Forensic Science International-Genetics最新文献

{"title":"Nanopore sequencing of MiniHap biomarkers for forensic DNA mixture deconvolution: A proof-of-principle study","authors":"Jian Zhang ,&nbsp;Xiaoting Mo ,&nbsp;Weiqiang Li ,&nbsp;Cheng Cheng ,&nbsp;Yu Feng ,&nbsp;Yiwen Zhang ,&nbsp;Shengbin Li","doi":"10.1016/j.fsigen.2025.103272","DOIUrl":"10.1016/j.fsigen.2025.103272","url":null,"abstract":"<div><div>Mixture deconvolution remains one of the major challenges in the field of forensic science. Currently, genetic markers are used and studied in the field of forensic genetics, including short tandem repeat (STR), insertion/deletion polymorphism (InDel), single nucleotide polymorphism (SNP), InDel closely linked to STR (DIP-STR), SNP closely linked to STR (SNP-STR), InDel closely linked to SNP (DIP-SNP) and microhaplotype (MH), all of which have been studied for DNA mixture analysis and have their own advantages and disadvantages. Mini-haplotype (MiniHap), as a novel haplotype genetic marker, contains 5 or more SNPs. A previous study has substantiated its significant high polymorphic characteristics, and it is expected to have potential applications in individual identification, paternity testing, ancestry inference, and mixture deconvolution. In this study, we first screened 22 MiniHaps with high polymorphism potential and constructed a panel based on the QNome nanopore sequencing device. Subsequently, we tested 100 unrelated Chinese Han individuals to evaluate the sequencing performance, allele (haplotype) frequencies, effective number of alleles (A_e) and forensic parameters of the 22 MiniHaps markers included in this novel assay. Next, a series of mixture simulations (two- or three-person mixtures with mixing ratios of 1:1–1:99 or 1:1:1–1:8:1) based on three standard materials (9947 A, 9948 and 2800 M) were detected by this MiniHap panel to explore its potential for DNA mixture deconvolution. The average A_e value was 10.9574, and 52.38 % of MiniHap loci had A_e values greater than 12.0000. The mean values of genetic diversity (GD) and power of discrimination (PD) were 0.8717 and 0.9457, respectively. Notably, most MiniHaps (85.71 %) had PD values exceeding 0.9000. The combined match probability (CMP) and combined power of exclusion (CPE) of this MiniHap panel were 4.4505 × 10⁻³¹ and 0.999999999999999996653, respectively. Moreover, the results of mixture analysis demonstrated that this MiniHap panel allowed detecting the components of minor contributor (s) even in imbalanced mixture samples, with detection limits of 1:39 and 1:8:1 for two- and three-person mixtures, respectively. In summary, MiniHap markers have remarkable application potential in mixture deconvolution, and it is necessary to conduct in-depth research on MiniHap markers for mixture analysis in the future.</div></div>","PeriodicalId":50435,"journal":{"name":"Forensic Science International-Genetics","volume":"78 ","pages":"Article 103272"},"PeriodicalIF":3.2,"publicationDate":"2025-03-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143644191","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Are microhaplotypes derived from the 1000 Genomes Project reliable for forensic purposes?","authors":"Yifan Wei ,&nbsp;Xi Li ,&nbsp;Qiang Zhu ,&nbsp;Tiantian Shan ,&nbsp;Haoyu Wang ,&nbsp;Xuan Dai ,&nbsp;Yufang Wang ,&nbsp;Ji Zhang","doi":"10.1016/j.fsigen.2025.103273","DOIUrl":"10.1016/j.fsigen.2025.103273","url":null,"abstract":"<div><div>Microhaplotypes (MHs) have emerged as an important genetic marker in forensic genetics. However, most studies have overlooked the potential for phasing errors within microhaplotypes based on the 1000 Genome Project (1kGP), which may impact the evaluation of various forensic parameters and lead to misleading results. In this study, we constructed a dense and extensive set of MHs across the human genome, using the expanded 1000 Genomes Project data aligned to GRCh38 reference genome. We applied three different SNP minor allele frequency (MAF) thresholds (0, 0.01, and 0.05) to evaluate the reliability of these markers. Utilizing pedigree data from 18 populations, which included a total of 602 trios, we scanned for and confirmed suspected phasing error events at these MH loci. We also sequenced 50 MHs for one trio of the Southern Han Chinese (CHS) population to further investigate these discrepancies. The results revealed the presence of phasing errors in MHs from 1kGP when analyzed using targeted enrichment and next-generation sequencing. The probability of suspected phasing error events was strongly and positively correlated with the effective number of alleles (Ae) and informativeness (In) of the markers. Additionally, these mismatch probabilities varied significantly across different continental populations. Additionally, when selecting loci, applying MAF filtering and avoiding regions such as the MHC can reduce the occurrence of such events to some extent. Based on these findings, we suggest that relying solely on sequencing data of the 1kGP for forensic purpose may be risky. A thorough investigation of the true forensic parameters of MHs is essential to ensure their reliability in forensic applications.</div></div>","PeriodicalId":50435,"journal":{"name":"Forensic Science International-Genetics","volume":"78 ","pages":"Article 103273"},"PeriodicalIF":3.2,"publicationDate":"2025-03-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143643609","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genetic predictions of eye and hair colour in the Danish population","authors":"Amaia Cabrejas-Olalla ,&nbsp;Frank G. Jørgensen ,&nbsp;Jade Y. Cheng ,&nbsp;Peter C. Kjærgaard ,&nbsp;Mikkel H. Schierup ,&nbsp;Thomas Mailund ,&nbsp;Georgios Athanasiadis","doi":"10.1016/j.fsigen.2025.103267","DOIUrl":"10.1016/j.fsigen.2025.103267","url":null,"abstract":"<div><div>Genetic predictions of eye and hair colour are prominent examples of forensic DNA phenotyping that can help resolve criminal cases. The advent of high-throughput genotyping technologies in forensic genetics opens up the possibility of applying polygenic risk scores in forensic settings. In this work, we compare the performance of HIrisPlex with PRSice-2 in predicting eye and hair colour to gain insights into the relative benefits of new approaches. Predictions were carried out on 584 Danish high school students for which genetic and self-reported phenotype data were available. Prediction of brown eye colour was very accurate (AUC = 0.98), followed by blue eye colour (AUC = 0.82), while it failed for intermediate eye colour (AUC = 0.57). As for hair colour, red and black were overall better predicted than blond and brown, and PRSice-2 performed better in all but the black hair colour. Despite the limitations of the study, HIrisPlex exhibited its usual high performance in the prediction of brown and blue eye colour, as well as red and black hair colour. However, PRSice-2 offered overall improvements in hair colour prediction over HIrisPlex suggesting that there is room for improvement in forensic DNA phenotyping by using polygenic risk scores.</div></div>","PeriodicalId":50435,"journal":{"name":"Forensic Science International-Genetics","volume":"78 ","pages":"Article 103267"},"PeriodicalIF":3.2,"publicationDate":"2025-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143577906","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Species level and SNP profiling of skin microbiome improve the specificity in identifying forensic fluid and individual","authors":"Litao Huang ,&nbsp;Jieyu Du ,&nbsp;Linying Ye ,&nbsp;Yangyang Zheng ,&nbsp;Xueyuan Liu ,&nbsp;Enping Huang ,&nbsp;Jiaqian Le ,&nbsp;Xuan Huang ,&nbsp;Weian Du ,&nbsp;Chao Liu ,&nbsp;Ling Chen","doi":"10.1016/j.fsigen.2025.103256","DOIUrl":"10.1016/j.fsigen.2025.103256","url":null,"abstract":"<div><div>Human skin possesses individual and body fluid-specific microbial signatures potentially useful for forensic identification. Previous studies mostly attribute individuals based on the relative abundance of microbiota at single time point, however fluctuations in taxonomy and phylogenetic structure may cause this to be unreliable. In this study, we assessed the skin microbiome of individuals at consecutive time-point from fingers, palm, arm and forehead sites using full-length 16S rRNA gene sequencing. At the species level, hand samples (fingers, palm, arm) differed significantly from forehead microbes. Additionally, skin flora of the present study differed significantly from the dominant species that have been reported for saliva, feces, and vaginal secretions samples. ANOSIM analysis of all skin samples showed that inter-individual differences were greater than intra-individual differences, yet accuracy of individual identification was only 52.5 %. At the microbial gene level, three machine learning models based on single nucleotide polymorphism (SNP) profiles of <em>Cutibacterium acnes</em> resulted in accurate classification of more than 97.5 % individuals. These results indicate that consideration of bacterial SNP profiling may provide new directions for forensic identification and may have potential applications in body fluid identification and individual identification in forensic.</div></div>","PeriodicalId":50435,"journal":{"name":"Forensic Science International-Genetics","volume":"78 ","pages":"Article 103256"},"PeriodicalIF":3.2,"publicationDate":"2025-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143592013","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The ReAct project: Bayesian networks for assessing the value of the results given activity level propositions","authors":"Peter Gill,&nbsp;Tacha Hicks,&nbsp;Angel Carracedo","doi":"10.1016/j.fsigen.2025.103223","DOIUrl":"10.1016/j.fsigen.2025.103223","url":null,"abstract":"","PeriodicalId":50435,"journal":{"name":"Forensic Science International-Genetics","volume":"76 ","pages":"Article 103223"},"PeriodicalIF":3.2,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142967653","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Corrigendum to “A preliminary report on the exploration of salivary bacterial diversity by the multiplex SNaPshot assay” [Forensic Sci. Int.: Genet. 70 (2024) 103032]","authors":"Shuangshuang Wang ,&nbsp;Feng Song ,&nbsp;Xiangnan Guo ,&nbsp;Liya Gu ,&nbsp;Weijia Tan ,&nbsp;Peiyan Wu ,&nbsp;Weibo Liang ,&nbsp;Haibo Luo ,&nbsp;Yanyun Wang","doi":"10.1016/j.fsigen.2025.103227","DOIUrl":"10.1016/j.fsigen.2025.103227","url":null,"abstract":"","PeriodicalId":50435,"journal":{"name":"Forensic Science International-Genetics","volume":"76 ","pages":"Article 103227"},"PeriodicalIF":3.2,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143018923","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A biogeographical ancestry inference pipeline using PCA-XGBoost model and its application in Asian populations","authors":"Chunnain Wang ,&nbsp;Shuaiqi Wang ,&nbsp;Yiru Zhao ,&nbsp;Jun Liu ,&nbsp;Deqin Zhang ,&nbsp;Fuyang Wang ,&nbsp;Hong Fan ,&nbsp;Caixia Li ,&nbsp;Li Jiang","doi":"10.1016/j.fsigen.2025.103239","DOIUrl":"10.1016/j.fsigen.2025.103239","url":null,"abstract":"<div><div>Biogeographical ancestry (BGA) inference plays a crucial role in genetics, anthropology, forensic science, and medical research. Current methods like principal component analysis (PCA) and ADMIXTURE, based on single nucleotide polymorphisms, are commonly used. Here, we introduce a bio-geographical ancestry inference pipeline that integrates prior population structure and clustering. Our pipeline first analyzes genetic structure on cleaned data to obtain optimal parameters and classification model labels. An XGBoost (eXtreme Gradient Boosting) classification model is constructed using principal components from PCA, and model predictions are evaluated with LR (likelihood ratio). The pipeline was applied to a dataset of Asian populations, with a first prediction accuracy of 96.27 % achieved. The LR-based evaluation accuracy reached 98.96 %, showing an improvement of 2.69 % with the introduction of LR assessment. This highlights the robust predictive capability of our pipeline and the improved accuracy in evaluation with LR. This successful application will benefit genetic research, human history studies, and criminal investigations. Additionally, the pipeline's versatility allows application to new datasets.</div></div>","PeriodicalId":50435,"journal":{"name":"Forensic Science International-Genetics","volume":"77 ","pages":"Article 103239"},"PeriodicalIF":3.2,"publicationDate":"2025-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143549849","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"DNA methylation-based semen age prediction using the markers identified in Koreans and Europeans","authors":"Ji Eun Lee ,&nbsp;Sohee Cho ,&nbsp;Moon Hyun So ,&nbsp;Hwan Young Lee","doi":"10.1016/j.fsigen.2025.103243","DOIUrl":"10.1016/j.fsigen.2025.103243","url":null,"abstract":"<div><div>In the forensic field, sexual assaults have consistently been the important issue, with semen frequently serving as the primary evidence. When the suspect is unidentified, estimating the perpetrator’s age using investigating semen can provide important information. The VISAGE consortium conducted research on the semen age prediction focused on European semen samples, but the age prediction model has remained undisclosed. Additionally, several studies have reported methylation differences across populations, indicating that the European semen age prediction model might not be broadly applicable to other groups. A study did explore semen age prediction in Koreans using Illumina’s Infinium Methylation450K BeadChip array, however recent developments in technology could enhance this approach. To address this, we conducted a study on Korean males aged 18–70 years. We initially analyzed 49 samples utilizing Illumina’s Infinium MethylationEPIC BeadChip array to identify age-related CpG sites. From this analysis, we identified 9 age-related CpG markers, excluding one due to difficulties in locus-specific analysis. As a result, we used 11 markers including 8 newly identified CpGs from the EPIC array and 3 CpG markers from previous research utilizing the SNaPshot assay. Furthermore, we incorporated 13 CpG markers from the European study to analyze a total of 159 semen samples using the Illumina Nextera MPS system. This approach enabled us to test age-related markers identified in Europeans within the Korean population and to construct a more accurate age prediction model using markers from both Korean and European sources.</div></div>","PeriodicalId":50435,"journal":{"name":"Forensic Science International-Genetics","volume":"77 ","pages":"Article 103243"},"PeriodicalIF":3.2,"publicationDate":"2025-02-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143519577","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Differences of tsRNA expression profiles efficiently discriminate monozygotic twins in peripheral blood","authors":"Meihui Tian ,&nbsp;Xiangnian Liu ,&nbsp;Danyang Wang ,&nbsp;Yuxi Wang ,&nbsp;Siwen Wang ,&nbsp;Jiayi Wei ,&nbsp;Dawei Guan ,&nbsp;Jun Yao","doi":"10.1016/j.fsigen.2025.103242","DOIUrl":"10.1016/j.fsigen.2025.103242","url":null,"abstract":"<div><div>Monozygotic twins (MZTs) share nearly identical genomic DNA sequences, making traditional forensic short tandem repeats (STR) genotyping methods ineffective for distinguishing between them. In recent years, the use of epigenetic factors in forensic applications has gained traction. The dynamic epigenetic factors can be influenced by inherited traits or acquired environmental factors. This study analyzed the expression profiles of transfer RNA-derived small RNAs (tsRNAs) in peripheral blood from four pairs of adult MZTs using Panoramic RNA Display by Overcoming RNA Modification Aborted Sequencing (PANDORA-seq). Differentially expressed tsRNAs (DEtsRNAs) were identified and validated using the reverse-transcriptase quantitative polymerase chain reaction (RT-qPCR) and droplet digital PCR (ddPCR) in both adult and newborn MZTs. The study also evaluated the longitudinal temporal stability, resistance to degradation, and suitability of DEtsRNAs for aged bloodstains. A total of 8795 expressed tsRNAs were identified in the four pairs of adult MZTs by PANDORA-seq. After screening with a normalized | log₂ (fold change) | &gt; 1 and an adjusted p-value &lt; 0.05, 10, 187, and 1520 DEtsRNAs were shared by 4, 3, and 2 pairs of MZTs. RT-qPCR and ddPCR confirmed the expression of the 10 DEtsRNAs identified by PANDORA-seq. Six candidate tsRNAs (tRNA-Gly-GCC, tRNA-Leu-TAA, tRNA-Lys-CTT, tRNA-Val-AAC_5_end, tRNA-iMet-CAT_5_end, and tsRNA-3023a/b-PheGAA) were identified as effective discrimination markers, even in neonatal MZTs which are largely unaffected by environment factors. Forensic applicability assessment revealed that tRNA-Gly-GCC and tRNA-Leu-TAA remained detectable in the 180-day-series bloodstains, while tRNA-Lys-CTT, tRNA-Val-AAC_5_end, and tRNA-iMet-CAT_5_end were relatively stable after 15 times of freeze-thaw cycles. Additionally, tRNA-Gly-GCC and tRNA-Lys-CTT exhibited long-term stability, with consistent expression over six months. In conclusion, this study demonstrates that differential tsRNAs expression can serve as a novel biomarker for MZT identification in forensic medicine.</div></div>","PeriodicalId":50435,"journal":{"name":"Forensic Science International-Genetics","volume":"77 ","pages":"Article 103242"},"PeriodicalIF":3.2,"publicationDate":"2025-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143474994","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"SCN5A missense variants and their contribution to deaths in Sudden Unexplained Nocturnal Death Syndrome (SUNDS)","authors":"Aummarin Chaloemthanetphong ,&nbsp;Kiattawee Choowongkomon ,&nbsp;Wikanda Worrapitirungsi ,&nbsp;Nattachai Thangsiriskul ,&nbsp;Tikumphorn Sathirapatya ,&nbsp;Poonyapat Sukawutthiya ,&nbsp;Hasnee Noh ,&nbsp;Ashfaque Ahmed Kanhar ,&nbsp;Pagparpat Varrathyarom ,&nbsp;Irin Lertparinyaphorn ,&nbsp;Napapat Natthasumon ,&nbsp;Saknan Bongsebandhu-Phubhakdi ,&nbsp;Vichaya Auvichayapat ,&nbsp;Kornkiat Vongpaisarnsin","doi":"10.1016/j.fsigen.2025.103237","DOIUrl":"10.1016/j.fsigen.2025.103237","url":null,"abstract":"<div><div>Sudden Unexplained Nocturnal Death Syndrome (SUNDS), locally known as Lai-tai in Thailand, leads to sudden death during sleep in otherwise healthy young males. Cardiac arrhythmias, including Brugada syndrome (BrS) and Long QT syndrome (LQTS), are often implicated, with mutations in the <em>SCN5A</em> gene, encoding the Na_v1.5 sodium channel, strongly linked to both conditions. This study characterized postmortem SUNDS cases in Thailand and analyzed <em>SCN5A</em> gene variants using whole exome sequencing (WES) and molecular modeling. Forensic autopsies were performed on 98 SUNDS victims from August 2020 to February 2023. WES was applied to 98 SUNDS-related genes, filtering variants based on dbNSFP annotations and public databases like the 1000 Genomes Project. Three <em>SCN5A</em> variants (A665S, R179Q, and R965C) were detected in five cases (approximate for 5 %). One case of A665S, which was reported for the first time in Thailand, was discovered. The R179Q variant was identified in an additional case, but it did not have a substantial electrostatic surface impact on Na_v1.5. In contrast, the R965C variant, which is frequently associated with BrS, was discovered in three cases (approximate for 3 %). These results imply that <em>SCN5A</em> variants are involved in the pathogenesis of SUNDS and may provide valuable genetic markers for the purpose of diagnosis and prevention.</div></div>","PeriodicalId":50435,"journal":{"name":"Forensic Science International-Genetics","volume":"76 ","pages":"Article 103237"},"PeriodicalIF":3.2,"publicationDate":"2025-02-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143445146","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}