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From cold case to conviction: How advanced DNA technologies such as mtDNA sequencing connected two brutal homicides 从悬案到定罪:先进的DNA技术如mtDNA测序如何将两起残忍的凶杀案联系起来
IF 3.1 2区 医学 Q2 GENETICS & HEREDITY Pub Date : 2025-11-26 DOI: 10.1016/j.fsigen.2025.103407
Patrick Dieltjes, Yvonne van de Wal, Marcelle Vos, Lisette Doodkorte, Natalie E.C. Weiler, Kristiaan J. van der Gaag, Titia Sijen
Cold case investigations involve revisiting case circumstances and prior evidentiary material. Novel or improved methods better suited to minute, mixed or degraded samples may provide new leads or higher evidential values. Here, we describe a reinvestigation started in 2016 of a 2004 murder case in which the body parts of a young woman were found in five double-bagged rubbish bags in the city of Amsterdam. Resampling and autosomal DNA-profiling of one of the rubbish bags knot areas resulted in a low LR for a man who had had sexual contact just before the victim went missing. This man became therefore suspect in this case. Detailed trace examination of stored upholstering of the backseat of the car of the 2004 victim revealed blood-stained sand particles and small botanical material. DNA profiling presented a match to a young woman who was found naked and brutally murdered on an embankment in Amsterdam in 2003. Both women worked as prostitutes but did not know each other. Moreover, the suspect in the 2004 case was found to have had sexual contact with the 2003 victim shortly before she deceased. A crucial DNA link between the two cases was provided through mitochondrial DNA (mtDNA) analysis of samplings of the rubbish bag knots. Because the 2004 DNA extracts contained insufficient material for autosomal analysis, massively parallel sequencing (MPS)-based mtDNA profiling was performed[1]. At that time, our laboratory had just validated and implemented MPS, allowing detection of minor mtDNA contributions as low as 3 % in mixtures. Remarkably, one sample yielded a match with both the 2004 victim and the suspect, while another matched the 2004 and the 2003 victim. A scenario could be that the suspect used the car of the 2004 victim to dispose not only of her body parts but also of an artefact from the 2003 case. A 2021 court of appeal decision convicted the suspect for both these, and a third, homicide also involving a young prostitute. Looking back, several aspects contributed to resolving the cold case: saving evidentiary items so that these can be reanalysed in later years when methods have advanced, scrutinous trace examination detecting blood-stained sand and botanical particles, furthering (mt)DNA analyses to deal better with low-level mixtures, improved DNA profile interpretation presenting higher evidentiary values by applying a continuous probabilistic genotyping model, and daring to apply these novel techniques in cases and report to the court.
悬案调查涉及重审案件情况和先前的证据材料。新的或改进的方法更适合于分钟,混合或降解样品可能提供新的线索或更高的证据值。在这里,我们描述了2016年开始的对2004年谋杀案的重新调查,在阿姆斯特丹市的五个双袋垃圾袋中发现了一名年轻女子的身体部位。对其中一个垃圾袋结区的重新取样和常染色体dna分析显示,一名男子的LR较低,他在受害者失踪前曾与之发生过性接触。因此,这名男子成为本案的嫌疑人。对2004年受害者的汽车后座坐垫进行了详细的痕迹检查,发现了带有血迹的沙粒和小型植物物质。DNA分析显示,2003年在阿姆斯特丹的一个堤岸上发现了一名被残忍杀害的裸体年轻女子。两人都是妓女,但彼此并不认识。此外,2004年案件的嫌疑人被发现在2003年受害者死亡前不久与她发生过性接触。通过对垃圾袋结样本的线粒体DNA (mtDNA)分析,提供了这两起案件之间的关键DNA联系。由于2004年DNA提取液中含有的常染色体分析材料不足,因此我们于2010年进行了基于大规模平行测序(MPS)的mtDNA分析。当时,我们的实验室刚刚验证并实施了MPS,允许检测混合物中低至3 %的次要mtDNA贡献。值得注意的是,一个样本与2004年的受害者和嫌疑人都吻合,而另一个样本与2004年和2003年的受害者都吻合。一种可能的情况是,嫌疑人使用2004年受害者的车,不仅处理了她的身体部位,还处理了2003年案件中的一件文物。2021年,上诉法院的一项裁决判定,这名嫌疑人犯有这两项罪名,以及第三项涉及一名年轻妓女的杀人罪。回顾过去,有几个方面有助于解决这个悬案:保存证据,以便在以后的几年里,当方法先进时,可以重新分析这些证据,仔细的痕量检测检测血迹的沙子和植物颗粒,进一步(mt)DNA分析,以更好地处理低水平的混合物,改进DNA图谱解释,通过应用连续概率基因分型模型提供更高的证据价值,并敢于将这些新技术应用于案件并向法院报告。
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引用次数: 0
Oral microbiomes as forensic markers of origin and migration: Insights from an underrepresented population, Nigeria 口腔微生物组作为起源和迁移的法医标记:来自尼日利亚代表性不足人口的见解
IF 3.1 2区 医学 Q2 GENETICS & HEREDITY Pub Date : 2025-11-25 DOI: 10.1016/j.fsigen.2025.103395
Nengi Ogbanga , Andrew Nelson , Darren Smith , Richard Somiari , Noemi Procopio
The oral microbiome is shaped by environmental and host-associated factors, suggesting its utility for human profiling in forensics, particularly as an indicator of geographic origin and human migration. Using high-throughput sequencing and machine learning models, the predictive ability of the oral microbiome was assessed to determine the country of origin of the donors, using samples of individuals across 6 countries. The impact of migration on the predictive ability of the oral microbiome was also assessed through a longitudinal study of Nigerian migrants over a six-month period following migration. By analysing the oral microbiome at various time points during this timeframe, this study explores the influence of migration on the oral microbiome to provide insights into its applicability in forensic investigations. Our findings demonstrate that distinct microbial profiles correlate with the six geographic regions assessed in this study. Furthermore, the longitudinal sampling of Nigerian migrants revealed initial shifts in their microbiome profile, followed by a recovery to the original microbiome profile of Nigerian locals, observed after six months. These results highlight the forensic potential of the oral microbiome for geographic origin attribution, in migration tracking, and for providing intelligence information useful for forensic purposes.
口腔微生物组是由环境和宿主相关因素塑造的,这表明它在法医中对人类分析的效用,特别是作为地理起源和人类迁移的指标。使用高通量测序和机器学习模型,评估了口腔微生物组的预测能力,以确定捐赠者的原籍国,使用了6个国家的个人样本。通过对移民后六个月的尼日利亚移民进行纵向研究,还评估了移民对口腔微生物组预测能力的影响。通过分析这一时间段内不同时间点的口腔微生物组,本研究探讨了迁移对口腔微生物组的影响,以深入了解其在法医调查中的适用性。我们的研究结果表明,不同的微生物剖面与本研究中评估的六个地理区域相关。此外,尼日利亚移民的纵向抽样揭示了他们的微生物组谱的最初变化,随后在六个月后观察到尼日利亚当地人的原始微生物组谱恢复。这些结果突出了口腔微生物组在地理起源归属、迁移跟踪以及为法医目的提供有用的情报信息方面的法医潜力。
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引用次数: 0
Forensic analysis of a parthenogenetic 46, XX/46, XY congenital chimera: A case report 孤雌生殖46、XX/46、XY先天性嵌合体1例法医分析。
IF 3.1 2区 医学 Q2 GENETICS & HEREDITY Pub Date : 2025-11-24 DOI: 10.1016/j.fsigen.2025.103394
Linlin Gao , Chenxia Li , Yuntian Xiao , Wenyan Ren , Shujuan Ma , Jingjing Zhang , Jiangwei Yan
In forensic identification, chimerism is an extremely rare phenomenon in which DNA samples can easily be misidentified as mixtures from two individuals. If only a single cell population from the chimera is collected, it may lead to false exclusions in paternity testing and errors in forensic conclusions. In China, short tandem repeat analysis is required for victim identification in homicide cases. This study originated from a murder case — the decedent's blood sample exhibited a mixed STR profile suggestive of two contributors. Therefore, 16 additional distinct types of organ tissues from the decedent were collected for comprehensive analysis. Autosomal STR testing revealed that the mixed STR profiles across the 17 different tissues were completely consistent, though the mixture ratios varied among tissues. No more than three alleles were observed at each locus, and the resolved male component M and female component F shared one identical allele at each locus. X-STR profiling showed that all 18 samples displayed no more than two alleles per locus, with consistent typing results. Both A-STR and X-STR findings indicated that components M and F originated from the same maternal chromosome. Copy number variation analysis confirmed the coexistence of two cell lines, 46, XX and 46, XY, in the decedent’s tissues. Cross-validation using multiple methods confirmed that the decedent was an intersex parthenogenetic chimera, with both cell lines randomly participating in tissue and organ differentiation. The resolved component F matched the decedent's son and husband in a parent-child relationship, consistent with a trio kinship. Meanwhile, the male component, together with the female component and the decedent’s sister, was inclined to be considered full siblings based on the combined identity by state score. These results ruled out the possibility that the mixed STR profile resulted from contamination and suggested the presence of normal oocytes in the decedent’s ovarian tissue, indicating that germline cells might not be chimeric. This study provides a deeper exploration of the mechanisms underlying chimerism and offers new insights and references for forensic identification. Future DNA studies of autopsy material may help clarify the incidence, subtypes, and pathogenesis of chimerism, while also determining the optimal tissue types for detecting chimerism and screening for chimerism, thereby supporting related research and practice.
在法医鉴定中,嵌合是一种极其罕见的现象,在这种现象中,DNA样本很容易被误认为是来自两个人的混合物。如果只收集来自嵌合体的单个细胞群,可能会导致亲子鉴定中的错误排除和法医结论的错误。在中国,杀人案件的受害人鉴定需要短串联重复序列分析。这项研究起源于一起谋杀案,死者的血液样本显示出混合的STR特征,表明有两个贡献者。因此,从死者身上收集了16种不同类型的器官组织进行综合分析。常染色体STR检测显示,17种不同组织的混合STR谱完全一致,尽管不同组织的混合比例不同。在每个位点上观察到的等位基因不超过3个,在每个位点上分解的雄性成分M和雌性成分F共享一个相同的等位基因。X-STR分析显示,所有18个样本每个位点的等位基因不超过2个,分型结果一致。A-STR和X-STR结果表明,成分M和F来自同一母系染色体。拷贝数变异分析证实在死者组织中存在46、XX和46、XY两个细胞系。采用多种方法进行交叉验证,证实该死者为双性孤雌嵌合体,两种细胞系随机参与组织和器官分化。已解决的分量F与死者的儿子和丈夫在亲子关系中相匹配,符合三人亲属关系。同时,男性成分、女性成分和被遗属的姐妹在状态得分的综合认同上倾向于被认为是全兄妹。这些结果排除了混合STR谱由污染引起的可能性,并表明在死者的卵巢组织中存在正常卵母细胞,表明生殖系细胞可能不是嵌合的。本研究对嵌合的机制进行了深入的探索,为法医鉴定提供了新的见解和参考。未来对尸检材料的DNA研究可能有助于阐明嵌合的发病率、亚型和发病机制,同时确定检测嵌合和筛选嵌合的最佳组织类型,从而支持相关研究和实践。
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引用次数: 0
A hexaplex droplet digital PCR assay for DNA methylation-based age prediction from blood samples targeting ELOVL2, FHL2, and TRIM59 一项针对ELOVL2、FHL2和TRIM59的血液样本DNA甲基化年龄预测的六重液滴数字PCR试验
IF 3.1 2区 医学 Q2 GENETICS & HEREDITY Pub Date : 2025-11-22 DOI: 10.1016/j.fsigen.2025.103396
Rita Fakhr , Un Na Koh , So Eun Lee , Si-Keun Lim
DNA methylation analysis has emerged as a promising approach, offering valuable information in forensic investigations. This study presents the development of a hexaplex droplet digital PCR (ddPCR) assay for forensic age prediction based on three well-established age-associated markers: ELOVL2, FHL2, and TRIM59. The assay reliably distinguished methylation levels as low as 1 %, with no cross-reactivity or signal interference in the multiplex format. To evaluate the assay’s predictive performance, two statistical methods were used: hold-out cross-validation and 5-fold cross-validation. In both methods, all three markers showed strong correlations with chronological age. In the hold-out method, the model achieved a mean absolute error (MAE) of 2.80 years for the test set. Comparable performance was observed in 5-fold cross-validation, with an average MAE of 3.13 years. Prediction accuracy was higher in younger individuals and decreased with older age. The hexaplex assay allows all markers to be analyzed under identical experimental conditions, enhancing consistency, minimizing technical variability, and reducing reagent costs. Future work will include validation studies in accordance with the Scientific Working Group on DNA Analysis Methods (SWGDAM) guidelines and application to real forensic casework to further confirm the assay’s practical utility.
DNA甲基化分析已经成为一种很有前途的方法,为法医调查提供了有价值的信息。本研究提出了一种基于ELOVL2、FHL2和TRIM59三种成熟的年龄相关标记物的法医年龄预测的六重液滴数字PCR (ddPCR)检测方法。该分析可靠地区分甲基化水平低至1 %,在多重格式中没有交叉反应性或信号干扰。为了评估该方法的预测性能,采用了两种统计方法:保留交叉验证和5倍交叉验证。在这两种方法中,所有三个标记都显示出与实足年龄的强烈相关性。在hold-out方法中,模型对测试集的平均绝对误差(MAE)为2.80年。在5倍交叉验证中观察到可比的性能,平均MAE为3.13年。预测准确性在年轻人中较高,随着年龄的增长而下降。六联分析允许在相同的实验条件下分析所有标记物,增强一致性,最大限度地减少技术变化,并降低试剂成本。未来的工作将包括根据DNA分析方法科学工作组(SWGDAM)指南进行验证研究,并将其应用于实际的法医案例,以进一步确认该分析的实际效用。
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引用次数: 0
Pharmabiome analyses in tandem with chemometrics can help trace the provenance of falsified medicines: A proof-of-concept study 药物组学分析与化学计量学相结合可以帮助追踪伪造药物的来源:一项概念验证研究
IF 3.1 2区 医学 Q2 GENETICS & HEREDITY Pub Date : 2025-11-20 DOI: 10.1016/j.fsigen.2025.103392
Carla Perez-Mon , Alberto Roncone , Aiman Abrahim , Marivil Islam , Cathrin Hauk , Celine Caillet , Hamid A. Merchant , Rabia Farzand , Luana Bontempo , Simon D. Kelly , Daniel Blessborn , Joel Tarning , Rachel Kline , Victoria Nicheva , Dominic T. Kurian , Paul N. Newton , Rob Ogden
A lack of robust analytical approaches limits our ability to investigate the clandestine manufacturing origins of falsified medicines. We conducted a proof-of-concept study to test the feasibility of geolocating the production sites of falsified medicines, based on the identification of site-specific biological and chemo-isotopic features using a combination of environmental DNA metabarcoding, Direct Analysis in Real Time - Mass Spectrometry and Isotope Ratio Mass Spectrometry as profiling techniques. We produced tablets at two distant locations (England vs. Thailand), using controlled manufacturing methods, excipient composition and environmental conditions. Sets of tablets produced at separate locations showed distinct bacterial and eukaryotic diversity, particularly influenced by the incorporation of water used during tableting and the background environmental biosignatures of the production site. Tablets showed corresponding site-specific chemometric profiles, but the factors contributing to the observed chemical differences were unclear. When reference samples of known origin are available, our study suggests that site-specific biological and chemical features can be used in modelling approaches to successfully predict product origin. We developed a new mapping approach to exploit the geographic information within the eukaryotic pharmabiome of the falsifications; based on eDNA-derived species identification and the integration of publicly available species distribution data. In the absence of reference samples of known origin, the application of this workflow to our dataset provided partial clues about the product’s origin, with limitations likely due to taxonomic resolution and the presence of species with wide distribution ranges. Collectively, our research provides experimental support for the development of integrated, multifaceted tools for tracing the origin of falsified medicines, advancing efforts to combat this pervasive but neglected global health problem.
缺乏强有力的分析方法限制了我们调查假药秘密生产来源的能力。我们进行了一项概念验证研究,以测试假药生产地点地理定位的可行性,该研究基于使用环境DNA元条形码、实时质谱直接分析和同位素比质谱作为分析技术的组合来识别特定地点的生物和化学同位素特征。我们在两个遥远的地方(英国和泰国)生产片剂,使用受控的制造方法、辅料成分和环境条件。在不同地点生产的片剂组显示出不同的细菌和真核生物多样性,特别是受到片剂期间使用的水掺入和生产地点的背景环境生物特征的影响。片剂显示出相应的位点特异性化学计量谱,但导致观察到的化学差异的因素尚不清楚。当已知来源的参考样本可用时,我们的研究表明,特定地点的生物和化学特征可以用于建模方法,以成功预测产品来源。我们开发了一种新的制图方法来利用真核药物组中的伪造物的地理信息;基于edna衍生的物种鉴定和整合公开可用的物种分布数据。在缺乏已知来源的参考样本的情况下,将此工作流程应用于我们的数据集提供了关于产品来源的部分线索,可能由于分类分辨率和分布范围广泛的物种的存在而受到限制。总的来说,我们的研究为开发追踪假药来源的综合、多方面工具提供了实验支持,推动了与这一普遍但被忽视的全球卫生问题作斗争的努力。
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引用次数: 0
Microhaplotypes in forensic genetics: From exploration to application in degraded DNA specimens 法医遗传学中的微单倍型:从探索到降解DNA标本的应用。
IF 3.1 2区 医学 Q2 GENETICS & HEREDITY Pub Date : 2025-11-17 DOI: 10.1016/j.fsigen.2025.103391
Chiara Turchi , Filomena Melchionda , Fabiano Gentile , Alberto Marino , Domenico Colloca , Mauro Pesaresi , Andrew J. Pakstis , Kenneth K. Kidd
Microhaplotypes have emerged as powerful forensic markers over the past decade. This paper sets out the development of a MPS panel of microhaps and its potential for application to identification, analysis of degraded DNA, ancestry inference, and identification of close biological relationships. To make it more effective when dealing with fragmented DNA, the MPS assay was designed to ensure a reduced amplicon size of less than 140 bp. After MPS assay validation, a panel of 76 microhaps, comprised of 299 different SNPs and spread across the autosomal human genome, was established. A total of 102 Italian individuals were analyzed to estimate the genotype and haplotype frequencies. The effective number of alleles at each locus (Ae) for the Italian population ranges from 1.926 to 6.187, with 59 MHs that have values greater than 3.0. The matching probability (PI) ranges from 0.055 to 0.345 and the cumulative PI value is 11.763E-66. Complete and reliable profiles were obtained with as little as 0.05 ng. The MHs panel was then validated on real forensic specimens chosen on the basis of their DNA content and degradation level. The majority of the casework samples analyzed showed complete or nearly complete MH profiles even in degraded samples. To assess the informative power of MH profiles in forensic casework, probabilistic genotyping on partial MH profiles has been used. The resulting likelihood ratio values range from 7.84E+09 to 2.70E+34, thus defining an extremely strong support for the hypothesis that the genetic profile in a casework sample comes from the reference sample. Pairwise kinship simulations using allele frequencies from Italian population samples showed that full- and half-sibling relationships can be readily distinguished from unrelated individuals. For evaluation of the 76 MH panel’s utility for ancestry informativeness, PCA and STRUCTURE analyses are also presented comparing the newly collected sample from Ancona Italy with the 26 populations of the 1000 Genomes Project.
The results of the analysis confirmed the effectiveness of these short microhaplotypes in typing, with high sensitivity, samples with highly degraded DNA typically encountered in forensic cases.
在过去的十年里,微单倍型已经成为强有力的法医标记。本文阐述了微可能的MPS面板的发展及其在鉴定、分析降解DNA、祖先推断和鉴定密切生物关系方面的应用潜力。为了使其在处理片段DNA时更有效,MPS测定被设计为确保扩增子大小小于140 bp。在MPS测定验证后,建立了一个由299个不同的snp组成的76个microhaps小组,分布在常染色体人类基因组中。分析了102个意大利人的基因型和单倍型频率。意大利种群各位点(Ae)有效等位基因数为1.926 ~ 6.187个,其中59个等位基因值大于3.0。匹配概率(PI)取值范围为0.055 ~ 0.345,累计PI值为11.763E-66。获得完整可靠的谱图,误差最小为0.05 ng。然后根据其DNA含量和降解水平选择真实的法医标本对mhhs面板进行验证。分析的大多数案例样品即使在降解的样品中也显示出完整或几乎完整的MH谱。为了评估MH档案在法医案件工作中的信息能力,对部分MH档案进行了概率基因分型。由此得出的似然比值范围为7.84E+09 ~ 2.70E+34,从而为案例样本的遗传图谱来自参考样本的假设提供了极其有力的支持。利用来自意大利人群样本的等位基因频率进行的成对亲属关系模拟表明,完全和半兄弟姐妹关系可以很容易地从不相关的个体中区分出来。为了评估76个MH面板在祖先信息方面的效用,还提出了PCA和STRUCTURE分析,将意大利安科纳新收集的样本与1000基因组计划的26个群体进行了比较。分析结果证实了这些短微单倍型在分型中具有高灵敏度的有效性,这些样品具有高度降解的DNA,通常在法医案件中遇到。
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引用次数: 0
MHappaMundi: A custom AmpliSeq microhaplotype panel for ancestry inference MHappaMundi:用于祖先推断的自定义AmpliSeq微单倍型面板
IF 3.1 2区 医学 Q2 GENETICS & HEREDITY Pub Date : 2025-11-12 DOI: 10.1016/j.fsigen.2025.103389
Pedro Rodrigues , Nádia Pinto , Maria João Prata , Rodrigo Flores-Espinoza , Germán Burgos , Hirohaki Nakanishi , Jamila A. Perini , Paulo Cesar Basta , Claus Børsting , Leonor Gusmão , Vania Pereira
Recent advancements in massively parallel sequencing technologies have led to the exploration of a new class of genetic markers called microhaplotypes (MHs). MHs exhibit unique characteristics that highlight their potential as viable alternatives to STRs and SNPs in addressing challenges commonly faced in forensic investigations. Different studies have detailed the development of MH panels for distinct purposes in forensics (e.g., human identification, mixture deconvolution, kinship testing, or biogeographic ancestry inference). However, MH panels with the sole purpose of ancestry inference are scarce and show some limitations that hinder a broader acceptance within the community. A new ancestry-informative MH panel, named MHappaMundi, was developed with the specific aim of differentiating Sub-Saharan African, European, South Asian, East Asian, and Native American ancestries. The selection method involved computing pairwise FST for all the MHs present in the MicroHapDB database between all pairs of continental groups, based on the 1000 Genomes Project (1kGP) populations. This approach aimed to establish a final panel ensuring balanced genetic distances between each population pair. From this selection method, 100 MHs were recruited for the panel. The performance of MHappaMundi was assessed by sequencing 147 European (Danes and Portuguese), 120 East Asian (Mainland and Okinawan Japanese), and 101 Native American (Brazilian and Ecuadorian) individuals on the Ion GeneStudio™ S5 System. A total of 8 loci were excluded due to insufficient read depth or technical inconsistencies. The final panel included 92 MHs and 466 allele-defining SNPs. Population genetic clustering was evaluated through STRUCTURE analysis, Principal Component Analysis, and Multidimensional scaling for the genotyped populations from this study and available online data from the 1kGP and Middle Eastern populations. In these analyses, the panel demonstrated great effectiveness in separating the five continental groups, particularly the Europeans and South Asians, which had presented challenges in previous MH ancestry panels. Moreover, the panel revealed an effective estimation of ancestry proportions in admixed individuals. In conclusion, the MHappaMundi serves as a potential asset for ancestry inference in forensic and population genetics.
近年来,大规模平行测序技术的进步导致了一种称为微单体型(MHs)的新型遗传标记的探索。MHs表现出独特的特征,突出了它们作为STRs和snp的可行替代品在解决法医调查中普遍面临的挑战方面的潜力。不同的研究详细介绍了MH面板在法医鉴定中的不同用途(例如,人类鉴定、混合反褶积、亲属关系检测或生物地理血统推断)。然而,以祖先推断为唯一目的的MH面板很少,并且显示出一些限制,阻碍了社区内更广泛的接受。一个名为MHappaMundi的新的提供祖先信息的MH小组被开发出来,其具体目的是区分撒哈拉以南非洲、欧洲、南亚、东亚和美洲原住民的祖先。选择方法包括基于1000基因组计划(1kGP)群体,计算MicroHapDB数据库中所有对大陆群体之间所有mh的成对FST。这种方法旨在建立一个最终的面板,确保每个种群对之间的遗传距离平衡。通过这种选择方法,招募了100名医务人员加入专家组。MHappaMundi的表现通过在Ion GeneStudio™S5系统上对147个欧洲人(丹麦人和葡萄牙人)、120个东亚人(大陆和冲绳日本人)和101个美洲原住民(巴西人和厄瓜多尔人)进行测序来评估。由于读取深度不足或技术不一致,共有8个位点被排除。最后一组包括92个mh和466个等位基因定义snp。通过结构分析、主成分分析和多维标度对来自本研究的基因分型群体和来自1kGP和中东人群的在线数据进行群体遗传聚类评估。在这些分析中,该小组在分离五个大陆群体方面表现出了极大的有效性,特别是欧洲人和南亚人,这在以前的MH祖先小组中提出了挑战。此外,该小组还揭示了对混合个体祖先比例的有效估计。总之,MHappaMundi可以作为法医和群体遗传学中祖先推断的潜在资产。
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引用次数: 0
Multi-kingdom microbiota dynamics in exposed saliva: Integrating relative and absolute abundance across bacteria and fungi 暴露唾液中的多界微生物群动态:整合细菌和真菌的相对和绝对丰度
IF 3.1 2区 医学 Q2 GENETICS & HEREDITY Pub Date : 2025-11-11 DOI: 10.1016/j.fsigen.2025.103390
Linying Ye , Jiaqian Le , Jieyu Du , Litao Huang , Weibin Wu , Mingyue Zhao , Quyi Xu , Changhui Liu , Chengliang Yang , Chao Liu , Ling Chen
As an important body fluid of the human body, saliva harbors a diverse microbial community, yet the dynamic succession of its microbiota following environmental exposure remains incompletely understood. Most current studies focus solely on relative abundance and community structure derived from sequencing, which may lead to misinterpretation of microbial dynamics. Moreover, existing research has almost exclusively centered on bacterial communities, largely overlooking the role of fungi. In this study, we conducted a 90-day exposure experiment in two environments (an incubator and an indoor setting) and used 16S rRNA gene and ITS absolute quantification sequencing to characterize the structure and abundance of bacterial and fungal communities. Despite prolonged environmental exposure, core bacterial genera in saliva, such as Streptococcus, Actinomyces, Rothia, Neisseria, Veillonella, and Prevotella, persisted in the samples. An interaction between salivary and environmental bacterial communities was observed, which strengthened over time. Relative and absolute abundance analyses revealed different patterns: relative abundance suggested a moderately stable community structure with individual specificity, whereas absolute quantification demonstrated a significant decrease in total bacterial load over time. Fungal communities were nearly undetectable in fresh saliva but became detectable after 25 days of exposure in the incubator and subsequently increased in abundance, dominated by Aspergillus. In contrast to the significant decline in bacterial absolute abundance over time, fungi exhibited a continuous increase, with a negative correlation between the two. Relative abundance was more effective for individual identification, while absolute abundance performed better in time since deposition (TsD) estimation. Further incorporation of fungal data enhanced the accuracy of the TsD prediction model, as indicated by a mean absolute error (MAE) of 7.485 days and an R² of 0.905, highlighting the advantage of multi-kingdom microbial analysis.
唾液作为人体重要的体液,蕴藏着多种多样的微生物群落,但其微生物群在环境暴露后的动态演替尚不完全清楚。目前大多数研究只关注测序所得的相对丰度和群落结构,这可能导致对微生物动力学的误解。此外,现有的研究几乎完全集中在细菌群落上,很大程度上忽视了真菌的作用。在本研究中,我们在两种环境(培养箱和室内环境)中进行了90天的暴露实验,并使用16S rRNA基因和ITS绝对定量测序来表征细菌和真菌群落的结构和丰度。尽管长时间暴露在环境中,唾液中的核心细菌属,如链球菌、放线菌、罗氏菌、奈瑟菌、细孔菌和普雷沃氏菌,在样品中持续存在。观察到唾液和环境细菌群落之间的相互作用,这种相互作用随着时间的推移而加强。相对丰度和绝对丰度分析揭示了不同的模式:相对丰度表明具有个体特异性的中等稳定的群落结构,而绝对量化显示随着时间的推移,总细菌负荷显著减少。真菌群落在新鲜唾液中几乎检测不到,但在培养箱中暴露25天后可以检测到,随后丰度增加,以曲霉为主。与细菌绝对丰度随时间的显著下降相反,真菌的绝对丰度呈现出持续的增加,两者之间呈负相关。相对丰度在个体识别上更有效,而绝对丰度在沉积时间(TsD)估计上表现更好。进一步纳入真菌数据提高了TsD预测模型的准确性,平均绝对误差(MAE)为7.485天,R²为0.905,突出了多界微生物分析的优势。
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引用次数: 0
A proof-of-principle study: Species identification based on mitochondrial 12S rRNA gene using QNome nanopore sequencing 一项原理验证研究:基于线粒体12S rRNA基因的物种鉴定,使用QNome纳米孔测序。
IF 3.1 2区 医学 Q2 GENETICS & HEREDITY Pub Date : 2025-11-10 DOI: 10.1016/j.fsigen.2025.103388
Mengyao Zhao , Haowen Song , Yangyang Zheng , Liu Qin , Xueyuan Liu , Shiying Deng , Jing Liu , Ling Chen , Weian Du , Zheng Wang
Accurate species identification can provide crucial evidence to aid criminal investigations and preserve species diversity. DNA barcoding is an effective tool to ascertain the origin of degraded, trace, or processed samples, and the mitochondrial 12S rRNA gene serving as a potential marker due to its low intraspecific variation and high interspecific variation. QNome nanopore sequencing, with its flexible read lengths, real-time analysis, and portable device size, offers new means for species identification. In this proof-of-principle study, we collected 12S rRNA gene reference sequences of 120 common species from Genbank genetic sequence database and conducted sequence similarity analysis to evaluate the applicability of this genetic marker. The automated species identification pipeline, ClassIdent, based on QNome nanopore sequencing of the 12S rRNA gene, was subsequently developed as an open-source tool. We sequenced 60 tested samples from different animals using the QNome sequencer, and ClassIdent was employed to detect matching proportions and generate consensus sequences. Out of the 60 tested samples, 53 matched the sequences of their corresponding species, while the remaining seven matched sequences from closely related species within the same genus or family. The average proportion of sequencing reads assigned to the reference sequence was 95.66 %, with an average sequence similarity of 99.11 %. The consensus sequences generated by ClassIdent demonstrated high accuracy, showing an average sequence similarity of 99.34 % compared to Sanger sequences. Overall, this pipeline demonstrated the potential of using 12S rRNA gene for species identification via Qnome nanopore sequencing. However, further research is needed to incorporate more DNA barcoding markers or to detect the whole mitochondrial genome based on long read sequencing technology.
准确的物种鉴定可以为刑事调查和保护物种多样性提供重要证据。DNA条形码是确定降解、痕量或加工样品来源的有效工具,线粒体12S rRNA基因由于其低种内变异和高种间变异而成为潜在的标记。QNome纳米孔测序具有灵活的读取长度,实时分析和便携式设备尺寸,为物种鉴定提供了新的手段。在这项原理验证性研究中,我们从Genbank基因序列数据库中收集了120个常见物种的12S rRNA基因参考序列,并进行了序列相似性分析,以评估该遗传标记的适用性。基于QNome纳米孔12S rRNA基因测序的自动物种鉴定管道ClassIdent随后被开发为开源工具。我们使用QNome测序仪对来自不同动物的60个测试样本进行测序,并使用ClassIdent检测匹配比例并生成一致序列。在60个测试样本中,53个与对应物种的序列相匹配,而其余7个与同一属或科中密切相关的物种的序列相匹配。测序reads分配给参考序列的平均比例为95.66 %,平均序列相似度为99.11 %。ClassIdent生成的一致性序列具有较高的准确性,与Sanger序列相比,平均序列相似度为99.34 %。总之,该管道显示了通过Qnome纳米孔测序使用12S rRNA基因进行物种鉴定的潜力。然而,进一步的研究需要纳入更多的DNA条形码标记或基于长读测序技术检测整个线粒体基因组。
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引用次数: 0
Bioinformatic processing of whole genome sequencing data with Tapir 貘全基因组测序数据的生物信息学处理
IF 3.1 2区 医学 Q2 GENETICS & HEREDITY Pub Date : 2025-11-08 DOI: 10.1016/j.fsigen.2025.103387
August E. Woerner , Briana N. Stowe , Jonathan L. King , Benjamin Crysup , Meng Huang , Michael D. Coble
Whole genome sequencing (WGS) has powerful potential to aid forensic investigations. The scale and complexity of WGS, however, present sizable barriers to its widespread adoption. In particular, some form of standardized pipeline is needed to provide certainty in and an accounting of the final genotypes. To that end, we introduce Tapir (two-step analysis pipeline for investigative reporting). Tapir is a reproducible end-to-end scientific workflow that ingests raw WGS data from Illumina platforms (i.e., BCL format) and produces a GEDmatch-compatible genotyping result. Tapir combines many extant (and some custom) tools for forensic assessments of WGS data, including two modern and powerful probabilistic genotyping algorithms: one that relies on genotype refinement/imputation (GLIMPSE) and another that uses maximum likelihood (BCFtools). Additionally, Tapir provides summary and inferential statistics relevant to the forensic audience (e.g., breadth and depth of coverage, estimation of mixture status). Tapir comes with both mamba- and conda-compatible YAML environment files and has been packaged in a virtual machine image that allows it to run on commodity x86-64 computers, including Microsoft Windows.
全基因组测序(WGS)在辅助法医调查方面具有强大的潜力。然而,WGS的规模和复杂性对其广泛采用构成了相当大的障碍。特别是,需要某种形式的标准化管道来提供最终基因型的确定性和核算。为此,我们介绍了Tapir(调查报告的两步分析管道)。Tapir是一个可重复的端到端科学工作流程,从Illumina平台(即BCL格式)摄取原始WGS数据,并产生gedmatch兼容的基因分型结果。Tapir结合了许多现有的(和一些定制的)工具来对WGS数据进行法医评估,包括两种现代且功能强大的概率基因分型算法:一种依赖于基因型优化/imputation (GLIMPSE),另一种使用最大似然(BCFtools)。此外,Tapir提供与法医受众相关的总结和推断统计(例如,覆盖的广度和深度,混合状态的估计)。Tapir附带了mamba和conda兼容的YAML环境文件,并打包在虚拟机映像中,允许它在商用x86-64计算机上运行,包括Microsoft Windows。
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引用次数: 0
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Forensic Science International-Genetics
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