Forensic Science International-Genetics最新文献_第5页

Massively parallel sequencing of 74 microhaplotypes for relationship testing in U.S. populations 74个微单倍型的大规模平行测序，用于美国人群的关系测试

IF 3.1 2区医学 Q2 GENETICS & HEREDITY

Forensic Science International-Genetics

Pub Date : 2025-11-06 DOI: 10.1016/j.fsigen.2025.103386

Fabio Oldoni , Chiara Della Rocca , Leena Yoon , Sathya Prakash Harihar , Aishwaryaa Subramanian , Daniele Podini

Microhaplotypes (MHs) are increasingly recognized as valuable forensic markers due to their low mutation rates, lack of stutter artifacts, and compatibility with massively parallel sequencing (MPS). These biomarkers have shown utility in human identification, mixture deconvolution, ancestry prediction and kinship testing. Although familial relationship testing has historically relied on fragment-sized analysis of STRs, it is now evolving with the advent of both MPS and MHs. While single nucleotide polymorphism (SNP) microarrays have also been used for kinship testing, they require high-quality and high-quantity DNA and are ineffective in the presence of mixtures—limitations that MHs can overcome due to their short amplicons and ability to deconvolute mixed DNA samples. This study specifically aimed to evaluate the performance of a previously designed 74-locus Ion AmpliSeq™ MH panel on the Ion GeneStudio S5 platform and compare it against a 29-fragment sized STR panel for kinship testing in four major U.S. populations. The 74plex MH panel was sequenced using a sample set of 372 family samples across African American, European American, Southwest Hispanic, and East Asian American population groups. Its performance was assessed on Familias software in differentiating between close and distant relatives, which included parent-child, full siblings, half-siblings, and cousins. For parent-child relationships, MHs and STRs showed clear separation, but MHs yielded consistently higher log₁₀LR values (>20) with tighter clustering, suggesting stronger discriminatory power than STRs. With full siblings, MHs consistently outperformed STRs, with their distributions showing higher log₁₀LRs. However, for half-siblings, both genetic markers struggled with significant overlap between related and unrelated pairs, though MHs showed higher log₁₀LR values than STRs. Neither 74 MHs nor 29 STRs were able to distinguish between cousins, exhibiting extensive overlap and log₁₀LRs near or below zero. In summary, the 74-locus Ion AmpliSeq™ MH panel offers enhanced discriminatory power for close kinship, particularly first-degree relationships. While MHs enhance second-degree resolution, the 74-MH struggles with more distant relationships like cousins. These findings underscore the need for larger MH panels (≥200 loci) to reliably resolve distant kinship, supporting their broader integration into forensic applications including kinship analysis, mixture deconvolution, and ancestry inference.

微单倍型（MHs）由于其低突变率、缺乏口吃产物以及与大规模平行测序（MPS）的兼容性，越来越被认为是有价值的法医标记。这些生物标志物在人类鉴定、混合反褶积、祖先预测和亲属关系检测中显示出效用。虽然家族关系测试历来依赖于str的片段大小分析，但随着MPS和mh的出现，它正在不断发展。虽然单核苷酸多态性（SNP）微阵列也被用于亲属关系检测，但它们需要高质量和高数量的DNA，并且在存在混合物的情况下无效——MHs可以克服这些限制，因为它们的扩增子短，并且能够反卷积混合DNA样本。本研究旨在评估先前在Ion GeneStudio S5平台上设计的74个位点Ion AmpliSeq™MH面板的性能，并将其与29个片段大小的STR面板进行比较，用于美国四个主要人群的亲属检测。74plex MH面板使用372个非裔美国人、欧洲美国人、西南西班牙人和东亚美国人群体的家庭样本进行测序。在Familias软件上对其性能进行了评估，以区分近亲和远亲，包括亲子，全兄弟姐妹，半兄弟姐妹和表兄弟姐妹。对于亲子关系，MHs和STRs表现出明显的分离，但MHs的log₁₀LR值始终较高（>20），聚类更紧密，表明区别力强于STRs。在全兄弟姐妹中，mh的表现始终优于str，其分布显示出更高的log₁₀lr。然而，对于同父异母的兄弟姐妹来说，两个遗传标记在相关和非相关对之间都存在显著的重叠，尽管MHs的log₁₀LR值高于STRs。74个mh和29个str都无法区分表兄弟，显示出广泛的重叠和log₁0 LRs接近或低于零。总之，74个位点的Ion AmpliSeq™MH面板为近亲，特别是一级亲属关系提供了增强的歧视性权力。虽然mh提高了二级分辨率，但74-MH却难以与表亲等更遥远的关系打交道。这些发现强调需要更大的MH面板（≥200个位点）来可靠地解决远亲关系，支持其更广泛地整合到法医应用中，包括亲属关系分析、混合反卷积和祖先推断。

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引用次数: 0

Development and validation of a 55-Plex X-STR NGS panel for forensic casework: Population genetics, mutation analysis, and kinship discrimination 55-Plex X-STR NGS法医案例面板的开发和验证：群体遗传学，突变分析和亲属歧视。

IF 3.1 2区医学 Q2 GENETICS & HEREDITY

Forensic Science International-Genetics

Pub Date : 2025-10-31 DOI: 10.1016/j.fsigen.2025.103385

Guanju Ma , Lihuan Zhu , Kailiang Liu , Chaolong Lu , Mengjie Zhang , Qian Wang , Guangping Fu , Junyan Wang , Bin Cong , Shujin Li , Lihong Fu

X-chromosome short tandem repeats (X-STRs) are valuable genetic markers in forensic genetics, particularly for complex kinship analysis and the analysis of male mixtures, due to their unique inheritance pattern. However, the application of X-STRs has been limited by the relatively small number of loci included in commonly used capillary electrophoresis (CE)-based assays, and the lack of sequence-level polymorphism information provided by CE. This study addresses these limitations by developing and validating a novel next-generation sequencing (NGS) panel comprising 55 X-STR markers. The panel was constructed using multiplexed PCR capture and sequenced on Illumina platforms. We performed comprehensive developmental validation studies according to the Scientific Working Group on DNA Analysis Methods (SWGDAM) guidelines, assessing repeatability, concordance, sensitivity, resistance to PCR inhibitors, performance with degraded DNA, analysis of DNA mixtures, and species specificity. The panel demonstrated excellent performance across all validation parameters. A minimum input of 0.5 ng of DNA is recommended for reliable genotyping. The system showed robust resistance to humic acid (up to 7 ng/μL) and hematin (up to 30 μM). Accurate genotyping was maintained even with degraded DNA samples. For DNA mixtures, the minor contributor alleles could be reliably detected up to a 1:19 ratio (male-male) and 1:9 (female-male). Furthermore, we conducted a population genetics survey of 268 individuals (154 females and 114 males) from the Han Chinese population in Hebei Province, including a subset of 128 unrelated individuals. A total of 648 alleles were identified across the 55 loci. No significant deviations from Hardy-Weinberg equilibrium (HWE) or linkage equilibrium (LE) were observed after Bonferroni correction, except for three LD pairs. Population genetic parameters, including power of discrimination (DP) and power of exclusion (PE), were calculated. Furthermore, paternal and maternal mutation rates were estimated based on 51 father-mother-children pedigrees including 102 offspring. Finally, we evaluated the panel^’s ability to distinguish second-degree kinship relationships using both real-world samples (67 pairs) and simulated data (44,000,000 pairs). The results demonstrated the panel^’s enhanced discriminatory power compared to existing X-STR systems, achieving overall accuracies of 80.47 % to 93.20 % in simulated second-degree kinship tests. This 55-plex X-STR NGS panel provides a powerful new tool for forensic casework, particularly for complex kinship analysis, and contributes valuable population data for the Han Chinese population. The study also highlights the importance of considering sequence variation in X-STR analysis and provides insights into X-STR mutation rates.

x染色体短串联重复序列（X-STRs）由于其独特的遗传模式，在法医遗传学，特别是复杂亲缘关系分析和雄性杂交分析中具有重要的应用价值。然而，由于常用的毛细管电泳（CE）检测方法中包含的基因座数量相对较少，并且缺乏毛细管电泳提供的序列水平多态性信息，X-STRs的应用受到限制。本研究通过开发和验证包含55个X-STR标记的新型下一代测序（NGS）面板来解决这些局限性。使用多重PCR捕获构建板，并在Illumina平台上测序。我们根据DNA分析方法科学工作组（SWGDAM）指南进行了全面的发育验证研究，评估了重复性、一致性、敏感性、对PCR抑制剂的抗性、降解DNA的性能、DNA混合物分析和物种特异性。该面板在所有验证参数中都表现出出色的性能。建议至少输入0.5 ng的DNA进行可靠的基因分型。该体系对腐植酸（高达7 ng/μL）和血素（高达30 μL）具有较强的抗性。即使DNA样本被降解，也能保持准确的基因分型。对于DNA混合物，次要贡献等位基因可以可靠地检测到高达1:19（男性-男性）和1:9（女性-男性）的比例。在此基础上，我们对河北省汉族人群中268个个体（雌性154个，雄性114个）进行了群体遗传学调查，其中包括128个无亲缘关系个体。55个位点共鉴定出648个等位基因。Bonferroni校正后，除三个LD对外，未观察到与Hardy-Weinberg平衡（HWE）或连锁平衡（LE）的显著偏差。计算群体遗传参数，包括辨别力（DP）和排除力（PE）。此外，根据包括102个后代在内的51个父系-母系-子女谱系，估计了父系和母系的突变率。最后，我们使用真实世界的样本（67对）和模拟数据（44,000,000对）来评估小组区分二级亲属关系的能力。结果表明，与现有的X-STR系统相比，该小组的歧视能力增强，在模拟二度亲属关系测试中，总体准确率为80.47 %至93.20 %。这个55层X-STR NGS面板为法医案件工作，特别是复杂的亲属关系分析提供了强大的新工具，并为汉族人口提供了宝贵的人口数据。该研究还强调了在X-STR分析中考虑序列变异的重要性，并提供了对X-STR突变率的见解。

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引用次数: 0

Preservation of proteomic and genomic genotypes in skeletal material from forensically treated cadavers 法医处理尸体骨骼材料中蛋白质组和基因组基因型的保存。

IF 3.1 2区医学 Q2 GENETICS & HEREDITY

Forensic Science International-Genetics

Pub Date : 2025-10-30 DOI: 10.1016/j.fsigen.2025.103384

Glendon Parker , Michelle Harrel , Jennifer Snedeker , Michelle Salemi , Trevor Borja , Rachel Houston

Skeletal material is often the only remaining evidence in missing persons cases, for mass burials, or disaster victim identification. Nuclear DNA can be highly degraded in these samples making it difficult to recover quality profiles for human identification or to deconvolute comingled remains. Proteins are chemically more stable than DNA and contain genetic information in the form of genetically variant peptides (GVPs) that can be used to infer non-synonymous SNP genotypes. To test chemical and genetic preservation of both biomolecular types, eight cadavers were examined using five treatments: embalming, burning, burial, and surface decomposition with and without subsequent formalin treatment (0–66 h in 36 % (w/v) formalin). Across the study DNA recoveries ranged from 210 ng to 0.08 ng in 50 mg of processed bone, a 2,600-fold range. Peptide recoveries, ranged from 22,000 ng to 5900 ng from the same amount of bone, a 3.7-fold range. At the information level the same peptide input (750 ng) could be obtained for all samples, and nucleotide level (0.8 ng) for most samples, although this consumed more sample than proteomic analysis. Of the 18 STR-profiles analyzed, 9 were CODIS-ineligible, yet all samples contained GVPs. This indicated that GVPs can be used to construct non-synonymous SNP genotypes in degraded bone samples that cannot provide usable STR-profiles. The relative quality of proteomic and genomic genetic data had a linear relationship (P < 0.0001) with a loss of 1 GVP for a 14 % loss of STR-alleles (97 % CI = 10–22 %), indicating that even correcting for chemical loss, information quality still decreased. SNaPshot™ genotyping of non-synonymous SNPs was less sensitive than GVP inference. Proteomic analysis of individual proteins in the sample indicated that collagen degradation was responsible for most protein loss, and chemical modifications were modest. Future studies are required to examine the stability of both DNA and protein in specific cadaver treatments, for further GVP discovery and validation, and optimization of proteomic sample processing. However, given the stability of GVP detection, even at this preliminary stage, protein-based genotyping is a valid option for extracting genetic information from samples with minimal or even no usable DNA detected. This is the first example of successful proteomic genotyping in forensically degraded bone and demonstrates that proteomic genotyping can be used for human identification and potential deconvolution of comingled remains.

在失踪人员案件中，骨骼材料往往是唯一剩下的证据，用于集体埋葬或灾难受害者的身份识别。核DNA在这些样品中可能被高度降解，这使得很难恢复用于人类鉴定的质量剖面或对混合遗骸进行反卷积。蛋白质在化学上比DNA更稳定，并以遗传变异肽（GVPs）的形式包含遗传信息，可用于推断非同义SNP基因型。为了测试这两种生物分子类型的化学和遗传保存，对8具尸体进行了五种处理：防腐、焚烧、埋葬和表面分解，随后进行了福尔马林处理（0-66 h，含36 % （w/v）福尔马林）。在整个研究中，在50 毫克加工过的骨头中，DNA回收率从210 ng到0.08 ng不等，范围是原来的2600倍。从相同数量的骨头中，肽回收率从22,000 ng到5900 ng不等，范围为3.7倍。在信息水平上，所有样品都可以获得相同的肽输入（750 ng），大多数样品的核苷酸水平（0.8 ng），尽管这比蛋白质组学分析消耗更多的样品。在分析的18个str谱中，9个不符合codis，但所有样本都含有GVPs。这表明GVPs可用于在无法提供可用str谱的降解骨样品中构建非同义SNP基因型。蛋白质组学和基因组遗传数据的相对质量呈线性关系(P

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引用次数: 0

The first population scale compendium of complete mitochondrial genomes from Flanders, Belgium 首个来自比利时佛兰德斯的全线粒体基因组种群规模纲要。

IF 3.1 2区医学 Q2 GENETICS & HEREDITY

Forensic Science International-Genetics

Pub Date : 2025-10-28 DOI: 10.1016/j.fsigen.2025.103382

Noah Gaens , Erika Souche , Toomas Kivisild , Jan Geypen , Sara Seneca , Francesc Calafell , Maarten H.D. Larmuseau

Mitochondrial DNA (mtDNA) plays a crucial role in forensics and population genetics, especially for analysing highly degraded samples. Yet, most mitogenomic reference datasets are still limited to control region (CR) sequences, that have limited discriminatory power. This is particularly true for Belgium, where despite the introduction of new legislation in 2024 to increase the use of mitochondrial DNA in familial searching, comprehensive mitogenomic reference data remain scarce. To fill this gap, we present a new forensic-grade dataset comprising complete mitochondrial genomes from 264 individuals with maternal ancestry from Flanders, the northern part of Belgium. Maternal lineages were verified through validated genealogical records extending prior to 1750. Our Flemish dataset reveals 252 unique haplotypes, a mean pairwise difference of 27.3, and a random match probability of 0.0042, demonstrating forensic resolution comparable to other high-quality European datasets. Haplogroups H, U, and T predominate in Flanders, aligning with broadly observed European patterns, while clustering analyses show close genetic affinities with neighbouring Western European populations. Furthermore, comparison with ancient genomes from the Middle Ages reveals notable continuity in maternal ancestry in Flanders throughout the historical era. Our data substantially expand the mitochondrial reference for Flanders, providing a high-quality resource based on autochthonous maternal lineages, suitable for forensic applications, genetic genealogical analyses, and microgeographic population studies.

线粒体DNA （mtDNA）在法医学和群体遗传学中起着至关重要的作用，特别是在分析高度降解的样本时。然而，大多数有丝分裂基因组参考数据集仍然局限于控制区（CR）序列，其鉴别能力有限。对于比利时来说尤其如此，尽管在2024年引入了新的立法，以增加在家族搜索中使用线粒体DNA，但全面的有丝分裂基因组参考数据仍然很少。为了填补这一空白，我们提出了一个新的法医级数据集，包括来自比利时北部佛兰德斯的母亲祖先的264个人的完整线粒体基因组。母亲的血统是通过有效的家谱记录来验证的，这些家谱记录可以追溯到1750年以前。我们的佛兰德语数据集揭示了252个独特的单倍型，平均成对差异为27.3，随机匹配概率为0.0042，证明了与其他高质量欧洲数据集相当的法医分辨率。单倍群H， U和T在佛兰德斯占主导地位，与广泛观察到的欧洲模式一致，而聚类分析显示与邻近的西欧人群有密切的遗传亲缘关系。此外，与中世纪古代基因组的比较显示，在整个历史时期，佛兰德斯的母系祖先具有显著的连续性。我们的数据大大扩展了法兰德斯人的线粒体参考，提供了基于本土母系的高质量资源，适用于法医应用、遗传谱系分析和微地理人口研究。

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引用次数: 0

Statistical interpretation of cases involving mixtures: A Spanish and Portuguese-Speaking Working Group (GHEP-ISFG) collaborative exercise 涉及混合病例的统计解释：西班牙语和葡萄牙语工作组（gep - isfg）合作练习。

IF 3.1 2区医学 Q2 GENETICS & HEREDITY

Forensic Science International-Genetics

Pub Date : 2025-10-28 DOI: 10.1016/j.fsigen.2025.103383

Camila Costa , Juan Carlos Álvarez , Sofia Angeletti , Sebastian Biagini , Mariela Caputo , Eugenia Carnevali , María Ignacia Castillo , Sandra Cordoba , Simon Cortes Sierra , María de la Puente , Agustina Dorigón , Oscar García , Santiago Ginart , Alejandra Guinudinik , Carina Merino Bedmar , Aline Minervino , Cecilia Miozzo , Ana Mosquera-Miguel , Maria Eugenia Nicolotti , Martina Onofri , Nádia Pinto

The increasing complexity of forensic genetic samples has driven the development and implementation of probabilistic genotyping software (PGS) to assist experts in quantifying the weight of evidence. A common challenge lies in quantifying the likelihood that a person of interest (PoI) is a contributor to a DNA mixture, especially in samples with low quantity and quality, stochastic effects (drop-in allele, dropout, and/or heterozygotic peaks imbalance), shared alleles, and stutter peaks. PGS can be based on either qualitative models (allele presence/absence) or quantitative (including allele peak heights) to assess the likelihood ratio, which consists of comparing the probability of observing the evidence given two hypotheses: “H1 = The PoI is a contributor to the evidence” and “H2 = The PoI is not a contributor nor genetically related to any contributor”. Key parameters included in these calculations regarding population – allele frequency distributions, and co-ancestry coefficient –, analytical factors – drop-in, dropout, analytical threshold –, and stutter presence, can influence the outcomes depending on how they are set. This collaborative exercise, organized by the Spanish and Portuguese-speaking Working Group of the International Society for Forensic Genetics, aimed to assess the current state of knowledge, use, and implementation of PGS among forensic laboratories. The goal was to evaluate how non-binary informatics tools are applied in practice and to understand the methodologies used to statistically interpret complex DNA mixtures.Participants were asked to analyze 30 pairs of samples composed of DNA mixtures (with varying the number of contributors, mixture ratios, and degradation levels) and corresponding reference profiles, selected from the PROVEDIt database. Laboratories employed different tools and approaches to quantify the evidence’s weight, including decisions regarding the number of contributors (NoC), population, laboratory, and case-specific parameters, such as coancestry coefficient, minimum allele frequency, dropout frequency, drop-in (frequency and modeling), analytical threshold, and the modeling of stutter peaks and degradation. Even though all laboratories received the same genotypic and frequency data, methodological differences led to different LR results, particularly for more complex samples with low-template and degraded DNA. The greatest differences were observed in the interplay between analytical thresholds and NoC estimation, with discrepancies amplified when alleles from minor contributors overlapped with expected stutter positions. This exercise highlights the importance of expert training and underscores the need for a comprehensive understanding of the statistical models underlying PGS. Ensuring accurate and consistent interpretation of complex DNA evidence requires not only technical proficiency but also an integrated approach to parameter selection and genotypic data evaluation.

法医基因样本日益复杂，这推动了概率基因分型软件（PGS）的发展和实施，以帮助专家量化证据的权重。一个常见的挑战在于量化一个感兴趣的人（PoI）是DNA混合物的贡献者的可能性，特别是在数量和质量低、随机效应（缺失等位基因、缺失和/或杂合子峰不平衡）、共享等位基因和口吃峰的样本中。PGS可以基于定性模型（等位基因存在/缺失）或定量模型（包括等位基因峰值高度）来评估似然比，其中包括比较观察到两个假设的证据的概率：“H1 = PoI是证据的贡献者”和“H2 = PoI不是贡献者，也与任何贡献者没有遗传关系”。这些计算中包含的关键参数包括种群——等位基因频率分布和共同祖先系数——、分析因素——失学、失学、分析阈值——和口吃的存在，这些都可能影响结果，具体取决于它们的设置方式。这次合作演习由国际法医遗传学学会的西班牙语和葡萄牙语工作组组织，旨在评估法医实验室对PGS的知识、使用和实施的现状。目的是评估非二进制信息学工具在实践中的应用，并了解用于统计解释复杂DNA混合物的方法。参与者被要求分析由DNA混合物组成的30对样本（具有不同的贡献者数量，混合比例和降解水平）和相应的参考档案，从PROVEDIt数据库中选择。实验室采用不同的工具和方法来量化证据的权重，包括有关贡献者数量（NoC）、人群、实验室和特定病例参数的决定，如共祖系数、最小等位基因频率、辍学频率、辍学（频率和建模）、分析阈值以及口吃峰值和退化的建模。尽管所有实验室都收到了相同的基因型和频率数据，但方法的差异导致了不同的LR结果，特别是对于具有低模板和降解DNA的更复杂的样品。在分析阈值和NoC估计之间的相互作用中观察到最大的差异，当来自次要贡献者的等位基因与预期的口吃位置重叠时，差异会被放大。这项工作突出了专家培训的重要性，并强调了全面了解PGS基础统计模型的必要性。确保准确和一致地解释复杂的DNA证据不仅需要技术熟练，而且需要综合的方法来选择参数和基因型数据评估。

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引用次数: 0

Developmental validation of a whole genome sequencing workflow for use in a forensic laboratory 用于法医实验室的全基因组测序工作流程的开发验证。

IF 3.1 2区医学 Q2 GENETICS & HEREDITY

Forensic Science International-Genetics

Pub Date : 2025-10-27 DOI: 10.1016/j.fsigen.2025.103380

Jennifer C. Cihlar , August E. Woerner , Jonathan L. King , Jessica Broner Hawkins , Michael D. Coble

The generation of large single nucleotide variant (SNV) profiles are at the forefront of the minds of many forensic practitioners, largely in response to the growing demand for forensic genetic genealogy (FGG) analyses on both missing persons and forensic cases. Current options available to laboratories today include PCR-based targeted amplification, SNV microarrays, and whole genome sequencing, each with multiple commercially available kits from which to choose. In addition to molecular considerations, bioinformatic workflows (and accompanying tools) must be constructed, validated, and implemented. To aid this process, a developmental validation study of a whole genome sequencing workflow was completed. This workflow consisted of library preparation with the KAPA HyperPrep Kit and sequencing on the NovaSeq 6000. Validation of this workflow included studies on PCR optimization, library stability, and library plexity. Sensitivity studies (ranging from 10 nanograms to 50 picograms of DNA) demonstrated the dynamic range and limit of detection. Libraries were generated by multiple individuals to allow for assessment of reproducibility. The potential for contamination was assessed through evaluation of negative controls for evidence of exogenous DNA. Finally, mock casework samples and mixtures at ratios ranging from 1:1–1:49 were sequenced to determine performance with potentially challenging samples. A portable end-to-end bioinformatic workflow (Tapir) was developed, allowing for a seamless transition from raw data from Illumina instruments (BCL) to sample genotypes in a format compatible with GEDmatch. Tapir includes various summaries of sample composition, including information on coverage (breadth and depth), duplication rates and call rates, and it supports both modern genotype imputation (i.e., genotype refinement) as well as classical genotyping techniques. The detailed breakdown of this workflow and the associated validation data will serve as an important tool in enabling the implementation of whole genome sequencing in forensic laboratories.

大单核苷酸变异（SNV）谱的生成是许多法医从业者的前沿思想，主要是为了响应对失踪人员和法医案件的法医遗传谱系（FGG）分析日益增长的需求。目前可供实验室选择的选项包括基于pcr的靶向扩增，SNV微阵列和全基因组测序，每个都有多个市售试剂盒可供选择。除了分子方面的考虑外，生物信息学工作流程（和附带的工具）必须被构建、验证和实施。为了帮助这一过程，完成了全基因组测序工作流程的发展验证研究。该工作流程包括使用KAPA HyperPrep试剂盒制备文库和在NovaSeq 6000上测序。该工作流程的验证包括PCR优化、文库稳定性和文库复杂性的研究。灵敏度研究（范围从10纳克到50皮克DNA）证明了动态范围和检测极限。库是由多个个体生成的，以便对可重复性进行评估。通过评估外源DNA证据的阴性对照来评估污染的可能性。最后，对1:1-1:49比例的模拟案例样品和混合物进行测序，以确定潜在挑战性样品的性能。开发了便携式端到端生物信息学工作流（Tapir），允许从Illumina仪器（BCL）的原始数据无缝过渡到与GEDmatch兼容的格式的样本基因型。Tapir包括样品组成的各种摘要，包括覆盖（广度和深度）、重复率和调用率的信息，它既支持现代基因型插入（即基因型精化），也支持经典基因分型技术。该工作流程的详细分解和相关的验证数据将作为在法医实验室实施全基因组测序的重要工具。

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引用次数: 0

Murder in cold blood? Forensic and bioarchaeological identification of the skeletal remains of Béla, Duke of Macsó (c. 1245–1272) 冷血谋杀？对Macsó公爵b<s:1>拉西亚（约1245-1272年）骨骼遗骸的法医和生物考古鉴定。

IF 3.1 2区医学 Q2 GENETICS & HEREDITY

Forensic Science International-Genetics

Pub Date : 2025-10-26 DOI: 10.1016/j.fsigen.2025.103381

Tamás Hajdu , Noémi Borbély , Zsolt Bernert , Ágota Buzár , Tamás Szeniczey , István Major , Claudio Cavazzuti , Mihály Molnár , Anikó Horváth , László Palcsu , Barna Árpád Kelentey , János Angyal , Balázs Gusztáv Mende , Kristóf Jakab , Zsuzsa Lisztes-Szabó , Ágoston Takács , Olivia Cheronet , Ron Pinhasi , David Emil Reich , Martin Trautmann , Anna Szécsényi-Nagy

In 1915, the remains of a male were discovered in a 13th-century monastery on Margaret Island, Budapest. Historical context suggested that the remains might have belong to Duke Béla of Macsó (c. 1245–1272), grandson of King Béla IV of Hungary (House of Árpád) and son of Duke Rostislav (Rurik dynasty). We applied a complex approach to identify the individual and reconstruct the circumstances of his death. Radiocarbon dating, when adjusted for freshwater reservoir effects linked to a high-protein diet, placed the burial in the mid-13th century. Skeletal features corresponded to a young adult male. Stable isotope and dental calculus analyses indicated a high-status diet rich in animal proteins and C3 cereals. Ancient DNA confirmed descent from King Béla III (Árpád dynasty) and Y-chromosomal affiliation with the Rurikid lineage. Forensic evidence revealed 26 perimortem injuries, suggesting a coordinated, premeditated assassination involving at least three assailants. The pattern of injuries indicated both planning and intense emotional involvement. Our findings provide the first genetic identification of a medieval royal, and resolve a century-old archaeological question, and illustrate the power of integrating multidisciplinary methods to confirm historical hypotheses and reconstruct violent deaths from the past with unprecedented detail.

Teaser

With unprecedented details, this study shows the impact of integrating multidisciplinary methods to confirm historical hypotheses and reconstruct violent deaths from the past.

1915年，在布达佩斯玛格丽特岛一座13世纪的修道院中发现了一具男性遗骸。历史背景表明，遗骸可能属于Macsó（约1245年至1272年），匈牙利国王b拉西亚四世（Árpád家族）的孙子和公爵Rostislav（留里克王朝）的儿子。我们采用了一种复杂的方法来识别这个人，并重建了他死亡的情况。放射性碳定年法，在考虑到与高蛋白饮食有关的淡水水库效应后，确定了这个埋葬在13世纪中期。骨骼特征与年轻成年男性相符。稳定同位素和牙石分析表明，他们的饮食中富含动物蛋白和C3谷物。古代DNA证实了他的祖先是国王b拉西三世（Árpád王朝），y染色体上与Rurikid家族有亲缘关系。法医证据显示有26处死前伤，表明这是一起有组织、有预谋的暗杀，涉及至少三名袭击者。伤口的模式表明有预谋和强烈的情感介入。我们的发现首次提供了中世纪皇室成员的基因鉴定，解决了一个百年的考古问题，并说明了整合多学科方法的力量，以证实历史假设，并以前所未有的细节重建过去的暴力死亡。导语：这项研究以前所未有的细节展示了整合多学科方法来证实历史假设和重建过去暴力死亡的影响。

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引用次数: 0

Assessing the value of bacteria, plants, fungi and arthropods characterized via DNA metabarcoding for separation of forensic-like surface soils at varied spatial scales 利用DNA元条形码技术评估细菌、植物、真菌和节肢动物在不同空间尺度上的鉴定价值。

IF 3.1 2区医学 Q2 GENETICS & HEREDITY

Forensic Science International-Genetics

Pub Date : 2025-10-24 DOI: 10.1016/j.fsigen.2025.103379

Kelly A. Meiklejohn , Melissa K.R. Scheible , Tiffany Layne , Teresa M. Tiedge , Kim Love , Jack Hietpas , Jodi B. Webb , Libby A. Stern

Geological materials, including soil and dust, are ubiquitous and often inadvertently transferred during crime events. Forensic geologists use a range of particle-based analytical approaches to characterize the inorganic fraction for sample-to-sample comparisons. While analysis of the inorganic component often provides sufficient information to answer case related questions, there are inevitably cases where analysis of the organic fraction could be beneficial. In this study we assessed whether the biological communities associated with the organic fraction of North Carolina surface soils could allow for sample separation at four spatial scales: 1) sub-site samples – three samples collected 1 m apart, 2) small – A and B sites at a single location in close proximity (median distance of 66 m apart), 3) moderate – multiple locations within the same research station (median distance of 1.1 km apart), and 4) large – multiple locations within each physiographic region (Coastal Plain, Mountains, Piedmont) separated by up to 250 km. DNA metabarcoding coupled with Illumina® sequencing was used to amplify ∼200 bp regions of the following in each surface soil sample (n = 180): 1) 16S for bacteria, 2) ITS1 for fungi, 3) ITS2 and p6 loop of the trnL-UAA intron for plants, and 4) COI for arthropods. Generated sequences were taxonomically classified and subsequently organized into eight taxonomic combinations each analyzed at four data levels (unique sequence level and family rank, with and without removal of the 25 % most common taxa). Beta diversity was used as input for ANOSIM and PCA analyses to determine the optimal biological communities and data level to permit separation across the four spatial scales. The biological communities that permitted separation between samples varied based on the spatial scale being examined. At small spatial scales, datasets that included bacteria had the highest success of separating samples. At moderate spatial scales, the combination of plants + fungi or plants alone provided the highest success of separation. Finally, at the examined largest spatial scale, all combinations of biological communities tested performed comparably, likely due to the large diversity in habitat, land-use and geologic parent material between locations. Across all examined spatial scales, the optimal biological community combinations performed best when analyzed at the most granular unique sequence level. The results of this study demonstrate the value of biological communities for differentiating soils across varying spatial scales, providing a complementary analysis method for samples where the inorganic fraction lacked exclusionary differences.

地质物质，包括土壤和灰尘，无处不在，经常在犯罪事件中不经意地转移。法医地质学家使用一系列基于颗粒的分析方法来表征样品间比较的无机部分。虽然无机成分的分析通常提供足够的信息来回答与案例相关的问题，但不可避免地，有机部分的分析可能是有益的。在这项研究中，我们评估了与北卡罗来纳州表层土壤有机组分相关的生物群落是否可以在四个空间尺度上进行样本分离：1)子样点——三个样点之间相距1 m， 2)小样点——A和B样点之间距离较近（中间距离为66 m）， 3)中等样点——同一研究站内多个样点（中间距离为1.1 km）， 4)大样点——每个地理区域（沿海平原、山区、山前山区）内多个样点之间距离可达250 km。利用DNA元条形码结合Illumina®测序，在每个表层土壤样品中扩增出以下区域的~ 200 bp (n = 180):1)细菌的16S， 2)真菌的ITS1, 3)植物trnL-UAA内含子的ITS2和p6环，4)节肢动物的COI。对生成的序列进行分类，然后将其组织为8个分类组合，每个组合在4个数据水平上进行分析（唯一序列水平和家族等级，去除或不去除25% %最常见的分类群）。利用Beta多样性作为ANOSIM和PCA分析的输入，以确定四个空间尺度上允许分离的最佳生物群落和数据水平。允许样本之间分离的生物群落根据所检查的空间尺度而变化。在小的空间尺度上，包含细菌的数据集在分离样本方面取得了最高的成功。在中等空间尺度下，植物+ 真菌组合或植物单独分离成功率最高。最后，在研究的最大空间尺度上，所有被测试的生物群落组合都具有可比性，这可能是由于不同地点之间栖息地、土地利用和地质母质的巨大差异。在所有研究的空间尺度上，当在最颗粒的独特序列水平上分析时，最佳生物群落组合表现最佳。本研究的结果证明了生物群落在不同空间尺度上区分土壤的价值，为无机组分缺乏排他性差异的样品提供了一种补充分析方法。

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引用次数: 0

Construction of a succession model for the microbiome in water from submerged corpses based on single-molecule real-time sequencing 基于单分子实时测序的沉尸水体微生物群演替模型构建

IF 3.1 2区医学 Q2 GENETICS & HEREDITY

Forensic Science International-Genetics

Pub Date : 2025-10-24 DOI: 10.1016/j.fsigen.2025.103378

Xiaoxin Hu , Mengqi Wu , Bolei Zhao , Tingyu Xu , Zhenjun Jia , Xingchun Zhao

Decomposition of corpses in aquatic environments is regulated by multiple factors, and traditional methods for estimating the postmortem submerged interval (PMSI) have clear limitations. To explore the microbial succession patterns in the water of submerged corpses and their potential application in PMSI estimation, this study submerged rat carcasses in both river water and tap water, collecting water samples on days 0, 2, 6, 9, 14, 20, 27, 40, 54, and 70 postmortem. The microbial succession dynamics in the water were analyzed using single-molecule real-time sequencing. The results indicated that, although the response patterns to decomposition differed between the two water sources, key microorganisms common to various decomposition stages were identified, suggesting their important role in the process. This study characterized the microbial community succession trajectory at the species level and identified several species with potential for PMSI indication. Based on this, we constructed a simple random forest prediction model. During the 70-day decomposition period, the mean absolute errors (MAE) of the river water model and the tap water model were 5.8745 days and 4.8599 days, respectively. This research elucidates the microbial community succession patterns induced by corpse submersion in water, constructs a methodological framework for PMSI estimation based on water microbiomes, and provides crucial support for the development of more versatile PMSI inference models.

尸体在水生环境中的分解受到多种因素的调控，传统的估算死后淹没时间间隔（PMSI）的方法存在明显的局限性。为了探索浸泡尸水中微生物演替模式及其在PMSI估计中的潜在应用，本研究将大鼠尸体浸泡在河流和自来水中，在死后0、2、6、9、14、20、27、40、54和70天采集水样。采用单分子实时测序技术对水体微生物演替动态进行了分析。结果表明，尽管两种水源对分解的响应模式不同，但在不同分解阶段共有的关键微生物被鉴定出来，表明它们在分解过程中起着重要作用。本研究在物种水平上对微生物群落演替轨迹进行了表征，并确定了几个具有潜在PMSI指示的物种。在此基础上，我们构建了一个简单的随机森林预测模型。在70 d分解期内，河流水模型和自来水模型的平均绝对误差（MAE）分别为5.8745天和4.8599天。本研究阐明了尸体淹水导致的微生物群落演替模式，构建了基于水体微生物组的PMSI估算方法框架，为开发更通用的PMSI推断模型提供了重要支持。

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引用次数: 0

So much promise, so little delivery: Underuse of biological evidence collected from sexual assault victims treated in an Italian specialised hospital centre 承诺太多，兑现太少：从意大利一家专门医院中心治疗的性侵犯受害者身上收集的生物证据未得到充分利用

IF 3.1 2区医学 Q2 GENETICS & HEREDITY

Forensic Science International-Genetics

Pub Date : 2025-10-21 DOI: 10.1016/j.fsigen.2025.103377

A. Riem , E. Chierto , S. Aneli , F. Lupariello , S. Gino , M. La Porta , M. Omedei , N. Staiti , A. Canavese , P. Castagna , C. Robino

In an Italian hospital centre treating victims of sexual assault, requests for genetic testing of biological samples collected during forensic medical examinations (GT cases) were identified from 2003 to 2023, and details of the results of body fluid identification (BFI) and DNA analysis were obtained from the designated laboratories. Elements that could influence the decision to perform forensic DNA analysis were derived from the medical records of GT cases and a comparison group of patients whose samples were not genetically tested.

The overall proportion of GT cases was 7.8 %, remaining limited even after the implementation of the National DNA Database (BDN-DNA) in 2017 (14.3 % in 2023). Items that were significantly more common in GT cases compared to the comparison group included: a positive sperm microscopy result; short time since intercourse (TSI) (<24 h in >80 % of GT cases); reported ejaculation; aggression by a stranger; group violence; absence of injuries.

Male DNA profiles were obtained from 52.1 % of samples using a direct-to-DNA approach, and from 39.2 % using a traditional strategy involving differential extraction, depending on the preliminary BFI results. The success rate was significantly higher for shorter TSI and positive BFI test for semen, although male DNA profiles could be obtained in 18–27 % of semen negative samples. Only 25.0 % of eligible DNA profiles obtained after 2017 were uploaded to BDN-DNA.

The results show the underuse of biological evidence in the investigation of sexual violence cases in the Italian criminal justice system and the lack of awareness of the potential of BDN-DNA.

在意大利一家治疗性侵犯受害者的医院中心，从2003年至2023年确认了对法医检查（GT案件）期间收集的生物样本进行基因检测的请求，并从指定实验室获得了体液鉴定（BFI）和DNA分析结果的详细信息。可能影响进行法医DNA分析决定的因素来自GT病例的医疗记录和一组患者的比较，这些患者的样本未进行基因检测。GT病例的总比例为7.8% %，即使在2017年实施国家DNA数据库（BDN-DNA）后仍然有限（2023年为14.3% %）。与对照组相比，GT病例中更常见的项目包括：精子显微镜结果阳性；距性交时间短（TSI）（>； 80% % GT病例中<；24 h）；报道射精;陌生人的攻击；集团暴力;没有受伤。根据初步的BFI结果，使用直接提取DNA的方法从52.1% %的样本中获得雄性DNA谱，使用涉及差异提取的传统策略从39.2% %的样本中获得雄性DNA谱。尽管在18 - 27% %的精液阴性样本中可以获得男性DNA图谱，但较短TSI和阳性BFI测试的成功率显著更高。在2017年之后获得的符合条件的DNA图谱中，只有25.0 %上传到BDN-DNA。研究结果表明，意大利刑事司法系统在调查性暴力案件时没有充分利用生物证据，也缺乏对BDN-DNA潜力的认识。

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引用次数: 0