Forensic Science International-Genetics最新文献

{"title":"Shotgun DNA sequencing for human identification: Dynamic SNP selection and likelihood ratio calculations accounting for errors","authors":"Mikkel Meyer Andersen ,&nbsp;Marie-Louise Kampmann ,&nbsp;Alberte Honoré Jepsen ,&nbsp;Niels Morling ,&nbsp;Poul Svante Eriksen ,&nbsp;Claus Børsting ,&nbsp;Jeppe Dyrberg Andersen","doi":"10.1016/j.fsigen.2024.103146","DOIUrl":"10.1016/j.fsigen.2024.103146","url":null,"abstract":"<div><p>Shotgun sequencing is a DNA analysis method that potentially determines the nucleotide sequence of every DNA fragment in a sample, unlike PCR-based genotyping methods that is widely used in forensic genetics and targets predefined short tandem repeats (STRs) or predefined single nucleotide polymorphisms (SNPs). Shotgun DNA sequencing is particularly useful for highly degraded low-quality DNA samples, such as ancient samples or those from crime scenes. Here, we developed a statistical model for human identification using shotgun sequencing data and developed formulas for calculating the evidential weight as a likelihood ratio (<span><math><mrow><mi>L</mi><mi>R</mi></mrow></math></span>). The model uses a dynamic set of binary SNP loci and takes the error rate from shotgun sequencing into consideration in a probabilistic manner. To our knowledge, the method is the first to make this possible. Results from replicated shotgun sequencing of buccal swabs (high-quality samples) and hair samples (low-quality samples) were arranged in a genotype-call confusion matrix to estimate the calling error probability by maximum likelihood and Bayesian inference. Different genotype quality filters may be applied to account for genotyping errors. An error probability of zero resulted in the commonly used <span><math><mrow><mi>L</mi><mi>R</mi></mrow></math></span> formula for the weight of evidence. Error probabilities above zero reduced the <span><math><mrow><mi>L</mi><mi>R</mi></mrow></math></span> contribution of matching genotypes and increased the <span><math><mrow><mi>L</mi><mi>R</mi></mrow></math></span> in the case of a mismatch between the genotypes of the trace and the person of interest. In the latter scenario, the <span><math><mrow><mi>L</mi><mi>R</mi></mrow></math></span> increased from zero (occurring when the error probability was zero) to low positive values, which allow for the possibility that the mismatch may be due to genotyping errors. We developed an open-source R package, <span>wgsLR</span>, which implements the method, including estimation of the calling error probability and calculation of <span><math><mrow><mi>L</mi><mi>R</mi></mrow></math></span> values. The R package includes all formulas used in this paper and the functionalities to generate the formulas.</p></div>","PeriodicalId":50435,"journal":{"name":"Forensic Science International-Genetics","volume":"74 ","pages":"Article 103146"},"PeriodicalIF":3.2,"publicationDate":"2024-09-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S187249732400142X/pdfft?md5=21c59d83082c09c3567c36aad86c5b15&pid=1-s2.0-S187249732400142X-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142172820","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":"The role of cats in human DNA transfer","authors":"Heidi Monkman ,&nbsp;Roland A.H. van Oorschot ,&nbsp;Mariya Goray","doi":"10.1016/j.fsigen.2024.103132","DOIUrl":"10.1016/j.fsigen.2024.103132","url":null,"abstract":"<div><p>Domestic animals, such as cats and dogs, are present in the majority of Australian households. Recently, questions regarding the possibility that domestic animals can serve as silent witnesses, from whom evidence can be collected, or act as vectors of contamination and transfer, have started to be raised. Yet, little is known regarding the transfer and prevalence of human DNA to and from cats. This study investigated if cats are reservoirs and vectors for human DNA transfer. Twenty cats from 15 households were sampled from 4 different areas (head (fur), back (fur), left (skin) and right (fur)) to obtain information on the background DNA that may be found on an animal. Further, transfer of human DNA to and from an animal, after a short patting contact, was tested. Human DNA was found to be prevalent on all cats. Of the areas sampled, most DNA was collected from the top of the fur from the back followed by the head and right/fur. No or very low quantities of human DNA was recovered from the left (skin) area. Most of the human DNA originated from the owners, but DNA from others was also often present (47 % of samples). Further, the transfer tests demonstrated that human DNA transferred readily to (detected in 45 % of samples) and from (detected in 80 % of samples) cats during patting. These results show that animals can act as reservoirs of human DNA and vectors for human DNA transfer that may need to be considered during evaluative DNA reporting. Furthermore, if an interaction between an animal and a perpetrator is suspected, consideration should be given to collecting DNA evidence from suspected contact areas on an animal.</p></div>","PeriodicalId":50435,"journal":{"name":"Forensic Science International-Genetics","volume":"74 ","pages":"Article 103132"},"PeriodicalIF":3.2,"publicationDate":"2024-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1872497324001285/pdfft?md5=3dc3013ec1b088fdd77c512db8f346a4&pid=1-s2.0-S1872497324001285-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142147182","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":"Exploring legal age estimation using DNA methylation","authors":"M. Boullón-Cassau ,&nbsp;A. Ambroa-Conde ,&nbsp;M.A. Casares de Cal ,&nbsp;A. Gómez-Tato ,&nbsp;A. Mosquera-Miguel ,&nbsp;J. Ruiz-Ramírez ,&nbsp;A. Cabrejas-Olalla ,&nbsp;J. González-Bao ,&nbsp;L. Casanova-Adán ,&nbsp;M. de la Puente ,&nbsp;A. Rodríguez ,&nbsp;C. Phillips ,&nbsp;MV. Lareu ,&nbsp;A. Freire-Aradas","doi":"10.1016/j.fsigen.2024.103142","DOIUrl":"10.1016/j.fsigen.2024.103142","url":null,"abstract":"<div><p>Minors (subjects under the legal age, established at this study at 18 years) benefit from a series of legal rights created to protect them and guarantee their welfare. However, throughout the world there are many minors who have no way to prove they are underaged, leading to a great interest in predicting legal age with the highest possible accuracy. Current methods, mainly involving X-ray analysis, are highly invasive, so new methods to predict legal age are being studied, such as DNA methylation. To further such studies, we created two age prediction models based on five epigenetic markers: cg21572722 (<em>ELOVL2</em>), cg02228185 (<em>ASPA</em>), cg06639320 (<em>FHL2</em>), cg19283806 (<em>CCDC102B</em>) and cg07082267 (no associated gene), that were analysed in blood samples to determine possible limitations regarding DNA methylation as an effective tool for legal age estimation. A wide age range prediction model was created using a broad set of samples (14–94 years) yielding a mean absolute error (MAE) of ±4.32 years. A second model, the constrained age prediction model, was created using a reduced range of samples (14–25 years) yielding an MAE of ±1.54 years. Both models, in addition to Horvath’s Skin &amp; Blood epigenetic clock, were evaluated using a test set comprising 732 pairs of 18-year-old twins (N=426 monozygotic (MZ) and N=306 dizygotic (DZ) pairs), representing a relevant age of study. Through analysis of the two former age prediction models, we found that constraining the age of the samples forming the training set around the desired age of study significantly reduced the prediction error (from MAE: ±4.07 and ±4.27 years for MZ and DZ twins, respectively; to ±1.31 and ±1.3 years). However, despite low prediction errors, DNA methylation models are still prone to classify same-aged individuals in different categories (minors or adults), despite each sample belonging to the same twin pair. Additional evaluation of Horvath’s Skin &amp; Blood model (391 CpGs) led to similar results in terms of age prediction errors than if using only five epigenetic markers (MAE: ±1.87 and ±1.99 years for MZ and DZ twins, respectively).</p></div>","PeriodicalId":50435,"journal":{"name":"Forensic Science International-Genetics","volume":"74 ","pages":"Article 103142"},"PeriodicalIF":3.2,"publicationDate":"2024-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1872497324001388/pdfft?md5=a27f6df0ba85539c0c136678454ec197&pid=1-s2.0-S1872497324001388-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142147180","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":"Really the best of both? Application of an mRNA/miRNA multiplex assay to casework samples, animal samples, and a storage study","authors":"Malte Bamberg,&nbsp;Maria Bruder,&nbsp;Sebastian N. Kunz,&nbsp;Theresa Wöhrle,&nbsp;Peter Wiegand","doi":"10.1016/j.fsigen.2024.103129","DOIUrl":"10.1016/j.fsigen.2024.103129","url":null,"abstract":"<div><p>The identification of body fluids is an important area of forensic genetics. In particular, the susceptibility to degradation of casework samples is of crucial importance, as the traces can often be exposed to different environmental conditions over a long period of time. RNAs especially are used as molecular markers for the identification of body fluids in forensics. Messenger RNAs (mRNAs) show an increased susceptibility to degradation, e.g. under humidity and UV radiation but are highly body fluid-specific. The shorter micro RNAs (miRNAs), however, are less susceptible to degradation, but only a few body fluid-specific markers could be investigated. In this study, a self-developed mRNA/miRNA multiplex assay for capillary electrophoresis from a preliminary study was further adapted and validated. The approach was applied to casework samples, animal samples, and a storage study. The advantages and disadvantages of the mRNA/miRNA assay were investigated in order to review a possible application for forensic casework. Some miRNA markers were also detected in animal samples, which once again underlines the possible non-specificity of miRNAs. In the storage study, the different markers were detected for different lengths of time depending on the body fluid examined. For almost all body fluids, the miRNA markers were still detectable after a period of 35 days under environmental conditions compared to the mRNA markers. The mRNA peaks were often already clearly reduced or no longer detectable after 14 days. The results show the advantage of the new mRNA/miRNA assay compared to established mRNA approaches, especially for older and degraded samples, but the assay has its limitations due to the limited number of specific miRNA markers.</p></div>","PeriodicalId":50435,"journal":{"name":"Forensic Science International-Genetics","volume":"74 ","pages":"Article 103129"},"PeriodicalIF":3.2,"publicationDate":"2024-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S187249732400125X/pdfft?md5=d926e15a0e45775d22405b1768083e18&pid=1-s2.0-S187249732400125X-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142147181","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 mathematical framework for genetic relatedness analysis involving X chromosome aneuploidies","authors":"Marisa Faustino ,&nbsp;Leonor Gusmão ,&nbsp;António Amorim ,&nbsp;Daniel Kling ,&nbsp;Nádia Pinto","doi":"10.1016/j.fsigen.2024.103128","DOIUrl":"10.1016/j.fsigen.2024.103128","url":null,"abstract":"<div><p>The unique features of the X chromosome can be crucial to complement autosomal profiling or to disentangle complex kinship problems, providing in some cases a similar or even greater power than autosomes in paternity/maternity investigations. While theoretical and informatics approaches for pairwise X-linked kinship analyses are well established for euploid individuals, these are still lacking for individuals with an X chromosome aneuploidy. To trigger the fulfilment of this gap, this research presents a mathematical framework that enables the quantification of DNA evidence in pairwise kinship analyses, involving two non-inbred individuals, one of whom with a non-mosaic X chromosome aneuploidy: Trisomy X (47, XXX), Klinefelter (47, XXY) or Turner (45, X0) syndrome. As previously developed for a regular number of chromosomes, this approach relies on the probability of related individuals sharing identical-by-descent (IBD) alleles at one specific locus and it can be applied to any set of independently transmitted markers, with no gametic association in the population. The kinship hypotheses mostly considered in forensic casework are specifically addressed in this work, but the reasoning and procedure can be applied to virtually any pairwise kinship problem under the referred assumptions. Algebraic formulae for joint genotypic probabilities cover all the possible genotypic configurations and pedigrees. Compared with the analyses assuming individuals with a regular number of chromosomes, complicating factors rely on the different possibilities for both the parental origin of the error (either maternal or paternal), and the type of error occurred (either meiotic or post-zygotic mitotic). These imply that a non-inbred female with Triple X or a male with Klinefelter syndrome may carry two IBD alleles at the same locus. Thus, and contrarily to what occurs for the standard case, IBD partitions depend not only on the kinship hypothesis under analysis but also on the genotypic configuration of the analyzed individuals. For some cases, parameters of interest can be inferred, while for others recommended values based on the available literature are provided. This work is the starting point to analyze X-chromosomal data under the scope of kinship problems, involving individuals with aneuploidies, as it will enhance the quantification of the DNA evidence not only in forensics but also in the medical genetics field. We hope it will trigger the development of approaches including other complicating factors, as a greater number of individuals, possibility of the occurrence of mutations and/or silent alleles, as well as the analysis of linked markers.</p></div>","PeriodicalId":50435,"journal":{"name":"Forensic Science International-Genetics","volume":"74 ","pages":"Article 103128"},"PeriodicalIF":3.2,"publicationDate":"2024-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1872497324001248/pdfft?md5=1be7df89b7b68597975297630b20e6ad&pid=1-s2.0-S1872497324001248-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142147178","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":"Comparison of next generation sequencing (NGS) - (SNPs) and capillary electrophoresis (CE) - (STRs) in the genetic analysis of human remains","authors":"Stavros Kokotas ,&nbsp;Bruce Budowle ,&nbsp;Athanasios Papatheodorou ,&nbsp;Eugenia Bolanaki ,&nbsp;Aikaterini Kondili ,&nbsp;Aristea Metheniti ,&nbsp;Maria Vouropoulou ,&nbsp;Georgios Koukouvinos ,&nbsp;Emmanouil Palaigeorgiou ,&nbsp;Polyzois Makras","doi":"10.1016/j.fsigen.2024.103131","DOIUrl":"10.1016/j.fsigen.2024.103131","url":null,"abstract":"<div><p>A pilot study was performed using two different DNA technology platforms conducted by two laboratories to analyze DNA extracted from 83-year-old, human male skeletal remains from 16 individuals, of which there are no other viable means to identify these war victims. The workflow of the more recent developed ForenSeq Kintelligence Kit and next generation sequencing was compared to that of the standard capillary electrophoresis – short tandem repeat (STR) method (Power Plex ESX17 and Y23 Systems). The findings indicate that greater amount of useful genetic data can be gained with the Kintelligence system across the range of samples under study and particularly for samples in which partial or no STR profiles are obtained. SNP data are more likely to be obtained from degraded samples, like the ones analyzed in this study. Moreover, high volume SNP data are suitable for long distance kinship associations and genetic genealogy databases to develop more investigative leads for future kinship and missing persons cases, a process not feasible by STR typing.</p></div>","PeriodicalId":50435,"journal":{"name":"Forensic Science International-Genetics","volume":"74 ","pages":"Article 103131"},"PeriodicalIF":3.2,"publicationDate":"2024-08-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142147179","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":"Transfer and persistence of intruder DNA within an office after reuse by owner","authors":"Monique Zacher ,&nbsp;Roland A.H. van Oorschot ,&nbsp;Oliva Handt ,&nbsp;Mariya Goray","doi":"10.1016/j.fsigen.2024.103130","DOIUrl":"10.1016/j.fsigen.2024.103130","url":null,"abstract":"<div><p>The heightened sensitivity of DNA typing techniques, paired with the extensive use of trace DNA in forensic investigations, has resulted in an increased need to understand how and when DNA is deposited on surfaces of interest. This study focussed on the transfer, persistence, and prevalence of trace DNA in a single occupation of an office space by an intruder, when all contacts made during occupation and for the two hours prior and post occupation were known. The extent to which DNA could be recovered from contacted/not contacted surfaces was investigated. This study investigates the impacts of these movements and use of an office space when the duration of occupancy, surface contact histories and shedder status of participants are known. Contacts were documented and surfaces in the office space were targeted for sampling. Categories were set for target sampling that included different types of contact. Direct and indirect DNA transfer was detected in 55 % and 6 % of samples, respectively. Contactless DNA transfer was detected in 0.5 % of samples. The owner was observed as the sole/major/majority contributor in 77 % of the samples and as minor contributor in 10 % of samples. The intruder was observed as the sole/major/majority contributor in 14 % of samples and as the minor contributor in 16 %. An increased number of contacts increased the relative DNA contribution of the individual making the contact, however, not all observed direct contacts resulted in detectable DNA transfer. The outcome of this study will aid in better sample targeting strategies and contribute to the pool of data assisting in the development of activity level assessments.</p></div>","PeriodicalId":50435,"journal":{"name":"Forensic Science International-Genetics","volume":"73 ","pages":"Article 103130"},"PeriodicalIF":3.2,"publicationDate":"2024-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1872497324001261/pdfft?md5=6ce733f1573f85b0673f497af5641fc0&pid=1-s2.0-S1872497324001261-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142094626","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":"Forensic efficiency evaluation of a mtDNA whole genome sequencing system constructed with long fragment amplification strategy on DNA nanoball sequencing platform","authors":"Man Chen ,&nbsp;Chong Chen ,&nbsp;Ning Li ,&nbsp;Yuerong Su ,&nbsp;Wei Cui ,&nbsp;Yan Huang ,&nbsp;Meiming Cai ,&nbsp;Bofeng Zhu","doi":"10.1016/j.fsigen.2024.103126","DOIUrl":"10.1016/j.fsigen.2024.103126","url":null,"abstract":"<div><p>Mitochondrial DNA (mtDNA) is an important genetic marker for degraded biological sample identification, maternal pedigree tracing, and population genetic structure study owing to its characteristics of high copy number, anti-degradable ring structure, and maternal inheritance. Whole mtDNA genome sequencing is an optimal method for the analysis of mtDNA polymorphism and heterogeneity because it allows for the comprehensive use of maternal genetic information. However, because of lacking quantitative evaluations for sequencing data, the scientific interpretation standards for mtDNA sequencing results of the previously used sequencing systems are often different, and false positive or false negative results are prone to occur when faced with the interference of nuclear genomic DNA, or the heterogeneities of mtDNA sequence and structure. In this study, we evaluated a novel mtDNA whole genome sequencing system using long fragment amplification strategy on the DNA nanoball (DNB) sequencing platform. This system demonstrated high sequencing quality and specific mtDNA sequencing efficiencies on positive control DNA and FTA bloodstain samples, as the average Q20 and Q30 values of the corresponding samples were 97.17 % and 91.93 %; 97.37 % and 92.48 %, respectively. The mean mapping percentages for the reference sequences of whole genome DNA (wgDNA), mtDNA, and nuclear genomic DNA (ngDNA) in the corresponding samples were 99.98 %, 99.97 %, 0.03 %, and 99.91 %, 99.40 %, 0.60 %; respectively. The average error calling rates for the bases A, C, G, and T of the whole mtDNA genome were 0.2519 %, 0.2550 %, 0.2906 %; and 0.2392 %, respectively. The efficacy of heteroplasmy identification was assessed using a set of theoretical sites with predetermined rates. These sites were created by combining the samples with known mtDNA haplotypes in certain proportions. The absolute errors between observed and theoretical heteroplasmy values were 89.59 %, 74.68 %, 50.20 %, 12.65 %, 8.31 %, and 4.85 %, while the theoretical heteroplasmy values were 5 %, 10 %, 20 %, 80 %, 90 %, and 95 %, respectively. The absolute error exhibited relative stability when the mtDNA sequencing depth exceeded 500×. Furthermore, the system sequencing efficiency was also confirmed among different kinds of samples, and these samples included natural samples (e.g., peripheral blood samples preserved on FTA cards for 2 and 11 years, and on filter paper for 6 and 9 years), degraded samples, sensitivity samples, samples derived from various bodily fluids, and maternal pedigree samples. In summary, the whole mtDNA genome sequencing system used for forensic identification demonstrated high performance in analyzing mtDNA sequence information, and showed significant prospects for forensic application and maternal genetic research.</p></div>","PeriodicalId":50435,"journal":{"name":"Forensic Science International-Genetics","volume":"73 ","pages":"Article 103126"},"PeriodicalIF":3.2,"publicationDate":"2024-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142094625","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":"Comprehensive body fluid identification and contributor assignment by combining targeted sequencing of mRNA and coding region SNPs","authors":"Maximilian Neis ,&nbsp;Theresa Groß ,&nbsp;Harald Schneider ,&nbsp;Peter M. Schneider ,&nbsp;Cornelius Courts","doi":"10.1016/j.fsigen.2024.103125","DOIUrl":"10.1016/j.fsigen.2024.103125","url":null,"abstract":"<div><p>Forensic genetic analyses aim to retrieve as much information as possible from biological trace material recovered from crime scenes. While standard short tandem repeat (STR) profiling is essential to individualize biological traces, its significance is diminished in crime scenarios where the presence of a suspect's DNA is acknowledged by all parties. In such cases, forensic (m)RNA analysis can provide crucial contextualizing information on the source level about a trace’s composition, i.e., body fluids/tissues, and has therefore emerged as a powerful tool for modern forensic investigations. However, the question which of several suspects contributed a specific component (body fluid) to a mixed trace cannot be answered by RNA analysis using conventional methods. This individualizing information is stored within the sequence of the mRNA transcripts. Massively parallel sequencing (MPS) represents a promising alternative, offering not only higher multiplex capacity, but also the typing of individual coding region SNPs (cSNPs) to enable the assignment of contributors to mixture components, thereby reducing the risk of association fallacies. Herein, we describe the development of an extensive mRNA/cSNP panel for targeted sequencing on the IonTorrent S5 platform. Our panel comprises 30 markers for the detection of six body fluids/tissues (blood, saliva, semen, skin, vaginal and menstrual secretion), along with 70 linkage-controlled cSNPs for contributor assignment. It exhibited high reliable detection sensitivity with RNA inputs down to 0.75 ng and a conservatively calculated probability of identity of 0.03 – 6 % for individual body fluid-specific cSNP profiles. Limitations and areas for future work include RNA-related allele imbalances, inclusion of markers to correctly identify rectal mucosa and the optimization of specific markers. In summary, our new panel is intended to be a major step forward to interpret biological evidence at sub-source and source level based on cSNP attribution of a body fluid component to a suspect and victim, respectively.</p></div>","PeriodicalId":50435,"journal":{"name":"Forensic Science International-Genetics","volume":"73 ","pages":"Article 103125"},"PeriodicalIF":3.2,"publicationDate":"2024-08-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1872497324001212/pdfft?md5=c9df79a13c65d7776a6353482f2598a4&pid=1-s2.0-S1872497324001212-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142048002","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":"Analysis of rapidly mutating Y-STRs enables almost complete discrimination of unrelated and related males from the African continent","authors":"Filippo Barni,&nbsp;Arwin Ralf,&nbsp;Chiara Della Rocca,&nbsp;Federica Cannistrà,&nbsp;Marco Gigliucci,&nbsp;Beniamino Trombetta,&nbsp;Andrea Berti,&nbsp;Manfred Kayser,&nbsp;Fulvio Cruciani","doi":"10.1016/j.fsigen.2024.103127","DOIUrl":"10.1016/j.fsigen.2024.103127","url":null,"abstract":"","PeriodicalId":50435,"journal":{"name":"Forensic Science International-Genetics","volume":"73 ","pages":"Article 103127"},"PeriodicalIF":3.2,"publicationDate":"2024-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142122179","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}