Forensic Science International: Genetics Supplement Series最新文献

Update of aims population data and test with the genogeographer admixture module 目标人口数据的更新和基因地理学混合模块的测试

Forensic Science International: Genetics Supplement Series Pub Date : 2022-12-01 DOI: 10.1016/j.fsigss.2022.09.006

H.S. Mogensen , T. Tvedebrink , V. Pereira , P.S. Eriksen , N. Morling

{"title":"Update of aims population data and test with the genogeographer admixture module","authors":"H.S. Mogensen , T. Tvedebrink , V. Pereira , P.S. Eriksen , N. Morling","doi":"10.1016/j.fsigss.2022.09.006","DOIUrl":"https://doi.org/10.1016/j.fsigss.2022.09.006","url":null,"abstract":"<div><p>Individuals from Slovenia, Greece, Albania, and Eritrea were typed with the Precision ID Ancestry Panel and included among GenoGeographer’s nine reference populations (Sub-Saharan Africa, Horn of Africa, North Africa, Middle East, Europe, South/Central Asia, East Asia, and East and West Greenland). We tested the performance of GenoGeographer with the Admixture Module on AIM profiles of 3548 individuals assumed to belong to one of the reference populations. A total of 3387 (95.5 %) profiles were assigned to one or more of the reference populations, either a single population or an admixture of two or more populations, while 161 (4.5 %) profiles were not assigned to any reference population or admixtures thereof. For 1486 AIM profiles with no reference population of origin in GenoGeographer, the rejection rate was more than 70 % for AIM profiles from North and South America and less than 20 % for those from Central, North, and Northeast Asia.</p></div>","PeriodicalId":56262,"journal":{"name":"Forensic Science International: Genetics Supplement Series","volume":"8 ","pages":"Pages 15-16"},"PeriodicalIF":0.0,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1875176822000063/pdfft?md5=4f46368ddd5376bafde8ca80ee5427a4&pid=1-s2.0-S1875176822000063-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71876089","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Empirical validation of a family-member prioritization approach to maximize statistical power in missing person cases 家庭成员优先排序方法的实证验证，以最大限度地提高失踪人口案件的统计能力

Forensic Science International: Genetics Supplement Series Pub Date : 2022-12-01 DOI: 10.1016/j.fsigss.2022.10.059

Martin Iungman, Sebastian Biagini, Malena Canteros, Luciana Rabitti, Jessica Maggiore, Tamara Samsonowicz, Mariana Herrera Piñero

引用次数: 0

A method to enable forensic genetic genealogy investigations from DNA mixtures 一种能够从DNA混合物中进行法医遗传谱系调查的方法

Forensic Science International: Genetics Supplement Series Pub Date : 2022-12-01 DOI: 10.1016/j.fsigss.2022.10.020

Rebecca Mitchell, Sana Enke, Kim Eskey, Tracy Ferguson, Rebecca Just

引用次数: 3

Discrete Laplace as applied to the SWGDAM-compliant U.S. subpopulations in the Y Chromosome Haplotype Reference Database 离散拉普拉斯应用于Y染色体单倍型参考数据库中符合swgdam的美国亚群

Forensic Science International: Genetics Supplement Series Pub Date : 2022-12-01 DOI: 10.1016/j.fsigss.2022.10.024

Brandon Letts , Steven Myers , Christopher Askew , Suzanne Barritt-Ross , Ann Marie Gross , Dixie Peters , Lutz Roewer , Jeanette Wallin , Sascha Willuweit

{"title":"Discrete Laplace as applied to the SWGDAM-compliant U.S. subpopulations in the Y Chromosome Haplotype Reference Database","authors":"Brandon Letts , Steven Myers , Christopher Askew , Suzanne Barritt-Ross , Ann Marie Gross , Dixie Peters , Lutz Roewer , Jeanette Wallin , Sascha Willuweit","doi":"10.1016/j.fsigss.2022.10.024","DOIUrl":"https://doi.org/10.1016/j.fsigss.2022.10.024","url":null,"abstract":"<div><p>Late in 2021, the Y Chromosome Haplotype Reference Database (YHRD) added the capability to perform discrete Laplace statistical calculations on searches performed against their SWGDAM-compliant U.S. subpopulations. Because discrete Laplace is not a commonly used or reported statistic in the United States, the SWGDAM Lineage Marker Committee, responsible for maintaining the SWGDAM Interpretation Guidelines for Y-Chromosome STR Testing, evaluated the feature to assess its ease of use and applicability to U.S. casework. Discrete Laplace calculates profile probabilities based on their genetic distance from sets of ancestral alleles and can yield much more informative probability estimates than the commonly used Clopper-Pearson 95% upper confidence interval (UCI). This is especially true for rare profiles with no database observations because, unlike the 95% UCI, the discrete Laplace calculation is not based upon how many times a profile is observed in the database. However, the statistic as applied by YHRD also has some limitations, such as a requirement that the query profile is complete for the ‘minimal’ kit and that expanded loci beyond those included in the Y17 kit cannot be included in the calculation. Here, we explain how discrete Laplace works and demonstrate how the results compare to those generated using the 95% UCI.</p></div>","PeriodicalId":56262,"journal":{"name":"Forensic Science International: Genetics Supplement Series","volume":"8 ","pages":"Pages 170-172"},"PeriodicalIF":0.0,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1875176822000634/pdfft?md5=ce224c40c9cb5601424bdcc1109b473c&pid=1-s2.0-S1875176822000634-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71876654","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Make it "SNPPY" - Updates to SRM 2391d: PCR-Based DNA Profiling Standard 使它“时髦”-更新到SRM 2391d:基于pcr的DNA分析标准

Forensic Science International: Genetics Supplement Series Pub Date : 2022-12-01 DOI: 10.1016/j.fsigss.2022.09.004

Carolyn R. Steffen, Erica L. Romsos, Kevin M. Kiesler, Lisa A. Borsuk, Katherine B. Gettings, Peter M. Vallone

{"title":"Make it \"SNPPY\" - Updates to SRM 2391d: PCR-Based DNA Profiling Standard","authors":"Carolyn R. Steffen, Erica L. Romsos, Kevin M. Kiesler, Lisa A. Borsuk, Katherine B. Gettings, Peter M. Vallone","doi":"10.1016/j.fsigss.2022.09.004","DOIUrl":"https://doi.org/10.1016/j.fsigss.2022.09.004","url":null,"abstract":"<div><p>Standard Reference Material (SRM) 2391d: PCR-Based DNA Profiling Standard was released to the forensic community in 2019. Next Generation Sequencing (NGS) was used as the primary method of certification, where certified values were assigned when a high coverage sequence string was available for a marker. Using NGS to assign values has allowed for additional marker sets beyond short tandem repeat (STR) loci, including single nucleotide polymorphisms (SNPs) and mitochondrial DNA (mtDNA) whole genome sequences, to be included in the Certificate of Analysis (COA). Since the 2019 release, several commercial NGS panels have become available including the Verogen ForenSeq mtDNA Control Region, mtDNA Whole Genome, MainstAY, and Kintelligence Kits. In addition, three community Ion AmpliSeq panels from Thermo Fisher (MH-74 Plex, VISAGE, and Y-SNP) are now available. While the mtDNA whole genome sequence for the components are already included and no new STR markers are introduced by MainstAY, the other recently released panels allow for the inclusion of > 11,000 additional SNPs (e.g., identity, ancestry, phenotype, kinship, and X- and Y-SNPs) and 74 microhaplotypes to the COA for SRM 2391d in an update completed by fall of 2022.</p></div>","PeriodicalId":56262,"journal":{"name":"Forensic Science International: Genetics Supplement Series","volume":"8 ","pages":"Pages 9-11"},"PeriodicalIF":0.0,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S187517682200004X/pdfft?md5=f96cd07a300153c6df19e67357df0148&pid=1-s2.0-S187517682200004X-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71876950","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Seven years of SNPs: An assessment of methods utilized for generating profiles for forensic genetic genealogy 七年的snp:用于法医遗传谱系生成档案的方法评估

Forensic Science International: Genetics Supplement Series Pub Date : 2022-12-01 DOI: 10.1016/j.fsigss.2022.11.002

Rachel H. Oefelein

引用次数: 1

Whole-genome sequencing of degraded DNA for investigative genetic genealogy 降解DNA的全基因组测序用于调查遗传谱系

Forensic Science International: Genetics Supplement Series Pub Date : 2022-12-01 DOI: 10.1016/j.fsigss.2022.09.008

Janet Cady, Ellen M. Greytak

引用次数: 2

Bayesian networks for DNA-based kinship analysis: Functionality and validation of the GENis missing person identification module 基于dna的亲属关系分析的贝叶斯网络:GENis失踪人员识别模块的功能和验证

Forensic Science International: Genetics Supplement Series Pub Date : 2022-12-01 DOI: 10.1016/j.fsigss.2022.10.008

Ariel Chernomoretz , Franco Marsico , Javier Iserte , Mariana Herrera Piñero , Maria Soledad Escobar , Manuel Balparda , Gustavo Sibilla

{"title":"Bayesian networks for DNA-based kinship analysis: Functionality and validation of the GENis missing person identification module","authors":"Ariel Chernomoretz , Franco Marsico , Javier Iserte , Mariana Herrera Piñero , Maria Soledad Escobar , Manuel Balparda , Gustavo Sibilla","doi":"10.1016/j.fsigss.2022.10.008","DOIUrl":"https://doi.org/10.1016/j.fsigss.2022.10.008","url":null,"abstract":"<div><p>GENis is a recently published open-source multi-tier information system developed to run forensic DNA databases. It relies on a Bayesian Networks framework and it is particularly well suited to efficiently perform large-size queries against databases of missing individuals. In this contribution we present a validation of the missing person identification capabilities of GENis. To that end we introduce <em>fbnet</em>, a free-software package written in the R statistical language that implements the complete GENis functionality to perform kinship analysis based on DNA profiles. With the aid of <em>fbnet</em>, we could validate likelihood ratios against estimations draw with <em>Familias</em> and <em>forrel</em> (two well-recognized R packages for kinship quantification) for complex pedigrees provided by the Argentinian reference databank (Banco Nacional de Datos Geneticos, BNDG). We found that our methodological approach presented an excellent performance in terms of accuracy and computation times.</p></div>","PeriodicalId":56262,"journal":{"name":"Forensic Science International: Genetics Supplement Series","volume":"8 ","pages":"Pages 131-132"},"PeriodicalIF":0.0,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1875176822000506/pdfft?md5=3a682bd32b94df4e7a042365cc2337ab&pid=1-s2.0-S1875176822000506-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71876371","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Haplogroup prediction in the Ghanaian population using haplotype data of 27 Yfiler® Plus loci and TaqMan SNP genotyping 利用27个Yfiler®Plus基因座单倍型数据和TaqMan SNP基因分型预测加纳人群的单倍型

Forensic Science International: Genetics Supplement Series Pub Date : 2022-12-01 DOI: 10.1016/j.fsigss.2022.10.015

Pet-Paul Wepeba , Chrissie S. Abaidoo , William H. Goodwin

{"title":"Haplogroup prediction in the Ghanaian population using haplotype data of 27 Yfiler® Plus loci and TaqMan SNP genotyping","authors":"Pet-Paul Wepeba , Chrissie S. Abaidoo , William H. Goodwin","doi":"10.1016/j.fsigss.2022.10.015","DOIUrl":"https://doi.org/10.1016/j.fsigss.2022.10.015","url":null,"abstract":"<div><p>This study describes the use of the 27 loci Yfiler® Plus kit and TaqMan™ SNP genotyping to characterise and predict the haplogroups of Y chromosomes within the four major ethnic populations of Ghana. Haplogroups were assigned using the desktop NevGen software (<span>https://www.nevgen.org/</span><svg><path></path></svg>). The E1b1a and E1b1b haplogroups are the most common in the Ghanaian population and form 95% of the dataset. The Mole-Dagomba sub-population had 4. 8% assigned to the haplogroups G, H, R1b, R2 and T. The Ewe had two samples assigned to haplogroups C and D whilst the Akan had one sample each assigned to haplogroups B, J1 and J2. The NevGen predicted haplogroups were further screened with TaqMan™ genotyping for confirmation. In conclusion, ≈ 95% of the dataset was classified as M-E1b1a using NevGen combined with TaqMan™ SNP Genotyping for confirmation. The TaqMan™ also revealed 5% as J1 and other haplogroups, using an in-house control from the J1 haplogroup.</p></div>","PeriodicalId":56262,"journal":{"name":"Forensic Science International: Genetics Supplement Series","volume":"8 ","pages":"Pages 147-148"},"PeriodicalIF":0.0,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1875176822000543/pdfft?md5=cb85b5371c9f5f709fb5abd4dffe0abf&pid=1-s2.0-S1875176822000543-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71876372","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Introducing eNoC – A simple, excel-based tool for improved assignment of the number of contributors (NoC) to a mixture 介绍eNoC -一个简单的，基于excel的工具，用于改进对混合物的贡献者数量(NoC)的分配

Forensic Science International: Genetics Supplement Series Pub Date : 2022-12-01 DOI: 10.1016/j.fsigss.2022.09.016

Jim Thomson, David Moore, Tim Clayton

{"title":"Introducing eNoC – A simple, excel-based tool for improved assignment of the number of contributors (NoC) to a mixture","authors":"Jim Thomson, David Moore, Tim Clayton","doi":"10.1016/j.fsigss.2022.09.016","DOIUrl":"https://doi.org/10.1016/j.fsigss.2022.09.016","url":null,"abstract":"<div><p>Assigning NoC in a mixed STR profile is an important preliminary step in computing a likelihood ratio (LR). A common metric is maximum allele count (MAC) whereby the locus exhibiting the largest number of alleles is used to set the NOC. This metric can be supplemented by considering total allele count (TAC) and locus allele count (LAC). TAC is the total number of alleles across all loci and is compared with probability distributions generated <em>in silico</em>. LAC works similarly, save that the probability distributions are generated at the locus level. Herein, we present a comparative analysis of these three metrics using a dataset of 10,000 of each of 2–7 person simulated ground truth mixtures. These datasets were used to generate parameter distributions for each NoC. This analysis showed LAC to be the most accurate single metric in all circumstances tested. We have developmentally validated an excel-based tool to automate calculations for use by operational caseworkers.</p></div>","PeriodicalId":56262,"journal":{"name":"Forensic Science International: Genetics Supplement Series","volume":"8 ","pages":"Pages 42-44"},"PeriodicalIF":0.0,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1875176822000166/pdfft?md5=f5583095331ee6f80a07ca1222804fba&pid=1-s2.0-S1875176822000166-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71876468","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0