Forensic Science International-Genetics最新文献

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Identification of individuals from low template blood samples using whole transcriptome shotgun sequencing 利用全转录组枪式测序从低模板血液样本中识别个体
IF 3.2 2区 医学
Forensic Science International-Genetics Pub Date : 2024-06-19 DOI: 10.1016/j.fsigen.2024.103089
Alberte Honoré Jepsen, Marie-Louise Kampmann, Stine Bøttcher Jacobsen, Claus Børsting, Jeppe Dyrberg Andersen
{"title":"Identification of individuals from low template blood samples using whole transcriptome shotgun sequencing","authors":"Alberte Honoré Jepsen,&nbsp;Marie-Louise Kampmann,&nbsp;Stine Bøttcher Jacobsen,&nbsp;Claus Børsting,&nbsp;Jeppe Dyrberg Andersen","doi":"10.1016/j.fsigen.2024.103089","DOIUrl":"https://doi.org/10.1016/j.fsigen.2024.103089","url":null,"abstract":"<div><p>Biological trace samples consisting of very few cells pose a challenge to conventional forensic genetic DNA analysis. RNA may be an alternative to DNA when handling low template samples. Whereas each cell only contains two copies of an autosomal DNA segment, the transcriptome retains much of the genomic variation replicated in abundant RNA fragments. In this study, we describe the development of a prototype RNA-based SNP selection set for forensic human identification from low template samples (50 pg gDNA). Whole blood from a subset of the Danish population (41 individuals) and blood stains subjected to degradation at room temperature for up to two weeks were analysed by whole transcriptome shotgun sequencing. Concordance was determined by DNA genotyping with the Infinium Omni5–4 SNP chip. In the 100 protein-coding genes with the most reads, 5214 bi-allelic SNPs with gnomAD minor allele frequencies &gt; 0.1 in the African/African American, East Asian, and (non-Finnish) European populations were identified. Of these, 24 SNPs in 21 genes passed screening in whole blood and degraded blood stains, with a resulting mean match probability of 4.5 ∙ 10<sup>−9</sup>. Additionally, ancestry informative SNPs and SNPs in genes useful for body fluid identification were identified in the transcriptome. Consequently, shotgun sequencing of RNA from low template samples may be used for a vast host of forensic genetics purposes, including simultaneous human and body fluid identification, leading to direct donor identification in the identified body fluid.</p></div>","PeriodicalId":50435,"journal":{"name":"Forensic Science International-Genetics","volume":null,"pages":null},"PeriodicalIF":3.2,"publicationDate":"2024-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1872497324000851/pdfft?md5=310a5ca9e7231c13df0a47984b1cd7c0&pid=1-s2.0-S1872497324000851-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141434577","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}
引用次数: 0
A collaborative study on the precision of the Markov chain Monte Carlo algorithms used for DNA profile interpretation 关于用于 DNA 图谱解读的马尔可夫链蒙特卡洛算法精确性的合作研究
IF 3.2 2区 医学
Forensic Science International-Genetics Pub Date : 2024-06-19 DOI: 10.1016/j.fsigen.2024.103088
Sarah Riman , Jo-Anne Bright , Kaitlin Huffman , Lilliana I. Moreno , Sicen Liu , Asmitha Sathya , Peter M. Vallone
{"title":"A collaborative study on the precision of the Markov chain Monte Carlo algorithms used for DNA profile interpretation","authors":"Sarah Riman ,&nbsp;Jo-Anne Bright ,&nbsp;Kaitlin Huffman ,&nbsp;Lilliana I. Moreno ,&nbsp;Sicen Liu ,&nbsp;Asmitha Sathya ,&nbsp;Peter M. Vallone","doi":"10.1016/j.fsigen.2024.103088","DOIUrl":"https://doi.org/10.1016/j.fsigen.2024.103088","url":null,"abstract":"<div><p>Several fully continuous probabilistic genotyping software (PGS) use Markov chain Monte Carlo algorithms (MCMC) to assign weights to different proposed genotype combinations at a locus. Replicate interpretations of the same profile in these software are expected not to produce identical weights and likelihood ratio (LR) values due to the Monte Carlo aspect. This paper reports a detailed precision study under reproducibility conditions conducted as a collaborative exercise across the National Institute of Standards and Technology (NIST), Federal Bureau of Investigation (FBI), and Institute of Environmental Science and Research (ESR). Replicate interpretations generated across the three laboratories used the same input files, software version, and settings but different random number seed and different computers. This work demonstrates that using different computers to analyze replicate interpretations does not contribute to any variations in LR values. The study quantifies the magnitude of differences in the assigned LRs that is only due to run-to-run MCMC variability and addresses the potential explanations for the observed differences.</p></div>","PeriodicalId":50435,"journal":{"name":"Forensic Science International-Genetics","volume":null,"pages":null},"PeriodicalIF":3.2,"publicationDate":"2024-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141438641","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}
引用次数: 0
Sequencing-induced artefacts in NGS STR data NGS STR 数据中由测序引起的伪差
IF 3.1 2区 医学
Forensic Science International-Genetics Pub Date : 2024-06-15 DOI: 10.1016/j.fsigen.2024.103086
Yao-Yuan Liu , Kevin Cheng , Rebecca Just , Sana Enke , Jo-Anne Bright
{"title":"Sequencing-induced artefacts in NGS STR data","authors":"Yao-Yuan Liu ,&nbsp;Kevin Cheng ,&nbsp;Rebecca Just ,&nbsp;Sana Enke ,&nbsp;Jo-Anne Bright","doi":"10.1016/j.fsigen.2024.103086","DOIUrl":"10.1016/j.fsigen.2024.103086","url":null,"abstract":"<div><p>Significant progress has been made in recent years in the development of techniques for Next Generation Sequencing (NGS), or Massively Parallel Sequencing (MPS), of forensically relevant short tandem repeat (STR) loci. However, as these technologies are investigated and adopted by forensic laboratories, new challenges unfold that require further scrutiny. In the analysis of DNA profiles generated using the MiSeq FGx sequencing system, we have observed noise sequences with relatively high readcounts that are challenging to distinguish from genuine alleles. These high read count noise sequences appear as allele sequences with one or a few substituted bases compared to a known allele sequence within the profile.</p><p>An examination of ForenSeq DNA Signature Prep Kit STR noise sequences revealed that the substituted base of a parent allele can align to the same position on the sequence across noise sequences. This suggests that these substitution events occur at specific positions within the amplicon, resulting in multiple noise reads with substitutions at the same position. Mapping of the noise events onto the original raw read positions revealed a high number of events, or “noise spikes”, occurring at</p><p>specific positions within a given sequencing run. These noise spikes affected reads across the entire run, agnostic of locus or sample, while the position, occurrence, and amplitude of the spikes differed across runs. The majority of noise sequences with high read counts in a DNA profile were generated from base changes at these spike positions, and could be classified as “noise spike artefacts”.</p><p>In this paper we present evidence of the noise spike artefacts and their genesis during the sequencing process in the sequencing-by-synthesis (SBS) cycles, as well as the methods developed to detect them. The information and methods will assist laboratories with detecting noise spikes in MiSeq FGx sequencing runs, differentiating authentic allele sequences from noise spike artefacts, and developing protocols for analyst review and handling of MiSeq FGx data.</p></div>","PeriodicalId":50435,"journal":{"name":"Forensic Science International-Genetics","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-06-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141412380","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}
引用次数: 0
Improved individual identification in DNA mixtures of unrelated or related contributors through massively parallel sequencing 通过大规模并行测序,在由无关联或有关联成分组成的 DNA 混合物中更好地识别个体
IF 3.1 2区 医学
Forensic Science International-Genetics Pub Date : 2024-06-12 DOI: 10.1016/j.fsigen.2024.103078
Zhiyong Liu , Enlin Wu , Ran Li , Jiajun Liu , Yu Zang , Bin Cong , Riga Wu , Bo Xie , Hongyu Sun
{"title":"Improved individual identification in DNA mixtures of unrelated or related contributors through massively parallel sequencing","authors":"Zhiyong Liu ,&nbsp;Enlin Wu ,&nbsp;Ran Li ,&nbsp;Jiajun Liu ,&nbsp;Yu Zang ,&nbsp;Bin Cong ,&nbsp;Riga Wu ,&nbsp;Bo Xie ,&nbsp;Hongyu Sun","doi":"10.1016/j.fsigen.2024.103078","DOIUrl":"10.1016/j.fsigen.2024.103078","url":null,"abstract":"<div><p>DNA mixtures are a common sample type in forensic genetics, and we typically assume that contributors to the mixture are unrelated when calculating the likelihood ratio (LR). However, scenarios involving mixtures with related contributors, such as in family murder or incest cases, can also be encountered. Compared to the mixtures with unrelated contributors, the kinship within the mixture would bring additional challenges for the inference of the number of contributors (NOC) and the construction of probabilistic genotyping models. To evaluate the influence of potential kinship on the individual identification of the person of interest (POI), we conducted simulations of two-person (2 P) and three-person (3 P) DNA mixtures containing unrelated or related contributors (parent-child, full-sibling, and uncle-nephew) at different mixing ratios (for 2 P: 1:1, 4:1, 9:1, and 19:1; for 3 P: 1:1:1, 2:1:1, 5:4:1, and 10:5:1), and performed massively parallel sequencing (MPS) using MGIEasy Signature Identification Library Prep Kit on MGI platform. In addition, in silico simulations of mixtures with unrelated and related contributors were also performed. In this study, we evaluated 1): the MPS performance; 2) the influence of multiple genetic markers on determining the presence of related contributors and inferring the NOC within the mixture; 3) the probability distribution of MAC (maximum allele count) and TAC (total allele count) based on in silico mixture profiles; 4) trends in LR values with and without considering kinship in mixtures with related and unrelated contributors; 5) trends in LR values with length- and sequence-based STR genotypes. Results indicated that multiple numbers and types of genetic markers positively influenced kinship and NOC inference in a mixture. The LR values of POI were strongly dependent on the mixing ratio. Non- and correct-kinship hypotheses essentially did not affect the individual identification of the major POI; the correct kinship hypothesis yielded more conservative LR values; the incorrect kinship hypothesis did not necessarily lead to the failure of POI individual identification. However, it is noteworthy that these considerations could lead to uncertain outcomes in the identification of minor contributors. Compared to length-based STR genotyping, using sequence-based STR genotype increases the individual identification power of the POI, concurrently improving the accuracy of mixing ratio inference using EuroForMix. In conclusion, the MGIEasy Signature Identification Library Prep kit demonstrated robust individual identification power, which is a viable MPS panel for forensic DNA mixture interpretations, whether involving unrelated or related contributors.</p></div>","PeriodicalId":50435,"journal":{"name":"Forensic Science International-Genetics","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141398521","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}
引用次数: 0
DNA preservation in compact and trabecular bone 密实骨和骨小梁中的 DNA 保存
IF 3.1 2区 医学
Forensic Science International-Genetics Pub Date : 2024-06-01 DOI: 10.1016/j.fsigen.2024.103067
Irena Zupanič Pajnič, Nika Kovačič
{"title":"DNA preservation in compact and trabecular bone","authors":"Irena Zupanič Pajnič,&nbsp;Nika Kovačič","doi":"10.1016/j.fsigen.2024.103067","DOIUrl":"https://doi.org/10.1016/j.fsigen.2024.103067","url":null,"abstract":"<div><p>Significant variation exists in the molecular structure of compact and trabecular bone. In compact bone full dissolution of the bone powder is required to efficiently release the DNA from hydroxyapatite. In trabecular bone where soft tissues are preserved, we assume that full dissolution of the bone powder is not required to release the DNA from collagen. To investigate this issue, research was performed on 45 Second World War diaphysis (compact bone)–epiphysis (trabecular bone) femur pairs, each processed with a full dissolution (FD) and partial dissolution (PD) extraction method. DNA quality and quantity were assessed using qPCR PowerQuant analyses, and autosomal STRs were typed to confirm the authenticity of isolated DNA. Our results support different mechanisms of DNA preservation in compact and trabecular bone because FD method was more efficient than PD method only in compact bone, and no difference in DNA yield was observed in trabecular bone, showing no need for full dissolution of the bone powder when trabecular bone tissue is processed. In addition, a significant difference in DNA yield was observed between compact and trabecular bone when PD was applied, with more DNA extracted from trabecular bone than compact bone. High suitability of trabecular bone processed with PD method is also supported by the similar quantities of DNA isolated by FD method when applied to both compact and trabecular bone. Additionally similar quantities of DNA were isolated when compact bone was extracted with FD method and trabecular bone was extracted with PD method. Processing trabecular bone with PD method in routine identification of skeletonized human remains shortens the extraction procedure and simplifies the grinding process.</p></div>","PeriodicalId":50435,"journal":{"name":"Forensic Science International-Genetics","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1872497324000632/pdfft?md5=162f014a1b38561ccfebf5d4679f1961&pid=1-s2.0-S1872497324000632-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141240152","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}
引用次数: 0
Identification of the body fluid donor in mixtures through target mRNA cSNP sequencing 通过目标 mRNA cSNP 测序鉴定混合物中的体液供体
IF 3.1 2区 医学
Forensic Science International-Genetics Pub Date : 2024-05-31 DOI: 10.1016/j.fsigen.2024.103066
Zidong Liu , Jiaqi Wang , Lishan Li, Hailing Yang, Huan Yu, Jiajia Fan, Mingming Zhang, Yuxin Zhang, Jinding Liu, Zeqin Li, Gengqian Zhang
{"title":"Identification of the body fluid donor in mixtures through target mRNA cSNP sequencing","authors":"Zidong Liu ,&nbsp;Jiaqi Wang ,&nbsp;Lishan Li,&nbsp;Hailing Yang,&nbsp;Huan Yu,&nbsp;Jiajia Fan,&nbsp;Mingming Zhang,&nbsp;Yuxin Zhang,&nbsp;Jinding Liu,&nbsp;Zeqin Li,&nbsp;Gengqian Zhang","doi":"10.1016/j.fsigen.2024.103066","DOIUrl":"https://doi.org/10.1016/j.fsigen.2024.103066","url":null,"abstract":"<div><p>In forensic practice, mixture stains containing various body fluids are common, presenting challenges for interpretation, particularly in multi-contributor mixtures. Traditional STR profiles face difficulties in such scenarios. Over recent years, RNA has emerged as a promising biomarker for body fluid identification, and mRNA polymorphism has shown excellent performance in identifying body fluid donors in previous studies. In this study, a massively parallel sequencing assay was developed, encompassing 202 coding region SNPs (cSNPs) from 45 body fluid/tissue-specific genes to identify both body fluid/tissue origin and the respective donors, including blood, saliva, semen, vaginal secretion, menstrual blood, and skin. The specificity was evaluated by examining the single-source body fluids/tissue and revealed that the same body fluid exhibited similar expression profiles and the tissue origin could be identified. For laboratory-generated mixtures containing 2–6 different components and mock case mixtures, the donor of each component could be successfully identified, except for the skin donor. The discriminatory power for all body fluids ranged from 0.997176329 (menstrual blood) to 0.99999999827 (blood). The concordance of DNA typing and mRNA typing for the cSNPs in this system was also validated. This cSNP typing system exhibits excellent performance in mixture deconvolution.</p></div>","PeriodicalId":50435,"journal":{"name":"Forensic Science International-Genetics","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141240156","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}
引用次数: 0
Shedding more light on shedders 进一步了解脱毛器
IF 3.1 2区 医学
Forensic Science International-Genetics Pub Date : 2024-05-30 DOI: 10.1016/j.fsigen.2024.103065
Piyamas Petcharoen , Madison Nolan , K. Paul Kirkbride , Adrian Linacre
{"title":"Shedding more light on shedders","authors":"Piyamas Petcharoen ,&nbsp;Madison Nolan ,&nbsp;K. Paul Kirkbride ,&nbsp;Adrian Linacre","doi":"10.1016/j.fsigen.2024.103065","DOIUrl":"https://doi.org/10.1016/j.fsigen.2024.103065","url":null,"abstract":"<div><p>We report on testing 100 individuals for their shedder status with the aim of demonstrating whether the process of cell staining is reproducible when testing a large number of people. A previous report using the same method was based on 11 donors and indicated that there may be a continuum of shedder types within this small sample set. In this report we also expand the time points post-handwashing to 0, 15, 30, 60, and 180 min. Triplicate samples were collected from both the right and left thumbs. Samples were collected by donors placing a thumb on a clean glass slide and then adding a DNA binding dye. The number of cells were recorded within three separate square millimetre areas (cells/mm<sup>2</sup>) at 220x magnification. The experiments were conducted in triplicate on three different days, giving a total of 72 thumbprints per individual. Finally, there were 3438 observed frames in the entire dataset. Of the 100 donors, 98 gave consistent and reproducible cell number deposition. There was no difference between the cells deposited by the left and right thumbs in 13 of 15 tested. Males tended to deposit more cells than females. If applying arbitrary boundary to a cell count to definitively determine shedder status, then many of the donors fell within two categories. This study based on 100 individuals strongly suggests that shedder status is a continuum phenomenon.</p></div>","PeriodicalId":50435,"journal":{"name":"Forensic Science International-Genetics","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1872497324000619/pdfft?md5=011dbe27ad1e78ca8b0a5ec7b17de195&pid=1-s2.0-S1872497324000619-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141292258","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}
引用次数: 0
A novel type of three band pattern at STR loci 一种新型的 STR 位点三带模式
IF 3.1 2区 医学
Forensic Science International-Genetics Pub Date : 2024-05-26 DOI: 10.1016/j.fsigen.2024.103064
B. Rolf, A. Phillip, K. Hannig, S. Köhler, I. Göttesdorfer
{"title":"A novel type of three band pattern at STR loci","authors":"B. Rolf,&nbsp;A. Phillip,&nbsp;K. Hannig,&nbsp;S. Köhler,&nbsp;I. Göttesdorfer","doi":"10.1016/j.fsigen.2024.103064","DOIUrl":"https://doi.org/10.1016/j.fsigen.2024.103064","url":null,"abstract":"<div><p>SE33 or ACTBP2 is the most polymorphic locus in many national DNA databases and in the commercial STR kits used to type both crime scene samples and reference samples to populate these databases. We describe the molecular reason for a three band pattern of SE33 seen in several samples. A SNP in the flanking SE33 region causes the binding of the unlabelled D3S1358 primer. As a result, a “chimeric” PCR product of the labelled SE33 primer and the D3S1358 primer is generated that is smaller than the regular SE33 amplicon. We call this “Type 3 three band pattern” as the genetic base differs from the Type 1 three band pattern caused by somatic mosaicism and the Type 2 that results from copy number variation.</p></div>","PeriodicalId":50435,"journal":{"name":"Forensic Science International-Genetics","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-05-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141240151","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}
引用次数: 0
Development of a two-layer machine learning model for the forensic application of legal and illegal poppy classification based on sequence data 开发基于序列数据的合法和非法罂粟分类法医应用双层机器学习模型
IF 3.1 2区 医学
Forensic Science International-Genetics Pub Date : 2024-05-22 DOI: 10.1016/j.fsigen.2024.103061
Hyung-Eun An , Min-Ho Mun , Adeel Malik , Chang-Bae Kim
{"title":"Development of a two-layer machine learning model for the forensic application of legal and illegal poppy classification based on sequence data","authors":"Hyung-Eun An ,&nbsp;Min-Ho Mun ,&nbsp;Adeel Malik ,&nbsp;Chang-Bae Kim","doi":"10.1016/j.fsigen.2024.103061","DOIUrl":"10.1016/j.fsigen.2024.103061","url":null,"abstract":"<div><p>Poppies are beneficial plants with a variety of applications, including medicinal, edible, ornamental, and industrial purposes. Some <em>Papaver</em> species are forensically significant plants because they contain opium, a narcotic substance. Internationally trafficked species of illegal poppies are being identified by DNA barcoding employing multiple markers in response to their forensic value. However, effective markers for precise species identification of legal and illegal poppies are still under discussion, with research on illegal poppies focusing on <em>Papaver somniferum</em> L., and species identification studies of <em>Papaver bracteatum</em> and <em>Papaver setigerum</em> DC. still lacking. As a result, in order to evaluate the performance of genetic markers and classify their DNA sequences in the genus <em>Papaver</em>, this study developed the first machine learning-based two-layer model, in which the first layer classifies legal and illegal poppies from the given sequence and the second layer identifies species of illegal poppies using their sequences. We constructed the dataset and investigated biological features from four markers, internal transcribed spacer 1 (ITS1), internal transcribed spacer 2 (ITS2), transfer RNA Leucine (trnL), transfer RNA Leucine - transfer RNA Phenylalanine intergenic spacer (trnL–trnF intergenic spacer) and their combination, using four machine learning algorithms, K-nearest neighbor (KNN), Naïve Bayes (NB), extreme gradient boost (XGBoost) and Random Forest (RF). According to our findings, for Layer 1 to classify legal and illegal poppies, KNN-based models using combined ITS region achieved the greatest performance of accuracy 0.846 and 0.889 using training and test sets, respectively. Additionally, for Layer 2 to identify illegal poppy species, KNN-based models using combined ITS region achieved the best performance of 0.833 and 1.000 for using training and test sets, respectively. To validate the model, the combined ITS region, which includes ITS 1 and 2 sequences, from blind poppy samples were used as a case study, with the Layer 1 correctly classifying legal and illegal poppies with over 0.830 accuracy. Layer 2 correctly identified <em>P. setigerum</em> DC., however, only one of the three <em>P. somniferum</em> L. species was accurately identified. Nevertheless, our research shows that machine learning can be used to classify and identify legal and illegal poppy species using DNA barcodes which can then be used as an efficient and effective forensic tool for improved law enforcement and a safer society.</p></div>","PeriodicalId":50435,"journal":{"name":"Forensic Science International-Genetics","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1872497324000553/pdfft?md5=b07331f0615a4fbf6f5400482d9c7b44&pid=1-s2.0-S1872497324000553-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141143312","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}
引用次数: 0
Corrigendum to “Biological amplification of low frequency mutations unravels laboratory culture history of the bio-threat agent Francisella tularensis” [Forensic Sci. Int.: Genet. 45 (2020) 102230] 对 "低频突变的生物扩增揭示了土拉弗氏菌的实验室培养历史 "的更正[Forensic Sci. Int.: Genet. 45 (2020) 102230]。
IF 3.1 2区 医学
Forensic Science International-Genetics Pub Date : 2024-05-18 DOI: 10.1016/j.fsigen.2024.103063
Chinmay Dwibedi , Pär Larsson , Jon Ahlinder , Petter Lindgren , Kerstin Myrtennäs , Malin Granberg , Eva Larsson , Caroline Öhrman , Andreas Sjödin , Per Stenberg , Mats Forsman , Anders Johansson
{"title":"Corrigendum to “Biological amplification of low frequency mutations unravels laboratory culture history of the bio-threat agent Francisella tularensis” [Forensic Sci. Int.: Genet. 45 (2020) 102230]","authors":"Chinmay Dwibedi ,&nbsp;Pär Larsson ,&nbsp;Jon Ahlinder ,&nbsp;Petter Lindgren ,&nbsp;Kerstin Myrtennäs ,&nbsp;Malin Granberg ,&nbsp;Eva Larsson ,&nbsp;Caroline Öhrman ,&nbsp;Andreas Sjödin ,&nbsp;Per Stenberg ,&nbsp;Mats Forsman ,&nbsp;Anders Johansson","doi":"10.1016/j.fsigen.2024.103063","DOIUrl":"10.1016/j.fsigen.2024.103063","url":null,"abstract":"","PeriodicalId":50435,"journal":{"name":"Forensic Science International-Genetics","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-05-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1872497324000590/pdfft?md5=173ab6eff4ff24611d6ea0cbe319584e&pid=1-s2.0-S1872497324000590-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140961266","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}
引用次数: 0
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