex中显著提高了检测到的高突变率和其辨别能力,但由于可能存在重复,这需要仔细解释。尽管如此,这些发现为RMplex在韩国人群中区分父系相关男性的适用性提供了证据。
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引用次数: 0
The (in)dependence of single-cell data inferences on model constructs 单细胞数据推断对模型构造的依赖性。
IF 3.2 2区 医学 Q2 GENETICS & HEREDITY Pub Date : 2025-01-03 DOI: 10.1016/j.fsigen.2024.103220
Catherine M. Grgicak , Klaas Slooten , Robert G. Cowell , Qhawe Bhembe , Desmond S. Lun
<div><div>Recent developments in single-cell analysis have revolutionized basic research and have garnered the attention of the forensic domain. Though single-cell analysis is not new to forensics, the ways in which these data can be generated and interpreted are. Modern interpretation strategies report likelihood ratios that rely on a model of the world that is a simplification of it. It is, therefore, plausible that different reasonable models will assign noticeably different weights of evidence (WoEs) to some of these data, resulting in inconsistent reports and protracted reviews of that evidence, potentially across years. With one goal of research being to identify and understand sources of inconsistencies during early stages, we undertake a study that evaluates WoE at the limit of one single-cell electropherogram (scEPG) across three architecturally distinct probabilistic models. The three are named EESCIt (Evidentiary Evaluation of Single Cells), TD (Top-Down), and DCM (Discrete Cell Model). To do this, we performance test the three models on a set of 996 individual scEPGs and conduct one H<sub>1</sub>-true, i.e., true contributor, and 201 H<sub>2</sub>-true, i.e., false contributor, tests, per scEPG. With the 201,192 outcomes per model, we confirm that scEPGs well resolve the hypotheses, regardless of what model was applied. We also observe that WoEs increase, on average, by 1 for every 1000 RFU of total intensity added until a plateau near the logarithm of the inverse of the random match probability is reached at ca. 22,000 RFU. By querying WoE calibration for each model, we determine if the evidence is over- or under-stated for any one of them. We find that for WoE ≥ -1 hardly any calibration discrepancy is observed. There were rare instances, however, for which WoEs that were ≤ -1 too strongly pointed in the negative direction, though H<sub>1</sub> was true. This was the result of five scEPGs that not only exhibited extreme signal in stutter positions, but also carried little information in other loci. These findings show that all three models appropriately stated WoEs for scEPGs when reporting positive WoE, and the two continuous model’s WoE reasonably represented the findings when WoE < -1 for most loci. To further explore, we continued with paired analyses that evaluated the agreement in WoE, per scEPG, across models. Unlike unpaired analyses, this evaluation determines if well performing models return equivalent results for the same scEPG. The paired analysis was summarized by way of intraclass correlations, which were at least 0.99997. Further, we found that 762 of 996 WoEs were within a range of 3 orders of magnitude of each other, though many of these were associated with WoEs that were large, i.e., > 9, in the first instance. When we more closely focus on scEPGs giving ranges ≥ 3, but whose WoE ≤ 9 for at least one of the models, we find there are 21 of them. When we perform a locus-by-locus investigation of these 21 and o
单细胞分析的最新发展使基础研究发生了革命性的变化,并引起了法医领域的注意。虽然单细胞分析对法医学来说并不新鲜,但产生和解释这些数据的方式却是新鲜的。现代解释策略报告的可能性比依赖于一个简化的世界模型。因此,不同的合理模型可能会给其中一些数据分配明显不同的证据权重(哀伤),从而导致不一致的报告和对证据的长期审查,可能会持续数年。研究的一个目标是在早期阶段识别和理解不一致的来源,我们进行了一项研究,在三个结构不同的概率模型中,在一个单细胞电泳(scEPG)的极限下评估WoE。这三种方法分别是EESCIt(单细胞证据评估)、TD(自上而下)和DCM(离散细胞模型)。为此,我们在一组996个单独的scEPG上对这三个模型进行性能测试,并对每个scEPG进行一次H1-true(即真贡献者)和201次 H2-true(即假贡献者)测试。每个模型有201,192个结果,我们证实,无论应用哪种模型,scepg都能很好地解决假设。我们还观察到,平均而言,每增加1000 RFU的总强度,灾难就会增加1,直到在大约22,000 RFU时达到随机匹配概率逆的对数附近的平台。通过查询每个模型的WoE校准,我们确定其中任何一个模型的证据是否被夸大或低估。我们发现,对于WoE≥ -1,几乎没有观测到任何校准差异。然而,在极少数情况下,尽管H1是正确的,但≤ -1的哀伤过于强烈地指向负面方向。这是5个scepg的结果,它们不仅在口吃位置表现出极端的信号,而且在其他位点上携带的信息很少。这些发现表明,当报告积极的WoE时,所有三个模型都适当地为scepg陈述了WoE,并且两个连续模型的WoE在第一次实例中合理地代表了WoE 9时的发现。当我们更仔细地关注范围≥ 3,但至少有一个模型的WoE≤ 9的scepg时,我们发现有21个。当我们对这21个基因座和5个基因座进行逐一调查时,我们发现极端口吃通常是造成这些挑战的原因。为了改善预测罕见但有影响的事件的差异,我们提供了超越手动解决现象的解释性适应。随着在EESCIt, TD和DCM的相关区域内校准WoE,我们将每个分类为满足其预期WoE范围内单细胞数据的合法性支柱。
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引用次数: 0
Expression of Concern “Population data of 17 Y-STR loci in Nanyang Han population from Henan Province, Central China” [Forensic Sci. Int. Gene. 13 (2014) 145–146]
IF 3.2 2区 医学 Q2 GENETICS & HEREDITY Pub Date : 2025-01-01
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引用次数: 0
Expression of concern “Population genetics of 17 Y-STR loci in Xibe ethnic minority from Liaoning Province, Northeast China” [Forensic Sci. Int. Genet. 16 (2015) 86–87]
IF 3.2 2区 医学 Q2 GENETICS & HEREDITY Pub Date : 2025-01-01
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引用次数: 0
Expression of Concern: “Genetic profile of 17 Y chromosome STRs in the Guizhou Han population of southwestern China” [Forensic Sci. Int. Genet. 25 (2016) e6–e7]
IF 3.2 2区 医学 Q2 GENETICS & HEREDITY Pub Date : 2025-01-01
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引用次数: 0
Expression of concern: “Genetic polymorphisms of 17 Y chromosomal STRs in She and Manchu ethnic populations from China” [Forensic Sci. Int.: Genet. 22 (2016) e12–e14]
IF 3.2 2区 医学 Q2 GENETICS & HEREDITY Pub Date : 2025-01-01
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引用次数: 0
Expression of Concern: “Genetic population data of Yfiler Plus kit from 1434 unrelated Hans in Henan Province (Central China)” [Forensic Sci. Int. Genet. 22 (2016) e25–e27]
IF 3.2 2区 医学 Q2 GENETICS & HEREDITY Pub Date : 2025-01-01
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引用次数: 0
期刊
Forensic Science International-Genetics
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