Forensic Science International-Genetics最新文献

{"title":"Improved understanding of sequence polymorphisms at 42 Y chromosome short tandem repeats for the Chinese Han population","authors":"Lei Miao ,&nbsp;Shuang Liu ,&nbsp;Kun-Peng Pan ,&nbsp;Rui-Lian Jiao ,&nbsp;Qian Zhang ,&nbsp;Tao-Yong Xu ,&nbsp;Shi-Yu Tong ,&nbsp;Ke-Lai Kang ,&nbsp;Jie Zhao ,&nbsp;Chi Zhang ,&nbsp;Kai-Di Wang ,&nbsp;An-Quan Ji ,&nbsp;Jian Wu ,&nbsp;Le Wang","doi":"10.1016/j.fsigen.2024.103181","DOIUrl":"10.1016/j.fsigen.2024.103181","url":null,"abstract":"<div><div>Y-chromosome short tandem repeat (Y-STR) is an important type of genetic markers in the human genome, widely used in molecular anthropology and forensic genetics. However, most Y-STR studies has been focused on the length-based variations resulting from differences in the number of repeat units. Less attention was paid to sequence-based Y-STR variations. Consequently, sequence-based variation characteristics of Y-STRs in Chinese populations remain insufficiently studied. In this study, targeted sequencing of 42 Y-STR loci was performed for 331 Chinese Han males (with an average sequencing depth of 612 ×), unveiling a total of 387 sequence allele types and their frequencies in the population. Repeat pattern variations were observed in seven loci containing multiple repeat units. Across all sequenced repeat and flanking regions, 46 single-nucleotide substitutions and insertion/deletion variations were identified, including 13 mutations not recorded in the dbSNP database. Twenty-seven previously unreported sequence-based alleles were identified. Additionally, differences in Y-STRs between the Chinese Han population and three American populations (African Americans, Caucasians, and Hispanics) were revealed from sequence-based data analysis. In summary, this study provides a detailed summary of the sequence features of 42 Y-STRs in the Chinese Han population, improving our understanding of Y-STRs and providing basic data of sequence variations for the application of Y-STRs.</div></div>","PeriodicalId":50435,"journal":{"name":"Forensic Science International-Genetics","volume":"75 ","pages":"Article 103181"},"PeriodicalIF":3.2,"publicationDate":"2024-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142697388","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":"Illicit drug distribution: Evaluation of DNA transfer between ziplock bags and capsules","authors":"Madison Nolan ,&nbsp;Adrian Linacre","doi":"10.1016/j.fsigen.2024.103182","DOIUrl":"10.1016/j.fsigen.2024.103182","url":null,"abstract":"<div><div>Powders containing illicit substances are frequently poured into capsules and then distributed in small bags to users, often via intermediaries. We report on the transfer of DNA between individuals involved in making, packing, and transporting capsules within ziplock bags (ZLB) via two pathways, each using 10 ZLBs. A two-person chain was created where participant A made and packed the capsules into ZLBs and participant C then carried the bags for four days. A three-person chain was devised where participant A made the capsules, participant B placed the capsules in bags, and participant C carried the bags. The ZLBs were sampled for DNA on the inside, the inner semi-protected portion of the opening, and the outside surface. The exterior of capsules were also sampled along with a storage container. DNA profiling using Verifiler™ Plus was performed with data deconvoluted by STRmix™. Informative DNA profiles were obtained from capsules despite evidence of DNA transfer from the capsules to both storage containers and the inside of the ZLB. The outside of ZLBs yielded complex mixtures, however, the inside of the bag and the exterior of capsules, which had greater protection, yielded profiles with predominately only one to two contributors. This highlights that the inside of the bags and exterior of capsules could be targeted to identify individuals involved in the early packaging stages of the illicit drug pathway while the outside provided more information on recent handling.</div></div>","PeriodicalId":50435,"journal":{"name":"Forensic Science International-Genetics","volume":"75 ","pages":"Article 103182"},"PeriodicalIF":3.2,"publicationDate":"2024-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142697387","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 multi-class support vector machine classification model based on 14 microRNAs for forensic body fluid identification","authors":"Suyu Li ,&nbsp;Jing Liu ,&nbsp;Wei Xu ,&nbsp;Shuyuan Zhang ,&nbsp;Mengyao Zhao ,&nbsp;Lu Miao ,&nbsp;Minxiao Hui ,&nbsp;Yuan Wang ,&nbsp;Yiping Hou ,&nbsp;Bin Cong ,&nbsp;Zheng Wang","doi":"10.1016/j.fsigen.2024.103180","DOIUrl":"10.1016/j.fsigen.2024.103180","url":null,"abstract":"<div><div>MicroRNAs (miRNAs) are promising biomarkers for forensic body fluid identification owing to their small size, stability against degradation, and differential expression patterns. However, the expression of most body fluid-miRNAs is relative (differentially expressed in certain body fluids) rather than absolute (exclusively expressed in a specific body fluid). Moreover, different body fluids contain heterogeneous cell types, complicating their identification. Therefore, appropriate normalization strategies to eliminate non-biological variations and robust models to interpret expression levels accurately are necessary prerequisites for applying miRNAs in body fluid identification. In this study, the expression stability of six candidate reference genes (RGs) across five body fluids was validated using geNorm, NormFinder, BestKeeper and RankAggreg, and the most suitable combination of RGs (hsa-miR-484 and hsa-miR-191–5p) was identified under our experimental conditions. Subsequently, we systematically evaluated the expression patterns of the 28 most promising body fluid-specific miRNA markers using TaqMan RT-qPCR and selected the optimal combination of markers (12 miRNAs) to establish a multi-class support vector machine (MSVM) classification model. An independent test set (60 samples) was used to validate the accuracy of the proposed classification model, while an additional 30 casework samples were used to assess its robustness. The MSVM model accurately predicted the body fluid origin for almost all (59/60) single-source samples. Moreover, this model demonstrated the capability to identify aged forensic samples and to predict the primary components of mixed stains to a certain extent. In summary, this study presented a miRNA-based MSVM classification model for forensic body fluid identification using the qPCR platform. However, extensive validation, especially inter-laboratory collaborative exercises, is necessary before miRNA can be routinely applied in forensic identification practice.</div></div>","PeriodicalId":50435,"journal":{"name":"Forensic Science International-Genetics","volume":"75 ","pages":"Article 103180"},"PeriodicalIF":3.2,"publicationDate":"2024-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142697389","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":"A molecular framework for enhancing quality control and sample integrity in forensic genome sequencing","authors":"Steven A. Bates ,&nbsp;Bruce Budowle ,&nbsp;Lee Baker ,&nbsp;Kristen Mittelman ,&nbsp;David Mittelman","doi":"10.1016/j.fsigen.2024.103179","DOIUrl":"10.1016/j.fsigen.2024.103179","url":null,"abstract":"<div><div>DNA typing is essential for identifying crime scene evidence and missing and unknown persons. Molecular tags historically have been incorporated into DNA typing reactions to improve result interpretation. Molecular tags like barcodes and unique identifiers are integral to MPS, aiding in sample tracking and error detection. However, these tags do not fully leverage sequence variation to enhance quality control. To address this need, molecular etches, which are synthetic oligonucleotides that serve as an internal molecular information management system, are introduced. Molecular etches encode detailed sample information improving sample workflow history, tracking, contamination detection, and authenticity verification. Validation studies demonstrate the robustness of molecular etches in genomic sequencing, making them a valuable quality tool for forensic DNA analysis.</div></div>","PeriodicalId":50435,"journal":{"name":"Forensic Science International-Genetics","volume":"75 ","pages":"Article 103179"},"PeriodicalIF":3.2,"publicationDate":"2024-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142696122","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":"Benchmarking for genotyping and imputation using degraded DNA for forensic applications across diverse populations","authors":"Elena I. Zavala ,&nbsp;Rori V. Rohlfs ,&nbsp;Priya Moorjani","doi":"10.1016/j.fsigen.2024.103177","DOIUrl":"10.1016/j.fsigen.2024.103177","url":null,"abstract":"<div><div>Advancements in sequencing and laboratory technologies have enabled forensic genetic analysis on increasingly low quality and degraded DNA samples. However, existing computational methods applied to genotyping and imputation for generating DNA profiles from degraded DNA have not been tested for forensic applications. Here we simulated sequencing data of varying qualities–coverage, fragment lengths, and deamination patterns–from forty individuals of diverse genetic ancestries. We used this dataset to test the performance of commonly used genotype and imputation methods (SAMtools, GATK, ATLAS, Beagle, and GLIMPSE) on five different SNP panels (MPS-plex, FORCE, two extended kinship panels, and the Human Origins array) that are used for forensic and population genetics applications. For genome mapping and variant calling with degraded DNA, we find use of parameters and methods (such as ATLAS) developed for ancient DNA analysis provides a marked improvement over conventional standards used for next generation sequencing analysis. We find that ATLAS outperforms GATK and SAMtools, achieving over 90 % genotyping accuracy for the four largest SNP panels with coverages greater than 10X. For lower coverages, decreased concordance rates are correlated with increased rates of heterozygosity. Genotype refinement and imputation improve the accuracy at lower coverages by leveraging population reference data. For all five SNP panels, we find that using a population reference panel representative of worldwide populations (e.g., the 1000 Genomes Project) results in increased genotype accuracies across genetic ancestries, compared to ancestry-matched population reference panels. Importantly, we find that the low SNP density of commonly used forensics SNP panels can impact the reliability and performance of genotype refinement and imputation. This highlights a critical trade-off between enhancing privacy by using panels with fewer SNPs and maintaining the effectiveness of genomic tools. We provide benchmarks and recommendations for analyzing degraded DNA from diverse populations with widely used genomic methods in forensic casework.</div></div>","PeriodicalId":50435,"journal":{"name":"Forensic Science International-Genetics","volume":"75 ","pages":"Article 103177"},"PeriodicalIF":3.2,"publicationDate":"2024-11-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142697382","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":"Estimation of population-specific values of theta for PowerPlex Y23 profiles","authors":"John S. Buckleton ,&nbsp;Taryn O. Hall ,&nbsp;Jo-Anne Bright ,&nbsp;Michael C. Yung ,&nbsp;Jérôme Goudet ,&nbsp;Maarten Kruijver ,&nbsp;Bruce S. Weir","doi":"10.1016/j.fsigen.2024.103175","DOIUrl":"10.1016/j.fsigen.2024.103175","url":null,"abstract":"<div><div>We examine 31,011 PPY23 profiles at the population, metapopulation and world levels. Most haplotypes appear only once but a few have higher counts, including a set of 23 matching profiles in Delhi, India and a set of 16 matching profiles in Burkina Faso with one additional matching American African profile. We estimate <span><math><msub><mrow><mi>F</mi></mrow><mrow><mi>S</mi><mi>T</mi></mrow></msub></math></span>values to be used as “theta” <em>(θ</em>) in match probability calculations, following the method we used in our earlier survey of autosomal STR data. Match probability estimates using <span><math><msub><mrow><mover><mi>F</mi><mo>ˆ</mo></mover></mrow><mrow><mi>S</mi><mi>T</mi></mrow></msub></math></span> or the κ method of Brenner for a previously unseen profile are similar but differ for any profile previously seen.</div></div>","PeriodicalId":50435,"journal":{"name":"Forensic Science International-Genetics","volume":"75 ","pages":"Article 103175"},"PeriodicalIF":3.2,"publicationDate":"2024-11-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142696128","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":"Ethical and legal reflections on secondary research using genetic data acquired for criminal investigation purposes","authors":"Martin Zieger ,&nbsp;Nathan Scudder","doi":"10.1016/j.fsigen.2024.103178","DOIUrl":"10.1016/j.fsigen.2024.103178","url":null,"abstract":"<div><div>Research with human genetic data or human beings more generally requires valid informed consent. However, several exceptions exist to this universal principle, usually for situations where it is impossible or at least impractical to obtain this consent. Those exceptions are usually bound to requirements of necessity, shared benefit for the concerned community and minimization of harmful impact. Research without consent is normally subject to approval by an ethics review board. However, secondary use for research may also be based on statutory research privileges in the law. We identified several legal provisions in different countries, permitting the secondary use of DNA data that has been collected without consent for law enforcement purposes, which raises ethical questions. Most of the respective laws seem to be connected to privacy rules and permit the use of de-identified data only. However, whether individual DNA profiles in suspect and offender databases can actually be de-identified must be questioned. What appears to be less critical in terms of re-identification risk are the frequently mentioned \"statistical indices\", most likely referring to aggregated allele frequencies. However, reflections about data anonymity and a narrow purpose limitation to research aiming at the improvement of calculations of weight of evidence seem not to be the sole reasons for permitting research with entries from criminal offender databases. Distinctions between convicted offenders and other people in the database suggest an assumption of forfeiting some level of privacy protection upon conviction underlying some of these provisions. The use of entries on national DNA databases could therefore amount to problematic additional punishment.</div></div>","PeriodicalId":50435,"journal":{"name":"Forensic Science International-Genetics","volume":"75 ","pages":"Article 103178"},"PeriodicalIF":3.2,"publicationDate":"2024-11-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142696138","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":"Validation of the IDseek® OmniSTR™ Global Autosomal STR Profiling kit, reverse complement PCR as an improved tool/method for routine massively parallel sequencing of short tandem repeats","authors":"Kristiaan J. van der Gaag ,&nbsp;Natalie Weiler ,&nbsp;Erik A.C. de Jong ,&nbsp;Jerry Hoogenboom ,&nbsp;Pieter van Oers ,&nbsp;Rick H. de Leeuw ,&nbsp;Elisabeth S.M. Graaf ,&nbsp;Thirsa Kraaijenbrink ,&nbsp;Joop Theelen ,&nbsp;Titia Sijen","doi":"10.1016/j.fsigen.2024.103174","DOIUrl":"10.1016/j.fsigen.2024.103174","url":null,"abstract":"<div><div>Massively Parallel Sequencing (MPS) has gained interest in the forensic community over the past decade. Most of the published MPS methods focus on specialty applications intended for use in a limited number of samples with protocols that are relatively laborious. Recent developments using Reverse-Complement PCR enable an efficient MPS protocol suited for routine analysis of high numbers of samples. This method is implemented in the IDseek® OmniSTR™ Global Autosomal STR Profiling kit (Nimagen) for sequencing 28 of the most commonly used forensic autosomal STRs, one Y-chromosomal STR and Amelogenin. This study describes the validation of this kit and focuses on sensitivity, inhibitor tolerance, sequence variation detection and performance with mixtures up to 5 contributors. Results are compared to a Capillary Electrophoresis method (the PowerPlex® Fusion 6 C system, Promega) and the first commercial forensic MPS kit (ForenSeq™ DNA Signature prep, Qiagen) and for a concordance study with data from the Powerseq® MPS kit as well. Analysis settings in FDSTools are deduced and discussed, and an almost completely automated analysis is achieved. Using FDSTools noise correction, contributions in a mixture down to a level of 1.5 % of the major allele of a marker can be detected.</div></div>","PeriodicalId":50435,"journal":{"name":"Forensic Science International-Genetics","volume":"74 ","pages":"Article 103174"},"PeriodicalIF":3.2,"publicationDate":"2024-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142645274","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":"Concurrent genotyping of mitochondrial DNA and nuclear DNA in rootless hair shafts and blood samples for enhanced analysis","authors":"Dan Peng ,&nbsp;Nana Wang ,&nbsp;Yu Zang ,&nbsp;Zhiyong Liu ,&nbsp;Zhentang Liu ,&nbsp;Jiaojiao Geng ,&nbsp;Bin Cong ,&nbsp;Hongyu Sun ,&nbsp;Riga Wu","doi":"10.1016/j.fsigen.2024.103176","DOIUrl":"10.1016/j.fsigen.2024.103176","url":null,"abstract":"<div><div>Hair is an important type of biological evidence at crime scenes. However, the highly degraded nature of DNA fragments in hair shafts poses challenges for the detection of nuclear DNA (nuDNA) through capillary electrophoresis-based short tandem repeat (STR) genotyping. In this study, an all-in-one multiplex system named MGIEasy Signature Identification Library Prep Kit (MGI Tech, China) was employed to the simultaneous genotyping of both mitochondrial DNA (mtDNA) and nuDNA in hair shafts. This system is based on massively parallel sequencing (MPS) technology and encompasses Amelogenin, STRs, single nucleotide polymorphisms (SNPs) and mtDNA hypervariable regions (HVRs) in a single reaction. A total of 370 hair shafts, together with 180 blood samples as the references, were examined. The mtDNA analysis of 110 unrelated blood samples unveiled a total of 150 homoplasmic variants and 105 distinct haplotypes, revealing population polymorphisms in the Guangdong Han Chinese. The study also delved into the detection of mtDNA heteroplasmy, revealing 8.18 % and 16.36 % of individuals with point heteroplasmies (PHPs) in blood and hair shaft samples, respectively. Additionally, hair shafts with DNA extracted using the Investigator method yielded higher average depth of coverage (DoC), lower drop-out rate for SNP genotyping, higher nuDNA genotyped rates and success rates, than those using the MinElute method. In the longitudinal research, a gradual decrease in the total DoC of mtDNA fragments was observed along the length of the hair shaft, from the proximal root to the distal end. In contrast, the DoC of nuDNA exhibited a relatively stable pattern along the length of the hair shafts. The study contributes valuable insights into the simultaneous detection of nuDNA and mtDNA in hair shafts, emphasizing the need for optimized DNA extraction and detection methods for these highly degraded samples.</div></div>","PeriodicalId":50435,"journal":{"name":"Forensic Science International-Genetics","volume":"75 ","pages":"Article 103176"},"PeriodicalIF":3.2,"publicationDate":"2024-11-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142683245","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":"Improving the forensic genetic workflow for countries with small geographical areas: What are the options and how cost effective are they?","authors":"Anabella De La Chica ,&nbsp;Jason Birkett ,&nbsp;Cynthia Akwei ,&nbsp;David Lamont ,&nbsp;Nick Dawnay","doi":"10.1016/j.fsigen.2024.103171","DOIUrl":"10.1016/j.fsigen.2024.103171","url":null,"abstract":"<div><div>Forensic services worldwide often encounter considerable challenges relating to funding and infrastructure. Smaller jurisdictions or areas where forensic resources are scarce are faced with complicated choices in how they approach criminal casework, with a number of options available. Often these involve trade-offs between cost, time and data quality. Faced with such decisions it becomes important for the field to acknowledge the realities facing such jurisdictions, discuss the pros and cons of each approach, and identify a framework for making such decisions. This novel paper, reviews the available literature and identifies three main solutions for consideration: 1) the use of satellite laboratories for sample triage, 2) the use of a main regional laboratory for full forensic analysis and 3) the use of rapid DNA by police for reducing backlogs. Alongside these strategies, the impacts of cost and quality in regard to each of the stated options are considered. While the literature supports the assertion that some methods can reduce downstream costs via the reduction in turnaround times, there is limited data highlighting the business case used to support decision making when considering these options including the use of cost:benefit analyses or case studies, emphasizing the novelty of this paper. This is likely due to the commercialized nature of the forensic sector preventing the publication of a private laboratory’s business approach. The lack of emphasis on the ‘business case’ in forensic literature has the potential to mislead R&amp;D scientists who may consequently fail to consider such factors when performing their own research.</div></div>","PeriodicalId":50435,"journal":{"name":"Forensic Science International-Genetics","volume":"74 ","pages":"Article 103171"},"PeriodicalIF":3.2,"publicationDate":"2024-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142651500","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}