1
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Huang Y, Wang M, Liu C, He G. Comprehensive landscape of non-CODIS STRs in global populations provides new insights into challenging DNA profiles. Forensic Sci Int Genet 2024; 70:103010. [PMID: 38271830 DOI: 10.1016/j.fsigen.2024.103010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 01/13/2024] [Accepted: 01/14/2024] [Indexed: 01/27/2024]
Abstract
The worldwide implementation of short tandem repeats (STR) profiles in forensic genetics necessitated establishing and expanding the CODIS core loci set to facilitated efficient data management and exchange. Currently, the mainstay CODIS STRs are adopted in most general-purpose forensic kits. However, relying solely on these loci failed to yield satisfactory results for challenging tasks, such as bio-geographical ancestry inference, complex DNA mixture profile interpretation, and distant kinship analysis. In this context, non-CODIS STRs are potent supplements to enhance the systematic discriminating power, particularly when combined with the high-throughput next-generation sequencing (NGS) technique. Nevertheless, comprehensive evaluation on non-CODIS STRs in diverse populations was scarce, hindering their further application in routine caseworks. To address this gap, we investigated genetic variations of 178 historically available non-CODIS STRs from ethnolinguistically different worldwide populations and studied their characteristics and forensic potentials via high-coverage whole genome sequencing (WGS) data. Initially, we delineated the genomic properties of these non-CODIS markers through sequence searching, repeat structure scanning, and manual inspection. Subsequent population genetics analysis suggested that these non-CODIS STRs had comparable polymorphism levels and forensic utility to CODIS STRs. Furthermore, we constructed a theoretical next-generation sequencing (NGS) panel comprising 108 STRs (20 CODIS STRs and 88 non-CODIS STRs), and evaluated its performance in inferring bio-geographical ancestry origins, deconvoluting complex DNA mixtures, and differentiating distant kinships using real and simulated datasets. Our findings demonstrated that incorporating supplementary non-CODIS STRs enabled the extrapolation of multidimensional information from a single STR profile, thereby facilitating the analysis of challenging forensic tasks. In conclusion, this study presents an extensive genomic landscape of forensic non-CODIS STRs among global populations, and emphasized the imperative inclusion of additional polymorphic non-CODIS STRs in future NGS-based forensic systems.
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Affiliation(s)
- Yuguo Huang
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu 610041, China.
| | - Mengge Wang
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu 610041, China
| | - Chao Liu
- Anti-Drug Technology Center of Guangdong Province, Guangzhou 510230, China; Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China.
| | - Guanglin He
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu 610041, China; Center for Archaeological Science, Sichuan University, Chengdu 610000, China.
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2
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Chiao A, Ge J. Determining lineages between individuals with high-density mitochondrial and Y-chromosomal single-nucleotide polymorphisms. Electrophoresis 2024; 45:843-851. [PMID: 38010138 DOI: 10.1002/elps.202300142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 10/19/2023] [Accepted: 11/12/2023] [Indexed: 11/29/2023]
Abstract
Genetic genealogy has been more frequently used in forensic investigations in identifying criminals. However, the current genetic genealogy applications usually do not consider lineage markers (including both Y and mitochondrial deoxyribonucleic acid (DNA)), which is probably because not all distant relatives share the same lineage markers. In addition, there is no study to show how to use lineage markers and what methods or thresholds should be applied in genetic genealogy. In this study, we developed a method to quickly determine if two single-nucleotide polymorphism (SNP) profiles are from the same paternal or material lineages by using a mismatch frequency of the SNPs in Y-chromosomal or mitochondrial DNA. For both Y and mitochondrial SNPs, profile pairs from the same or different lineages can be decided with high accuracies (i.e., 0.380% or 0.157% error rates with Y and mitochondrial DNA, respectively). With kinship coefficient filtering based on autosomal SNPs, the accuracies of determining maternal and paternal lineage can be further improved (i.e., 0.120% or 0.057% error rates with Y and mitochondrial DNA, respectively, using a threshold of kinship coefficient >0). This study shows that lineage markers can be very powerful tools with high accuracies to determine lineages, which could help solve cases and reduce costs for genetic genealogy investigations.
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Affiliation(s)
- Austin Chiao
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, Texas, USA
- Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, Fort Worth, Texas, USA
| | - Jianye Ge
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, Texas, USA
- Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, Fort Worth, Texas, USA
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3
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Salvo NM, Olsen GH, Berg T, Janssen K. Biogeographical Ancestry Analyses Using the ForenSeq TM DNA Signature Prep Kit and Multiple Prediction Tools. Genes (Basel) 2024; 15:510. [PMID: 38674444 PMCID: PMC11050699 DOI: 10.3390/genes15040510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Revised: 04/15/2024] [Accepted: 04/16/2024] [Indexed: 04/28/2024] Open
Abstract
The inference of biogeographical ancestry (BGA) can assist in police investigations of serious crime cases and help to identify missing people and victims of mass disasters. In this study, we evaluated the typing performance of 56 ancestry-informative SNPs in 177 samples using the ForenSeq™ DNA Signature Prep Kit on the MiSeq FGx system. Furthermore, we compared the prediction accuracy of the tools Universal Analysis Software v1.2 (UAS), the FROG-kb, and GenoGeographer when inferring the ancestry of 503 Europeans, 22 non-Europeans, and 5 individuals with co-ancestry. The kit was highly sensitive with complete aiSNP profiles in samples with as low as 250pg input DNA. However, in line with others, we observed low read depth and occasional drop-out in some SNPs. Therefore, we suggest not using less than the recommended 1ng of input DNA. FROG-kb and GenoGeographer accurately predicted both Europeans (99.6% and 91.8% correct, respectively) and non-Europeans (95.4% and 90.9% correct, respectively). The UAS was highly accurate when predicting Europeans (96.0% correct) but performed poorer when predicting non-Europeans (40.9% correct). None of the tools were able to correctly predict individuals with co-ancestry. Our study demonstrates that the use of multiple prediction tools will increase the prediction accuracy of BGA inference in forensic casework.
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Affiliation(s)
- Nina Mjølsnes Salvo
- Centre for Forensic Genetics, Department of Medical Biology, Faculty of Health Sciences, UiT The Arctic University of Norway, Post Box 6050, 9037 Tromsø, Norway
| | | | | | - Kirstin Janssen
- Centre for Forensic Genetics, Department of Medical Biology, Faculty of Health Sciences, UiT The Arctic University of Norway, Post Box 6050, 9037 Tromsø, Norway
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4
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Guo F, Liu Z, Long G, Zhang B, Liu D, Yu S. Performance and characterization of 94 identity-informative SNPs in Northern Han Chinese using ForenSeq ™ DNA signature prep kit. J Forensic Leg Med 2024; 103:102678. [PMID: 38522119 DOI: 10.1016/j.jflm.2024.102678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Revised: 03/05/2024] [Accepted: 03/17/2024] [Indexed: 03/26/2024]
Abstract
Target and flanking region (FR) variation at 94 identity-informative SNPs (iSNPs) are investigated in 635 Northern Han Chinese using the ForenSeq DNA Signature Prep Kit on the MiSeq FGx Forensic Genomics System. The dataset presents the following performance characteristics (average values): ≥60% bases with a quality score of 20 or higher (%≥ Q20); >700 × of depth of coverage (DoC) from both Sample Details Reports and Flanking Region Reports; >80% of effective reads; ≥60% of allele coverage ratio (ACR); and ≥70% of inter-locus balance, while some stable low-performance characteristics are also observed: low DoC at rs1736442, rs1031825, rs7041158, rs338882, rs2920816, rs1493232, rs719366, and rs2342747; high noise at rs891700; and imbalanced ACR at rs6955448 and rs338882. The average amplicon length is 69 bp, suitable for detecting degraded samples. Bioinformatic concordance achieves 99.99% between the ForenSeq Universal Analysis Software (UAS) and the Integrative Genomic Viewer (IGV) inspection. Discordance results from flanking region deletions of rs10776839, rs8078417, rs2831700, and rs1454361. Due to FR variants within amplicons detected by massively parallel sequencing (MPS), the increases in the number of unique alleles, effective alleles (Ae), and observed heterozygosity (Hobs) are 46.81%, 4.51%, and 3.29%, respectively. Twelve FR variants are first reported to dbSNP, such as rs1252699848, rs1665500714, rs1771121532, rs2097285015, rs1851671415, rs2045669877, rs2046758811, rs2044248635, rs1251308240, rs1968822112, rs1981638299, and rs1341756746. All 94 iSNPs from target and amplicon data are in Hardy-Weinberg equilibrium (HWE) and independent within autosomes. As expected, forensic parameters from the amplicon data increase significantly on the combined power of discrimination (CPD = 1 - 3.9876 × 10-38) and the combined power of exclusion (CPE = 1 - 6.6690 × 10-8). Additionally, the power of the system effectiveness (CPD = 1 - 6.7054 × 10-72 and CPE = 1 - 4.4719 × 10-20) with sequence-based 27 autosomal STRs and 94 iSNP amplicons in combination is substantially improved compared to one type of marker alone. In conclusion, we have established a traditional length-based and current sequence-based reference database with 58 STRs and 94 iSNPs in the Northern Han Chinese population. We hope these data can serve as a solid reference and foundation for forensic practice.
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Affiliation(s)
- Fei Guo
- Shenyang Medical College, Shenyang, Liaoning, 110034, PR China; Key Laboratory of Human Ethnic Specificity and Phenomics of Critical Illness in Liaoning Province, Shenyang, Liaoning, 110034, PR China; Key Laboratory of Phenomics in Shenyang City, Shenyang, Liaoning, 110034, PR China.
| | - Ze Liu
- DNA Laboratory of Forensic Science Center, Shenyang Public Security Bureau, Shenyang, Liaoning, 110002, PR China
| | - Guannan Long
- DNA Laboratory of Forensic Science Center, Shenyang Public Security Bureau, Shenyang, Liaoning, 110002, PR China
| | - Biao Zhang
- DNA Laboratory of Forensic Science Center, Shenyang Public Security Bureau, Shenyang, Liaoning, 110002, PR China
| | - Dahua Liu
- Department of Forensic Medicine, Jinzhou Medical University, Jinzhou, Liaoning, 121001, PR China
| | - Shaobo Yu
- DNA Laboratory of Forensic Science Center, Shenyang Public Security Bureau, Shenyang, Liaoning, 110002, PR China.
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Liu J, Li S, Su Y, Wen Y, Qin L, Zhao M, Hui M, Jiang L, Chen X, Hou Y, Wang Z. A proof-of-principle study: The potential application of MiniHap biomarkers in ancestry inference based on the QNome nanopore sequencing. Forensic Sci Int Genet 2024; 68:102947. [PMID: 37862770 DOI: 10.1016/j.fsigen.2023.102947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 09/25/2023] [Accepted: 10/16/2023] [Indexed: 10/22/2023]
Abstract
Haplotyped SNPs convey forensic-related information, and microhaplotypes (MHs), as the most representative of this kind of marker, have proved the potential value for human forensics. In recent years, nanopore sequencing technology has developed rapidly, with its outstanding ability to sequence long continuous DNA fragments and obtain phase information, making the detection of longer haplotype marker possible. In this proof-of-principle study, we proposed a new type of forensic marker, MiniHap, based on five or more SNPs within a molecular distance less than 800 bp, and investigated the haplotype data of 56 selected MiniHaps in five Chinese populations using the QNome nanopore sequencing. The sequencing performance, allele (haplotype) frequencies, forensic parameters, effective number of alleles (Ae), and informativeness (In) were subsequently calculated. In addition, we performed principal component analysis (PCA), phylogenetic tree, and structure analysis to investigate the population genetic relationships and ancestry components among the five investigated populations and 26 worldwide populations. MiniHap-04 exhibited remarkable forensic efficacy, with 148 haplotypes reported and the Ae was 66.9268. In addition, the power of discrimination (PD) was 0.9934, the probability of exclusion (PE) was 0.9898, and the In value was 0.7893. Of the 56 loci, 85.71% had PD values above 0.85, 66.07% had PE values above 0.54, 67.86% had Ae values over 7.0%, and 55.36% were with In values above 0.2 across all samples, indicating that most of the MiniHaps are suitable for individual identification, paternity testing, mixture deconvolution, and ancestry inference. Moreover, the results of PCA, phylogenetic tree and structure analysis demonstrated that this MiniHap panel had the competency in continental population ancestry inference, but the differentiation within intracontinental/linguistically restricted subpopulations was not ideal. Such findings suggested that the QNome device for MiniHap detection was feasible and this novel marker has the potential in ancestry inference. Yet, the establishment of a more comprehensive database with sufficient reference population data remains necessary to screen more suitable MiniHaps.
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Affiliation(s)
- Jing Liu
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Suyu Li
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Yonglin Su
- Department of Rehabilitation Medicine, West China Hospital Sichuan University, Chengdu 610041, China
| | - Yufeng Wen
- School of Life Sciences, Jilin University, Changchun 130012, China
| | - Liu Qin
- Qitan Technology Ltd., Chengdu 610044, China
| | - Mengyao Zhao
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Minxiao Hui
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Lirong Jiang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Xiacan Chen
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Yiping Hou
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Zheng Wang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China.
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Cai M, Li S, Zhang X, Xie W, Shi J, Yuan X, Yao J, Zhu B. Ancestral Information Analysis of Chinese Korean Ethnic Group via a Novel Multiplex DIP System. J Mol Evol 2023; 91:922-934. [PMID: 38006428 DOI: 10.1007/s00239-023-10143-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 11/07/2023] [Indexed: 11/27/2023]
Abstract
Deletion/insertion polymorphism (DIP) is one of the more promising genetic markers in the field of forensic genetics for personal identification and biogeographic ancestry inference. In this research, we used an in-house developed ancestry-informative marker-DIP system, including 56 autosomal diallelic DIPs, three Y-chromosomal DIPs, and an Amelogenin gene, to analyze the genetic polymorphism and ancestral composition of the Chinese Korean group, as well as to explore its genetic relationships with the 26 reference populations. The results showed that this novel panel exhibited high genetic polymorphism in the studied Korean group and could be effectively applied for forensic individual identification in the Korean group. In addition, the results of multiple population genetic analyses indicated that the ancestral component of the Korean group was dominated by northern East Asia. Moreover, the Korean group was more closely related to the East Asian populations, especially to the Japanese population in Tokyo. This study enriched the genetic data of the Korean ethnic group in China and provided information on the ancestry of the Korean group from the perspective of population genetics.
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Affiliation(s)
- Meiming Cai
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong, China
| | - Shuanglin Li
- School of Basic Medical Sciences, Shenzhen University Medical School, Shenzhen University, Shenzhen, Guangdong, China
| | - Xingru Zhang
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shanxi, China
| | - Weibing Xie
- School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong, China
| | - Jianfeng Shi
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shanxi, China
| | - Xi Yuan
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong, China
| | - Jun Yao
- Department of Forensic Genetics, School of Forensic Medicine, China Medical University, Shenyang, Liaoning, China.
| | - Bofeng Zhu
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong, China.
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Childebayeva A, Zavala EI. Review: Computational analysis of human skeletal remains in ancient DNA and forensic genetics. iScience 2023; 26:108066. [PMID: 37927550 PMCID: PMC10622734 DOI: 10.1016/j.isci.2023.108066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2023] Open
Abstract
Degraded DNA is used to answer questions in the fields of ancient DNA (aDNA) and forensic genetics. While aDNA studies typically center around human evolution and past history, and forensic genetics is often more concerned with identifying a specific individual, scientists in both fields face similar challenges. The overlap in source material has prompted periodic discussions and studies on the advantages of collaboration between fields toward mutually beneficial methodological advancements. However, most have been centered around wet laboratory methods (sampling, DNA extraction, library preparation, etc.). In this review, we focus on the computational side of the analytical workflow. We discuss limitations and considerations to consider when working with degraded DNA. We hope this review provides a framework to researchers new to computational workflows for how to think about analyzing highly degraded DNA and prompts an increase of collaboration between the forensic genetics and aDNA fields.
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Affiliation(s)
- Ainash Childebayeva
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Anthropology, University of Kansas, Lawrence, KS, USA
| | - Elena I. Zavala
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Department of Biology, University of Oregon, Eugene, OR, USA
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8
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Smith M, Miller S. The Evolution of Forensic Genomics: Regulating Massively Parallel Sequencing. JOURNAL OF BIOETHICAL INQUIRY 2023:10.1007/s11673-023-10316-w. [PMID: 37966660 DOI: 10.1007/s11673-023-10316-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 09/11/2023] [Indexed: 11/16/2023]
Abstract
Forensic genomics now enables law enforcement agencies to undertake rapid and detailed analysis of suspect samples using a technique known as massively parallel sequencing (MPS), including information such as physical traits, biological ancestry, and medical conditions. This article discusses the implications of MPS and provides ethical analysis, drawing on the concept of joint rights applicable to genomic data, and the concept of collective moral responsibility (understood as joint moral responsibility) that are applicable to law enforcement investigations that utilize genomic data. The widespread and unconstrained use of this technology without appropriate legal protections of individual moral rights and associated accountability mechanisms, could potentially not only involve violations of individual moral rights but also lead to an unacceptable shift in the balance of power between governments and the citizenry. We argue that in light of the rights of victims and the security benefits for society, there is a collective moral responsibility for individuals to submit their DNA to law enforcement and for MPS to be used where other, less invasive techniques are not effective. However, this application should be limited by legislation, including that any data obtained should be directly relevant to the investigation and should be destroyed at the conclusion of the investigation.
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Affiliation(s)
- Marcus Smith
- Charles Sturt University, 10 Brisbane Avenue, Canberra, ACT 2600, Australia.
| | - Seumas Miller
- Charles Sturt University, 10 Brisbane Avenue, Canberra, ACT 2600, Australia
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Wen Y, Liu J, Su Y, Chen X, Hou Y, Liao L, Wang Z. Forensic biogeographical ancestry inference: recent insights and current trends. Genes Genomics 2023; 45:1229-1238. [PMID: 37081293 DOI: 10.1007/s13258-023-01387-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 04/01/2023] [Indexed: 04/22/2023]
Abstract
BACKGROUND As a powerful complement to the paradigmatic DNA profiling strategy, biogeographical ancestry inference (BGAI) plays a significant part in human forensic investigation especially when a database hit or eyewitness testimony are not available. It indicates one's biogeographical profile based on known population-specific genetic variations, and thus is crucial for guiding authority investigations to find unknown individuals. Forensic biogeographical ancestry testing exploits much of the recent advances in the understanding of human genomic variation and improving of molecular biology. OBJECTIVE In this review, recent development of prospective ancestry informative markers (AIMs) and the statistical approaches of inferring biogeographic ancestry from AIMs are elucidated and discussed. METHODS We highlight the research progress of three potential AIMs (i.e., single nucleotide polymorphisms, microhaplotypes, and Y or mtDNA uniparental markers) and discuss the prospects and challenges of two methods that are commonly used in BGAI. CONCLUSION While BGAI for forensic purposes has been thriving in recent years, important challenges, such as ethics and responsibilities, data completeness, and ununified standards for evaluation, remain for the use of biogeographical ancestry information in human forensic investigations. To address these issues and fully realize the value of BGAI in forensic investigation, efforts should be made not only by labs/institutions around the world independently, but also by inter-lab/institution collaborations.
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Affiliation(s)
- Yufeng Wen
- Key Laboratory of Evidence Science (China University of Political Science and Law), Ministry of Education, Beijing, 100088, China
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, China
- School of Life Sciences, Jilin University, Changchun, 130012, China
| | - Jing Liu
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Yonglin Su
- Department of Rehabilitation Medicine, West China Hospital Sichuan University, Chengdu, 610041, China
| | - Xiacan Chen
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Yiping Hou
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Linchuan Liao
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, China.
| | - Zheng Wang
- Key Laboratory of Evidence Science (China University of Political Science and Law), Ministry of Education, Beijing, 100088, China.
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, China.
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10
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Jawad M, Adnan A, Rehman RA, Nazir S, Adeyemo OA, Amer SAM, Hadi S, Liu F, Wang CC, Rakha A. Evaluation of facial hair-associated SNPs: a pilot study on male Pakistani Punjabi population. Forensic Sci Med Pathol 2023; 19:293-302. [PMID: 35994154 DOI: 10.1007/s12024-022-00515-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/03/2022] [Indexed: 10/15/2022]
Abstract
Variation in facial hair is one of the most conspicuous features of facial appearance, particularly in South Asia and Middle East countries. A genome-wide association study in Latin Americans has identified multiple genetic variants at distinct loci being associated with facial hair traits including eyebrow thickness, beard thickness, and monobrow. In this pilot study, we have evaluated 16 SNPs associated with facial hair traits in 58 male individuals from the Punjabi population of Pakistan. In our sample, rs365060 in EDAR and rs12597422 in FTO showed significant association with monobrow, rs6684877 in MACF1 showed significant association with eyebrow thickness, and two SNPs in LOC105379031 (rs9654415 and rs7702331) showed significant association with beard thickness. Our results also suggest that genetic association may vary between ethnic groups and geographic regions. Although more data are needed to validate our results, our findings are of value in forensic molecular photofitting research in Pakistan.
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Affiliation(s)
- Muhammad Jawad
- Department of Forensic Sciences, University of Health Sciences, Lahore, Pakistan
| | - Atif Adnan
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen, China.
- Department of Forensic Sciences, College of Criminal Justice, Naif Arab University of Security Sciences, Riyadh, 11452, Kingdom of Saudi Arabia.
| | - Rahat Abdul Rehman
- Department of Forensic Sciences, University of Health Sciences, Lahore, Pakistan
| | - Shahid Nazir
- Department of Forensic Sciences, University of Health Sciences, Lahore, Pakistan
| | - Oyenike A Adeyemo
- Department of Cell Biology and Genetics, Faculty of Science, University of Lagos, AkokaLagos, Yaba, Nigeria
| | - S A M Amer
- Department of Forensic Sciences, College of Criminal Justice, Naif Arab University of Security Sciences, Riyadh, 11452, Kingdom of Saudi Arabia
| | - Sibte Hadi
- Department of Forensic Sciences, College of Criminal Justice, Naif Arab University of Security Sciences, Riyadh, 11452, Kingdom of Saudi Arabia
| | - Fan Liu
- Department of Forensic Sciences, College of Criminal Justice, Naif Arab University of Security Sciences, Riyadh, 11452, Kingdom of Saudi Arabia
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Chuan-Chao Wang
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen, China.
| | - Allah Rakha
- Department of Forensic Sciences, University of Health Sciences, Lahore, Pakistan.
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11
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Aneli S, Fariselli P, Chierto E, Bini C, Robino C, Birolo G. Recombulator-X: A fast and user-friendly tool for estimating X chromosome recombination rates in forensic genetics. PLoS Comput Biol 2023; 19:e1011474. [PMID: 37721960 PMCID: PMC10538763 DOI: 10.1371/journal.pcbi.1011474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 09/28/2023] [Accepted: 08/28/2023] [Indexed: 09/20/2023] Open
Abstract
Genetic markers (especially short tandem repeats or STRs) located on the X chromosome are a valuable resource to solve complex kinship cases in forensic genetics in addition or alternatively to autosomal STRs. Groups of tightly linked markers are combined into haplotypes, thus increasing the discriminating power of tests. However, this approach requires precise knowledge of the recombination rates between adjacent markers. The International Society of Forensic Genetics recommends that recombination rate estimation on the X chromosome is performed from pedigree genetic data while taking into account the confounding effect of mutations. However, implementations that satisfy these requirements have several drawbacks: they were never publicly released, they are very slow and/or need cluster-level hardware and strong computational expertise to use. In order to address these key concerns we developed Recombulator-X, a new open-source Python tool. The most challenging issue, namely the running time, was addressed with dynamic programming techniques to greatly reduce the computational complexity of the algorithm. Compared to the previous methods, Recombulator-X reduces the estimation times from weeks or months to less than one hour for typical datasets. Moreover, the estimation process, including preprocessing, has been streamlined and packaged into a simple command-line tool that can be run on a normal PC. Where previous approaches were limited to small panels of STR markers (up to 15), our tool can handle greater numbers (up to 100) of mixed STR and non-STR markers. In conclusion, Recombulator-X makes the estimation process much simpler, faster and accessible to researchers without a computational background, hopefully spurring increased adoption of best practices.
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Affiliation(s)
- Serena Aneli
- Department of Public Health Sciences and Pediatrics, University of Turin, Turin, Italy
| | - Piero Fariselli
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Elena Chierto
- Department of Public Health Sciences and Pediatrics, University of Turin, Turin, Italy
| | - Carla Bini
- Department of Medical and Surgical Sciences, Section of Legal Medicine, University of Bologna, Bologna, Italy
| | - Carlo Robino
- Department of Public Health Sciences and Pediatrics, University of Turin, Turin, Italy
- S.C. Medicina Legale, AOU Città della Salute e della Scienza, Turin, Italy
| | - Giovanni Birolo
- Department of Medical Sciences, University of Turin, Turin, Italy
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12
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Refn MR, Kampmann ML, Morling N, Tfelt-Hansen J, Børsting C, Pereira V. Prediction of chronological age and its applications in forensic casework: methods, current practices, and future perspectives. Forensic Sci Res 2023; 8:85-97. [PMID: 37621446 PMCID: PMC10445583 DOI: 10.1093/fsr/owad021] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 04/28/2023] [Indexed: 08/26/2023] Open
Abstract
Estimating an individual's age can be relevant in several areas primarily related to the clinical and forensic fields. In the latter, estimation of an individual's chronological age from biological material left by the perpetrator at a crime scene may provide helpful information for police investigation. Estimation of age is also beneficial in immigration cases, where age can affect the person's protection status under the law, or in disaster victim identification to narrow the list of potential missing persons. In the last decade, research has focused on establishing new approaches for age prediction in the forensic field. From the first forensic age estimations based on morphological inspections of macroscopic changes in bone and teeth, the focus has shifted to molecular methods for age estimation. These methods allow the use of samples from human biological material that does not contain morphological age features and can, in theory, be investigated in traces containing only small amounts of biological material. Molecular methods involving DNA analyses are the primary choice and estimation of DNA methylation levels at specific sites in the genome is the most promising tool. This review aims to provide an overview of the status of forensic age prediction using molecular methods, with particular focus in DNA methylation. The frequent challenges that impact forensic age prediction model development will be addressed, together with the importance of validation efforts within the forensic community.
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Affiliation(s)
- Mie Rath Refn
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Marie-Louise Kampmann
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Niels Morling
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jacob Tfelt-Hansen
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- The Department of Cardiology, The Heart Centre, Copenhagen University Hospital, Rigshospitalet, Copenhagen , Denmark
| | - Claus Børsting
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Vania Pereira
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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13
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Aguilar-Velázquez JA, Llamas-de-Dios BJ, Córdova-Mercado MF, Coronado-Ávila CE, Salas-Salas O, López-Quintero A, Ramos-González B, Rangel-Villalobos H. Accuracy of Eye and Hair Color Prediction in Mexican Mestizos from Monterrey City Based on ForenSeq TM DNA Signature Prep. Genes (Basel) 2023; 14:genes14051120. [PMID: 37239480 DOI: 10.3390/genes14051120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 05/14/2023] [Accepted: 05/18/2023] [Indexed: 05/28/2023] Open
Abstract
Forensic genomic systems allow simultaneously analyzing identity informative (iiSNPs), ancestry informative (aiSNPs), and phenotype informative (piSNPs) genetic markers. Among these kits, the ForenSeq DNA Signature prep (Verogen) analyzes identity STRs and SNPs as well as 24 piSNPs from the HIrisPlex system to predict the hair and eye color. We report herein these 24 piSNPs in 88 samples from Monterrey City (Northeast, Mexico) based on the ForenSeq DNA Signature prep. Phenotypes were predicted by genotype results with both Universal Analysis Software (UAS) and the web tool of the Erasmus Medical Center (EMC). We observed predominantly brown eyes (96.5%) and black hair (75%) phenotypes, whereas blue eyes, and blond and red hair were not observed. Both UAS and EMC showed high performance in eye color prediction (p ≥ 96.6%), but a lower accuracy was observed for hair color prediction. Overall, UAS hair color predictions showed better performance and robustness than those obtained with the EMC web tool (when hair shade is excluded). Although we employed a threshold (p > 70%), we suggest using the EMC enhanced approach to avoid the exclusion of a high number of samples. Finally, although our results are helpful to employ these genomic tools to predict eye color, caution is suggested for hair color prediction in Latin American (admixed) populations such as those studied herein, principally when no black color is predicted.
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Affiliation(s)
- José Alonso Aguilar-Velázquez
- Instituto de Investigación en Ciencias Biomédicas, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara (CUCS-UdeG), Guadalajara 44340, Jalisco, Mexico
- Departamento de Morfología, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara (CUCS-UdeG), Guadalajara 44340, Jalisco, Mexico
| | - Blanca Jeannete Llamas-de-Dios
- Licenciatura en Ciencias Forenses, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara (CUCS-UdeG), Guadalajara 44340, Jalisco, Mexico
| | - Miranda Fabiola Córdova-Mercado
- Instituto de Criminalística y Servicios Periciales, Fiscalía General de Justicia del Estado de Nuevo León (FGJNL), Monterrey 64720, Nuevo León, Mexico
| | - Carolina Elena Coronado-Ávila
- Instituto de Criminalística y Servicios Periciales, Fiscalía General de Justicia del Estado de Nuevo León (FGJNL), Monterrey 64720, Nuevo León, Mexico
| | - Orlando Salas-Salas
- Instituto de Criminalística y Servicios Periciales, Fiscalía General de Justicia del Estado de Nuevo León (FGJNL), Monterrey 64720, Nuevo León, Mexico
| | - Andrés López-Quintero
- Instituto de Nutrigenética y Nutrigenómica Traslacional, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara (CUCS-UdeG), Guadalajara 44340, Jalisco, Mexico
| | - Benito Ramos-González
- Instituto de Criminalística y Servicios Periciales, Fiscalía General de Justicia del Estado de Nuevo León (FGJNL), Monterrey 64720, Nuevo León, Mexico
| | - Héctor Rangel-Villalobos
- Instituto de Investigación en Genética Molecular, Centro Universitario de la Ciénega, Universidad de Guadalajara (CUCI-UdeG), Ocotlán 47820, Jalisco, Mexico
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14
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Pilli E, Palamenghi A, Marino A, Staiti N, Alladio E, Morelli S, Cherubini A, Mazzarelli D, Caccia G, Gibelli D, Cattaneo C. Comparing Genetic and Physical Anthropological Analyses for the Biological Profile of Unidentified and Identified Bodies in Milan. Genes (Basel) 2023; 14:genes14051064. [PMID: 37239424 DOI: 10.3390/genes14051064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 05/08/2023] [Accepted: 05/09/2023] [Indexed: 05/28/2023] Open
Abstract
When studying unknown human remains, the estimation of skeletal sex and ancestry is paramount to create the victim's biological profile and attempt identification. In this paper, a multidisciplinary approach to infer the sex and biogeographical ancestry of different skeletons, using physical methods and routine forensic markers, is explored. Forensic investigators, thus, encounter two main issues: (1) the use of markers such as STRs that are not the best choice in terms of inferring biogeographical ancestry but are routine forensic markers to identify a person, and (2) the concordance of the physical and molecular results. In addition, a comparison of physical/molecular and then antemortem data (of a subset of individuals that are identified during our research) was evaluated. Antemortem data was particularly beneficial to evaluate the accuracy rates of the biological profiles produced by anthropologists and classification rates obtained by molecular experts using autosomal genetic profiles and multivariate statistical approaches. Our results highlight that physical and molecular analyses are in perfect agreement for sex estimation, but some discrepancies in ancestry estimation were observed in 5 out of 24 cases.
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Affiliation(s)
- Elena Pilli
- Laboratorio di Antropologia Molecolare Forense, Dipartimento di Biologia, Università degli Studi di Firenze, Via del Proconsolo 12, 50122 Florence, Italy
| | - Andrea Palamenghi
- LABANOF-Laboratorio di Antropologia e Odontologia Forense, Dipartimento di Scienze Biomediche per la Salute, Università degli Studi di Milano, Via L. Mangiagalli 37, 20133 Milan, Italy
- LAFAS-Laboratorio di Anatomia Funzionale dell'Apparato Stomatognatico, Dipartimento di Scienze Biomediche per la Salute, Università degli Studi di Milano, Via L. Mangiagalli 31, 20133 Milan, Italy
| | - Alberto Marino
- Reparto Carabinieri Investigazioni Scientifiche di Parma, Sezione Biologia, 43121 Parma, Italy
| | - Nicola Staiti
- Reparto Carabinieri Investigazioni Scientifiche di Parma, Sezione Biologia, 43121 Parma, Italy
| | - Eugenio Alladio
- Department of Chemistry, University of Turin, 10124 Turin, Italy
| | - Stefania Morelli
- Laboratorio di Antropologia Molecolare Forense, Dipartimento di Biologia, Università degli Studi di Firenze, Via del Proconsolo 12, 50122 Florence, Italy
| | - Anna Cherubini
- Reparto Carabinieri Investigazioni Scientifiche di Parma, Sezione Biologia, 43121 Parma, Italy
| | - Debora Mazzarelli
- LABANOF-Laboratorio di Antropologia e Odontologia Forense, Dipartimento di Scienze Biomediche per la Salute, Università degli Studi di Milano, Via L. Mangiagalli 37, 20133 Milan, Italy
| | - Giulia Caccia
- LABANOF-Laboratorio di Antropologia e Odontologia Forense, Dipartimento di Scienze Biomediche per la Salute, Università degli Studi di Milano, Via L. Mangiagalli 37, 20133 Milan, Italy
| | - Daniele Gibelli
- LAFAS-Laboratorio di Anatomia Funzionale dell'Apparato Stomatognatico, Dipartimento di Scienze Biomediche per la Salute, Università degli Studi di Milano, Via L. Mangiagalli 31, 20133 Milan, Italy
| | - Cristina Cattaneo
- LABANOF-Laboratorio di Antropologia e Odontologia Forense, Dipartimento di Scienze Biomediche per la Salute, Università degli Studi di Milano, Via L. Mangiagalli 37, 20133 Milan, Italy
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15
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Kayser M, Sajantila A, Butler JM, Parson W, Salas A, Gill P, Parsons T, Phillips C, Egeland T, Marshall C. Special issue: Forensic Genetics: Unde venisti et quo vadis? Forensic Sci Int Genet 2023:102881. [PMID: 37173159 DOI: 10.1016/j.fsigen.2023.102881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 04/26/2023] [Indexed: 05/15/2023]
Affiliation(s)
- Manfred Kayser
- Department of Genetic Identification, Erasmus MC, University Medical Center Rotterdam, the Netherland.
| | - Antti Sajantila
- Department of Forensic Medicine, University of Helsinki and Finnish Institute for Health and Welfare, Helsinki, Finland
| | - John M Butler
- National Institute of Standards and Technology, Special Programs Office, Gaithersburg, MD, USA
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, Austria and Forensic Science Program, The Pennsylvania State University, University Park, PA, USA
| | - Antonio Salas
- Forensic Genetics Unit, Institute of Forensic Sciences and GenPoB Research Group, Institute of Health Research, Clinic Hospital, University of Santiago de Compostela, Spain
| | - Peter Gill
- Forensic Genetics Research Group, Oslo University Hospital and Department of Clinical Medicine, University of Oslo, Norway
| | - Thomas Parsons
- International Commission on Missing Persons, Den Haag, the Netherlands
| | - Chris Phillips
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Spain
| | - Thore Egeland
- Faculty of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, Aas, Norway
| | - Charla Marshall
- Emerging Technologies Section, Armed Forces Medical Examiner System's Armed Forces DNA Identification Laboratory (AFMES-AFDIL), Dover Air Force Base, DE, USA
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16
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Kayser M, Branicki W, Parson W, Phillips C. Recent advances in Forensic DNA Phenotyping of appearance, ancestry and age. Forensic Sci Int Genet 2023; 65:102870. [PMID: 37084623 DOI: 10.1016/j.fsigen.2023.102870] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 04/04/2023] [Indexed: 04/09/2023]
Abstract
Forensic DNA Phenotyping (FDP) comprises the prediction of a person's externally visible characteristics regarding appearance, biogeographic ancestry and age from DNA of crime scene samples, to provide investigative leads to help find unknown perpetrators that cannot be identified with forensic STR-profiling. In recent years, FDP has advanced considerably in all of its three components, which we summarize in this review article. Appearance prediction from DNA has broadened beyond eye, hair and skin color to additionally comprise other traits such as eyebrow color, freckles, hair structure, hair loss in men, and tall stature. Biogeographic ancestry inference from DNA has progressed from continental ancestry to sub-continental ancestry detection and the resolving of co-ancestry patterns in genetically admixed individuals. Age estimation from DNA has widened beyond blood to more somatic tissues such as saliva and bones as well as new markers and tools for semen. Technological progress has allowed forensically suitable DNA technology with largely increased multiplex capacity for the simultaneous analysis of hundreds of DNA predictors with targeted massively parallel sequencing (MPS). Forensically validated MPS-based FDP tools for predicting from crime scene DNA i) several appearance traits, ii) multi-regional ancestry, iii) several appearance traits together with multi-regional ancestry, and iv) age from different tissue types, are already available. Despite recent advances that will likely increase the impact of FDP in criminal casework in the near future, moving reliable appearance, ancestry and age prediction from crime scene DNA to the level of detail and accuracy police investigators may desire, requires further intensified scientific research together with technical developments and forensic validations as well as the necessary funding.
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Affiliation(s)
- Manfred Kayser
- Department of Genetic Identification, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands.
| | - Wojciech Branicki
- Institute of Zoology and Biomedical Research, Jagiellonian University, Kraków, Poland,; Institute of Forensic Research, Kraków, Poland
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria; Forensic Science Program, The Pennsylvania State University, PA, USA
| | - Christopher Phillips
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Spain
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17
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Staadig A, Hedman J, Tillmar A. Applying Unique Molecular Indices with an Extensive All-in-One Forensic SNP Panel for Improved Genotype Accuracy and Sensitivity. Genes (Basel) 2023; 14:genes14040818. [PMID: 37107576 PMCID: PMC10137749 DOI: 10.3390/genes14040818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 03/23/2023] [Accepted: 03/27/2023] [Indexed: 03/31/2023] Open
Abstract
One of the major challenges in forensic genetics is being able to detect very small amounts of DNA. Massively parallel sequencing (MPS) enables sensitive detection; however, genotype errors may exist and could interfere with the interpretation. Common errors in MPS-based analysis are often induced during PCR or sequencing. Unique molecular indices (UMIs) are short random nucleotide sequences ligated to each template molecule prior to amplification. Applying UMIs can improve the limit of detection by enabling accurate counting of initial template molecules and removal of erroneous data. In this study, we applied the FORCE panel, which includes ~5500 SNPs, with a QIAseq Targeted DNA Custom Panel (Qiagen), including UMIs. Our main objective was to investigate whether UMIs can enhance the sensitivity and accuracy of forensic genotyping and to evaluate the overall assay performance. We analyzed the data both with and without the UMI information, and the results showed that both genotype accuracy and sensitivity were improved when applying UMIs. The results showed very high genotype accuracies (>99%) for both reference DNA and challenging samples, down to 125 pg. To conclude, we show successful assay performance for several forensic applications and improvements in forensic genotyping when applying UMIs.
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18
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Chen M, Cui W, Bai X, Fang Y, Yao H, Zhang X, Lei F, Zhu B. Comprehensive evaluations of individual discrimination, kinship analysis, genetic relationship exploration and biogeographic origin prediction in Chinese Dongxiang group by a 60-plex DIP panel. Hereditas 2023; 160:14. [PMID: 36978173 PMCID: PMC10052841 DOI: 10.1186/s41065-023-00271-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 02/22/2023] [Indexed: 03/30/2023] Open
Abstract
BACKGROUND Dongxiang group, as an important minority, resides in Gansu province which is located at the northwest China, forensic detection system with more loci needed to be studied to improve the application efficiency of forensic case investigation in this group. METHODS A 60-plex system including 57 autosomal deletion/insertion polymorphisms (A-DIPs), 2 Y chromosome DIPs (Y-DIPs) and the sex determination locus (Amelogenin) was explored to evaluate the forensic application efficiencies of individual discrimination, kinship analysis and biogeographic origin prediction in Gansu Dongxiang group based on the 60-plex genotype results of 233 unrelated Dongxiang individuals. The 60-plex genotype results of 4582 unrelated individuals from 33 reference populations in five different continents were also collected to analyze the genetic background of Dongxiang group and its genetic relationships with other continental populations. RESULTS The system showed high individual discrimination power, as the cumulative power of discrimination (CPD), cumulative power of exclusion (CPE) for trio and cumulative match probability (CMP) values were 0.99999999999999999999997297, 0.999980 and 2.7029E- 24, respectively. The system could distinguish 98.12%, 93.78%, 82.18%, 62.35% and 39.32% of full sibling pairs from unrelated individual pairs, when the likelihood ratio (LR) limits were set as 1, 10, 100, 1000 and 10,000 based on the simulated family samples, respectively. Additionally, Dongxiang group had the close genetic distances with populations in East Asia, especially showed the intimate genetic relationships with Chinese Han populations, which were concluded from the genetic affinities and genetic background analyses of Dongxiang group and 33 reference populations. In terms of the effectiveness of biogeographic origin inference, different artificial intelligent algorithms possessed different efficacies. Among them, the random forest (RF) and extreme gradient boosting (XGBoost) algorithm models could accurately predict the biogeographic origins of 99.7% and 90.59% of three and five continental individuals, respectively. CONCLUSION This 60-plex system had good performance for individual discrimination, kinship analysis and biogeographic origin prediction in Dongxiang group, which could be used as a powerful tool for case investigation.
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Affiliation(s)
- Man Chen
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Wei Cui
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Xiaole Bai
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Yating Fang
- School of Basic Medical Sciences, Anhui Medical University, Hefei, 230031, Anhui, China
| | - Hongbin Yao
- Belt and Road Research Center for Forensic Molecular Anthropology, Key Laboratory of Evidence Science of Gansu Province, Gansu University of Political Science and Law, Lanzhou, 730070, China
| | - Xingru Zhang
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, 710004, China
| | - Fanzhang Lei
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Bofeng Zhu
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, 510515, China.
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, 710004, China.
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19
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Ruiz-Ramírez J, de la Puente M, Xavier C, Ambroa-Conde A, Álvarez-Dios J, Freire-Aradas A, Mosquera-Miguel A, Ralf A, Amory C, Katsara MA, Khellaf T, Nothnagel M, Cheung EYY, Gross TE, Schneider PM, Uacyisrael J, Oliveira S, Klautau-Guimarães MDN, Carvalho-Gontijo C, Pośpiech E, Branicki W, Parson W, Kayser M, Carracedo A, Lareu MV, Phillips C. Development and evaluations of the ancestry informative markers of the VISAGE Enhanced Tool for Appearance and Ancestry. Forensic Sci Int Genet 2023; 64:102853. [PMID: 36917866 DOI: 10.1016/j.fsigen.2023.102853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 02/15/2023] [Accepted: 03/02/2023] [Indexed: 03/07/2023]
Abstract
The VISAGE Enhanced Tool for Appearance and Ancestry (ET) has been designed to combine markers for the prediction of bio-geographical ancestry plus a range of externally visible characteristics into a single massively parallel sequencing (MPS) assay. We describe the development of the ancestry panel markers used in ET, and the enhanced analyses they provide compared to previous MPS-based forensic ancestry assays. As well as established autosomal single nucleotide polymorphisms (SNPs) that differentiate sub-Saharan African, European, East Asian, South Asian, Native American, and Oceanian populations, ET includes autosomal SNPs able to efficiently differentiate populations from Middle East regions. The ability of the ET autosomal ancestry SNPs to distinguish Middle East populations from other continentally defined population groups is such that characteristic patterns for this region can be discerned in genetic cluster analysis using STRUCTURE. Joint cluster membership estimates showing individual co-ancestry that signals North African or East African origins were detected, or cluster patterns were seen that indicate origins from central and Eastern regions of the Middle East. In addition to an augmented panel of autosomal SNPs, ET includes panels of 85 Y-SNPs, 16 X-SNPs and 21 autosomal Microhaplotypes. The Y- and X-SNPs provide a distinct method for obtaining extra detail about co-ancestry patterns identified in males with admixed backgrounds. This study used the 1000 Genomes admixed African and admixed American sample sets to fully explore these enhancements to the analysis of individual co-ancestry. Samples from urban and rural Brazil with contrasting distributions of African, European, and Native American co-ancestry were also studied to gauge the efficiency of combining Y- and X-SNP data for this purpose. The small panel of Microhaplotypes incorporated in ET were selected because they showed the highest levels of haplotype diversity amongst the seven population groups we sought to differentiate. Microhaplotype data was not formally combined with single-site SNP genotypes to analyse ancestry. However, the haplotype sequence reads obtained with ET from these loci creates an effective system for de-convoluting two-contributor mixed DNA. We made simple mixture experiments to demonstrate that when the contributors have different ancestries and the mixture ratios are imbalanced (i.e., not 1:1 mixtures) the ET Microhaplotype panel is an informative system to infer ancestry when this differs between the contributors.
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Affiliation(s)
- J Ruiz-Ramírez
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - M de la Puente
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain.
| | - C Xavier
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - A Ambroa-Conde
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - J Álvarez-Dios
- Faculty of Mathematics, University of Santiago de Compostela, 15705 Santiago de Compostela, Spain
| | - A Freire-Aradas
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - A Mosquera-Miguel
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - A Ralf
- Department of Genetic Identification, Erasmus MC, University Medical Center Rotterdam, 3015 CN Rotterdam, South Holland, the Netherlands
| | - C Amory
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - M A Katsara
- Cologne Center for Genomics, University of Cologne, 50823 Cologne, Germany
| | - T Khellaf
- Cologne Center for Genomics, University of Cologne, 50823 Cologne, Germany
| | - M Nothnagel
- Cologne Center for Genomics, University of Cologne, 50823 Cologne, Germany; University Hospital Cologne, 50937 Cologne, Germany
| | - E Y Y Cheung
- Institute of Legal Medicine, Faculty of Medicine and University Clinic, University of Cologne, 50823 Cologne, Germany
| | - T E Gross
- Institute of Legal Medicine, Faculty of Medicine and University Clinic, University of Cologne, 50823 Cologne, Germany
| | - P M Schneider
- Institute of Legal Medicine, Faculty of Medicine and University Clinic, University of Cologne, 50823 Cologne, Germany
| | - J Uacyisrael
- Fiji Police Forensic Biology and DNA Laboratory, Nasova, Suva, Fiji
| | - S Oliveira
- Departamento Genética e Morfologia, Universidade de Brasília, Brasília, DF, Brazil
| | | | - C Carvalho-Gontijo
- Departamento Genética e Morfologia, Universidade de Brasília, Brasília, DF, Brazil
| | - E Pośpiech
- Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - W Branicki
- Institute of Zoology and Biomedical Research, Jagiellonian University, 30-387 Kraków, Poland
| | - W Parson
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria; Forensic Science Program, The Pennsylvania State University, University Park, State College, PA 16802, USA
| | - M Kayser
- Department of Genetic Identification, Erasmus MC, University Medical Center Rotterdam, 3015 CN Rotterdam, South Holland, the Netherlands
| | - A Carracedo
- Fundación Pública Galega de Medicina Xenómica (FPGMX), Instituto de Investigación Sanitaria (IDIS),15706 Santiago de Compostela, Spain; Genomics Group, CIBERER, CIMUS, University of Santiago de Compostela, Spain
| | - M V Lareu
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - C Phillips
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain.
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20
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Stasi A, Mir TUG, Pellegrino A, Wani AK, Shukla S. Forty years of research and development on forensic genetics: A bibliometric analysis. Forensic Sci Int Genet 2023; 63:102826. [PMID: 36640637 DOI: 10.1016/j.fsigen.2023.102826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 12/31/2022] [Accepted: 01/02/2023] [Indexed: 01/05/2023]
Abstract
The current study aims to investigate the research publication trends in the field of forensic genetics using Bibliometric analysis. An extensive search of the Scopus database was conducted to identify scholarly articles on forensic genetics published between 1977 and 2022, and a data set comprising 2945 articles was obtained. The analysis was carried out using VOSviewer, RStudio, MS Excel and MS Access to investigate the annual publication trend, most productive journals, organizations/authors/countries, authorship and citation patterns, most cited documents/articles and co-occurrence of keywords. The results revealed the first article in the field of forensic genetics was published in 1977. By the end of 1999, only 15 articles were published. Since then, there has been a considerable increase in the yearly number of publications and post-2006, there were more than 100 yearly published articles. USA, China, Spain, Germany and United Kingdom were found to be the most productive countries. Among various organizations, the Institute of Legal Medicine, Innsbruck Medical University, Austria was found to be the most productive organization. In terms of the number of publications and citations, Morling N. was found to be the most prolific author. The highest number of articles were published in Forensic Science International: Genetics, contributing about 34% of the total articles published in different sources/journals. The document with the highest number of citations was "HOMER N, 2008, PLOS GENET", with a total of 750 citations. The most frequent keywords were forensic genetics and forensic science, followed by STR, population genetics, DNA, mt-DNA and DNA-typing. The results also revealed that there had been collaborative research among countries, organizations and authors, which helps in the exchange of ideas across disciplines, developing new skills, getting access to financial resources and generating quality results.
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Affiliation(s)
- Alessandro Stasi
- Mahidol University International College, 999 Phutthamonthon Sai 4 Rd, Salaya, Phutthamonthon District, Nakhon Pathom 73170, Thailand.
| | - Tahir Ul Gani Mir
- Department of Forensic Science, School of Bioengineering and Biosciences, Lovely Professional University, Phagwara 144411, Punjab, India.
| | - Alfonso Pellegrino
- Sasin School of Management, Chulalongkorn University, Chula soi 12, Wang Mai, Pathum Wan, Bangkok 10330, Thailand.
| | - Atif Khurshid Wani
- Department of Biotechnology, School of Bioengineering and Biosciences, Lovely Professional University, Phagwara 144411, Punjab, India.
| | - Saurabh Shukla
- Department of Forensic Science, School of Bioengineering and Biosciences, Lovely Professional University, Phagwara 144411, Punjab, India.
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Bardan F, Higgins D, Austin JJ. A custom hybridisation enrichment forensic intelligence panel to infer biogeographic ancestry, hair and eye colour, and Y chromosome lineage. Forensic Sci Int Genet 2023; 63:102822. [PMID: 36525814 DOI: 10.1016/j.fsigen.2022.102822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 11/02/2022] [Accepted: 12/09/2022] [Indexed: 12/14/2022]
Abstract
Massively parallel sequencing can provide genetic data for hundreds to thousands of loci in a single assay for various types of forensic testing. However, available commercial kits require an initial PCR amplification of short-to-medium sized targets which limits their application for highly degraded DNA. Development and optimisation of large PCR multiplexes also prevents creation of custom panels that target different suites of markers for identity, biogeographic ancestry, phenotype, and lineage markers (Y-chromosome and mtDNA). Hybridisation enrichment, an alternative approach for target enrichment prior to sequencing, uses biotinylated probes to bind to target DNA and has proven successful on degraded and ancient DNA. We developed a customisable hybridisation capture method, that uses individually mixed baits to allow tailored and targeted enrichment to specific forensic questions of interest. To allow collection of forensic intelligence data, we assembled and tested a custom panel of hybridisation baits to infer biogeographic ancestry, hair and eye colour, and paternal lineage (and sex) on modern male and female samples with a range of self-declared ancestries and hair/eye colour combinations. The panel correctly estimated biogeographic ancestry in 9/12 samples (75%) but detected European admixture in three individuals from regions with admixed demographic history. Hair and eye colour were predicted correctly in 83% and 92% of samples respectively, where intermediate eye colour and blond hair were problematic to predict. Analysis of Y-chromosome SNPs correctly assigned sex and paternal haplogroups, the latter complementing and supporting biogeographic ancestry predictions. Overall, we demonstrate the utility of this hybridisation enrichment approach to forensic intelligence testing using a combined suite of biogeographic ancestry, phenotype, and Y-chromosome SNPs for comprehensive biological profiling.
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Affiliation(s)
- Felicia Bardan
- Australian Centre for Ancient DNA, School of Biological Sciences, The University of Adelaide, South Australia, Australia
| | - Denice Higgins
- Australian Centre for Ancient DNA, School of Biological Sciences, The University of Adelaide, South Australia, Australia; School of Dentistry, Health and Medical Sciences, The University of Adelaide, South Australia, Australia
| | - Jeremy J Austin
- Australian Centre for Ancient DNA, School of Biological Sciences, The University of Adelaide, South Australia, Australia.
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Resutik P, Aeschbacher S, Krützen M, Kratzer A, Haas C, Phillips C, Arora N. Comparative evaluation of the MAPlex, Precision ID Ancestry Panel, and VISAGE Basic Tool for biogeographical ancestry inference. Forensic Sci Int Genet 2023; 64:102850. [PMID: 36924679 DOI: 10.1016/j.fsigen.2023.102850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 02/21/2023] [Accepted: 02/23/2023] [Indexed: 02/27/2023]
Abstract
Biogeographical ancestry (BGA) inference from ancestry-informative markers (AIMs) has strong potential to support forensic investigations. Over the past two decades, several forensic panels composed of AIMs have been developed to predict ancestry at a continental scale. These panels typically comprise fewer than 200 AIMs and have been designed and tested with a limited set of populations. How well these panels recover patterns of genetic diversity relative to larger sets of markers, and how accurately they infer ancestry of individuals and populations not included in their design remains poorly understood. The lack of comparative studies addressing these aspects makes the selection of appropriate panels for forensic laboratories difficult. In this study, the model-based genetic clustering tool STRUCTURE was used to compare three popular forensic BGA panels: MAPlex, Precision ID Ancestry Panel (PIDAP), and VISAGE Basic Tool (VISAGE BT) relative to a genome-wide reference set of 10k SNPs. The genotypes for all these markers were obtained for a comprehensive set of 3957 individuals from 228 worldwide human populations. Our results indicate that at the broad continental scale (K=6) typically examined in forensic studies, all forensic panels produced similar genetic structure patterns compared to the reference set (G'≈90%) and had high classification performance across all regions (average AUC-PR > 97%). However, at K= 7 and K= 8, the forensic panels displayed some region-specific clustering deviations from the reference set, particularly in Europe and the region of East and South-East Asia, which may be attributed to differences in the design of the respective panels. Overall, the panel with the most consistent performance in all regions was VISAGE BT with an average weighted AUC̅W score of 96.26% across the three scales of geographical resolution investigated.
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Affiliation(s)
- Peter Resutik
- Zurich Institute of Forensic Medicine, University of Zurich, Switzerland.
| | - Simon Aeschbacher
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Switzerland
| | - Michael Krützen
- Department of Evolutionary Anthropology, University of Zurich, Switzerland
| | - Adelgunde Kratzer
- Zurich Institute of Forensic Medicine, University of Zurich, Switzerland
| | - Cordula Haas
- Zurich Institute of Forensic Medicine, University of Zurich, Switzerland
| | - Christopher Phillips
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Spain
| | - Natasha Arora
- Zurich Institute of Forensic Medicine, University of Zurich, Switzerland.
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Single-cell transcriptome sequencing allows genetic separation, characterization and identification of individuals in multi-person biological mixtures. Commun Biol 2023; 6:201. [PMID: 36805025 PMCID: PMC9941516 DOI: 10.1038/s42003-023-04557-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 02/06/2023] [Indexed: 02/22/2023] Open
Abstract
Identifying individuals from biological mixtures to which they contributed is highly relevant in crime scene investigation and various biomedical research fields, but despite previous attempts, remains nearly impossible. Here we investigated the potential of using single-cell transcriptome sequencing (scRNA-seq), coupled with a dedicated bioinformatics pipeline (De-goulash), to solve this long-standing problem. We developed a novel approach and tested it with scRNA-seq data that we de-novo generated from multi-person blood mixtures, and also in-silico mixtures we assembled from public single individual scRNA-seq datasets, involving different numbers, ratios, and bio-geographic ancestries of contributors. For all 2 up to 9-person balanced and imbalanced blood mixtures with ratios up to 1:60, we achieved a clear single-cell separation according to the contributing individuals. For all separated mixture contributors, sex and bio-geographic ancestry (maternal, paternal, and bi-parental) were correctly determined. All separated contributors were correctly individually identified with court-acceptable statistical certainty using de-novo generated whole exome sequencing reference data. In this proof-of-concept study, we demonstrate the feasibility of single-cell approaches to deconvolute biological mixtures and subsequently genetically characterise, and individually identify the separated mixture contributors. With further optimisation and implementation, this approach may eventually allow moving to challenging biological mixtures, including those found at crime scenes.
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Zhang X, Zheng H, Liu C. Genetic diversity of 23 Y-STR loci of the Lisu ethnic minority residing in Chuxiong Yi Autonomous Prefecture, Yunnan province, Southwest China. Ann Hum Biol 2023; 50:356-359. [PMID: 37523197 DOI: 10.1080/03014460.2023.2224972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 05/17/2023] [Accepted: 05/30/2023] [Indexed: 08/01/2023]
Abstract
BACKGROUND The Lisu group is a unique minority in Yunnan province. However, there is a lack of Y-STR population data for Chinese Lisu and the genetic structure of the Lisu group and other populations is unclear. AIM To provide genetic data for 23 Y-STRs in the Chinese Lisu population from Chuxiong Yi Autonomous Prefecture, as well as to analyse population genetic relationships between Chinese Lisu ethnic minority and other reference groups. SUBJECTS AND METHODS 423 unrelated healthy Lisu males were genotyped using the PowerPlex® Y23 system. Forensic parameters were calculated according to the previously published studies. Genetic structure analysis among Chinese Lisu and other populations was conducted using the YHRD's AMOVA tools. RESULTS Gene diversity (GD) ranged from 0.2,466 (DYS438) to 0.8,945 (DYS385a/b) among the 23 Y-STR loci. According to haplotype analysis, 323 different haplotypes were obtained, out of which 271 were unique. The haplotype diversity (HD) and discrimination capacity (DC) were 0.9,977 and 0.7,636, respectively. MDS plot indicated that the Chuxiong Lisu group is genetically related to the Yunnan Yi group. CONCLUSIONS This is the first report on Y-STR population data for the Chinese Lisu population. These data would be valuable for forensic applications.
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Affiliation(s)
- Xiufeng Zhang
- School of Forensic Medicine, Kunming Medical University, Kunming, Yunnan Province, China
- Judicial Expertise Center, Kunming Medical University, Kunming, Yunnan Province, China
| | - Hecheng Zheng
- Chuxiong Public Security Bureau, Chuxiong, Yunnan Province, China
| | - Chengjing Liu
- Chuxiong Public Security Bureau, Chuxiong, Yunnan Province, China
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25
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Felkl AB, Avila E, Gastaldo AZ, Lindholz CG, Dorn M, Alho CS. Ancestry resolution of South Brazilians by forensic 165 ancestry-informative SNPs panel. Forensic Sci Int Genet 2023; 64:102838. [PMID: 36736201 DOI: 10.1016/j.fsigen.2023.102838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 01/15/2023] [Accepted: 01/22/2023] [Indexed: 01/24/2023]
Abstract
Forensic DNA phenotyping (FDP) includes biogeographic ancestry (BGA) inference and externally visible characteristics (EVCs) prediction directly from an evidential DNA sample as alternatives to provide valuable intelligence when conventional DNA profiling fails to achieve identification. In this context, the application of Massively Parallel Sequencing (MPS) methodologies, which enables simultaneous typing of multiple samples and hundreds of forensic markers, has been gradually implemented in forensic genetic casework. The Precision ID Ancestry Panel (Thermo Fisher Scientific, Waltham, USA) is a forensic multiplex assay consisting of 165 autosomal SNPs designed to provide biogeographic ancestry information. In this work, a sample of 250 individuals from Rio Grande do Sul (RS) State, southern Brazil, apportioned into four main population groups (African-, European-, Amerindian-, and Admixed-derived Gauchos), was evaluated with this panel, to assess the feasibility of this approach in a highly heterogeneous population. Forensic descriptive parameters estimated for each population group revealed that this panel has enough polymorphic and informative SNPs to be used as a supplementary instrument in forensic individual identification and kinship testing regardless of ethnicity. No statistically significant deviation from Hardy-Weinberg equilibrium was observed after Bonferroni correction. However, seven loci pairs displayed linkage disequilibrium in pairwise LD testing (p < 3.70 × 10-6). Interpopulation comparisons by FST analysis, MDS plot, and STRUCTURE analysis among the four RS population groups apart and along with 89 reference worldwide populations demonstrated that Admixed- and African-derived Gauchos present the highest levels of admixture and population stratification, whereas European- and Amerindian-derived exhibit a more homogeneous genetic conformation.
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Affiliation(s)
- Aline Brugnera Felkl
- Forensic Genetics Laboratory, School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, RS, Brazil; National Institute of Science and Technology - Forensic Science, Porto Alegre, RS, Brazil.
| | - Eduardo Avila
- Forensic Genetics Laboratory, School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, RS, Brazil; Technical Scientific Section, Federal Police Department in Rio Grande do Sul State, Porto Alegre, RS, Brazil; National Institute of Science and Technology - Forensic Science, Porto Alegre, RS, Brazil
| | - André Zoratto Gastaldo
- Forensic Genetics Laboratory, School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, RS, Brazil; National Institute of Science and Technology - Forensic Science, Porto Alegre, RS, Brazil
| | - Catieli Gobetti Lindholz
- Forensic Genetics Laboratory, School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Márcio Dorn
- Forensic Genetics Laboratory, School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, RS, Brazil; National Institute of Science and Technology - Forensic Science, Porto Alegre, RS, Brazil; Institute of Informatics, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Clarice Sampaio Alho
- Forensic Genetics Laboratory, School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, RS, Brazil; National Institute of Science and Technology - Forensic Science, Porto Alegre, RS, Brazil
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Wan W, Ren Z, Zhang H, Wang Q, Wang T, Yang Y, You J, He K, Huang J, Jin X. Insight into forensic efficiency and genetic structure of the Guizhou Dong group via a 64-plex panel. Front Ecol Evol 2023. [DOI: 10.3389/fevo.2022.988504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Insertion/deletion polymorphisms (InDels) show great application values in forensic research because they own superiorities of short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs). Whereas, InDels commonly display low genetic diversities in comparison to STRs. Therefore, they may provide limited genetic information in forensic kinship testing. Here, we evaluated forensic application efficiency of a novel multiplex amplification system including two STRs, 59 InDels, and three sex-determination loci in the Guizhou Dong group. In addition, we explored the genetic background of the Guizhou Dong group in comparison to other reported populations based on 59 InDels. We found that 59 InDels displayed relatively high genetic diversities in the Guizhou Dong group. Moreover, the cumulative forensic efficiency of two STRs and 59 InDels could meet the requirement of individual identification and paternity testing in the Guizhou Dong group. For these 59 InDels, we observed that some loci exhibited relatively high genetic differentiations among different continental populations, especially for African and Non-African populations, which could be viewed as candidate ancestry informative markers in the future. Genetic structure results indicated that the Dong group had close genetic relationships with East Asian and some Southern Chinese Han populations. To sum up, we stated that the 64-plex panel could be performed for forensic application of the Guizhou Dong group.
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27
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Feng Y, Wang T, Yang Y, You J, He K, Zhang H, Wang Q, Yang M, Huang J, Ren Z, Jin X. Genetic features and phylogenetic relationship analyses of Guizhou Han population residing in Southwest China via 38 X-InDels. PeerJ 2023; 11:e14964. [PMID: 36915656 PMCID: PMC10007965 DOI: 10.7717/peerj.14964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 02/06/2023] [Indexed: 03/11/2023] Open
Abstract
Background The insertion/deletion polymorphism (InDel), an ideal forensic genetic marker with a low spontaneous mutation rate and small amplification product fragments, is widely distributed in the genome, combining the advantages of STR and SNP genetic markers. The X-chromosome has high application value in complex paternity testing, and it is an excellent system for evaluating population admixture and studying evolutionary anthropology. However, further research is needed on the population genetics of X-chromosome InDels (X-InDels). Methods In this article, a system composed of 38 X-InDel loci was utilized to analyse and evaluate the forensic parameters of the Guizhou Han population in order to explore its forensic application efficiency. Results The results showed that expected heterozygosities spanned from 0.0189 to 0.5715, and the cumulative power of discrimination of the 32 X-InDels and three linkage blocks was 0.9999999954 and 0.999999999999741 for males and females, respectively. The combined mean exclusion chance of these loci for trios and duos is 0.999999 and 0.999747, respectively. Multiple methods like principal component analysis, Fst genetic distance, and phylogenetic reconstruction were employed for dissecting the genetic structure of the Guizhou Han population by comparing it with previously reported populations. As expected, the studied Han population displayed relatively close genetic affinities with the East Asian populations. At the same time, there were obvious genetic differentiations between the Guizhou Han population and other continental populations that were discerned, especially for the African populations. Conclusions This study further verified the applicability of 38 X-InDels for human personal identification and kinship analyses of Han Chinese, and also showed the application potential of X-InDels in population genetics.
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Affiliation(s)
- Yuhang Feng
- Shanghai Key Lab of Forensic Medicine, Key Lab of Forensic Science, Ministry of Justice, China, Academy of Forensic Science, Shanghai, China.,Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Ting Wang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Yunteng Yang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Jiangtao You
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Kun He
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Hongling Zhang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Qiyan Wang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Meiqing Yang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Jiang Huang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Zheng Ren
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Xiaoye Jin
- Shanghai Key Lab of Forensic Medicine, Key Lab of Forensic Science, Ministry of Justice, China, Academy of Forensic Science, Shanghai, China.,Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
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Jin X, Ren Z, Zhang H, Wang Q, Liu Y, Ji J, Yang M, Zhang H, Hu W, Wang N, Wang Y, Huang J. Development and forensic efficiency evaluations of a novel multiplex amplification panel of 17 Multi-InDel loci on the X chromosome. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.985933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Multi-InDel, as the novel genetic markers, showed great potential in forensic research. Whereas, most scholars mainly focused on autosomal Multi-InDels, which might provide limited genetic information in some complex kinship cases. In this study, we selected 17 Multi-InDels on the X chromosome and developed a multiplex amplification panel based on the next-generation sequencing (NGS) technology. Genetic distributions of these 17 loci in Beijing Han, Chinese Southern Han, and the studied Guizhou Han populations revealed that most loci showed relatively high forensic application values in these Han populations. In addition, more allelic variations of some loci were observed in the Guizhou Han than those in Beijing Han and Southern Han populations. Pairwise FST values, multi-dimensional analysis, and phylogenetic tree of different continental populations showed that selected 17 loci generally could differentiate African, European, East Asian, and South Asian populations. To sum up, the developed panel in this study is not only viewed as the high-efficient supplementary tool for forensic individual identification and paternity analysis, but it is also beneficial for inferring biogeographical origins of different continental populations.
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29
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Maltese Allelic Variants in Corneal Dystrophy Genes in a Worldwide Setting. Mol Diagn Ther 2022; 26:529-540. [PMID: 35799042 DOI: 10.1007/s40291-022-00602-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/06/2022] [Indexed: 10/17/2022]
Abstract
INTRODUCTION This study aimed to establish which worldwide population cohorts have a genetic make-up closest to that of a large sample of the Maltese population with regard to corneal dystrophy (CD) genes. METHODS Single nucleotide polymorphisms (SNPs) in the Maltese cohort were compared with worldwide cohorts. Fixation index (FST) values were calculated to evaluate population differentiation. The genetic prevalence of CD subtypes in worldwide and Maltese cohorts were calculated, and single nucleotide missense mutations present in the Maltese cohort were evaluated for potential pathogenicity. RESULTS FST values showed that CD-related genes differ substantially among the studied cohorts. FST values for each SNP showed greatest differentiation between the Maltese and African cohorts and least differentiation with the Puerto Rican, Mexican, and Colombian cohorts. One TGFBI casual CD mutation, 502V, which causes a Bowman's layer CD/atypical Thiel-Behnke CD was identified in the Maltese cohort. The KRT3 NC_000012.11:g.53186088G>C mutation was potentially deleterious. CONCLUSION Identifying populations with least genetic differentiation can facilitate and help guide future diagnostic and treatment strategies for Maltese individuals with CDs in the absence of comparable Maltese data. Analysing the previously unknown CD genetic pool present in a large Maltese cohort adds to the global genetic bank that researchers rely on for medical progress.
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Cao Y, Zhu Q, Huang Y, Li X, Wei Y, Wang H, Zhang J. An efficient ancestry informative SNPs panel for further discriminating East Asian populations. Electrophoresis 2022; 43:1774-1783. [PMID: 35749689 DOI: 10.1002/elps.202100349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 05/19/2022] [Accepted: 06/17/2022] [Indexed: 11/07/2022]
Abstract
In forensic genetics, the use of ancestry informative single-nucleotide polymorphisms (AISNPs) panels can narrow the direction of the investigation by estimating an individual's biogeographic ancestry. However, distinguishing subgroups within continental regions requires more specific panels. In this study, we screened 19 AISNPs from the 1000 Genomes Project (1KG) based on their FST values to distinguish target populations in East Asia and obtained genotypes through SNaPshot. The 19 AISNPs could divide the global population of the 1KG into five clusters and could further divide the East Asian population into four clusters: Japanese, Han Chinese, Dai Chinese, and Kinh in Ho Chi Minh City of Vietnam. In summary, the 19-AISNP panel may serve as a useful and cost-effective tool for forensic ancestry inference in East Asian populations at a finer scale.
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Affiliation(s)
- Yueyan Cao
- West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, P. R. China
| | - Qiang Zhu
- West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, P. R. China
| | - Yuguo Huang
- West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, P. R. China
| | - Xi Li
- West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, P. R. China
| | - Yifan Wei
- West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, P. R. China
| | - Haoyu Wang
- West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, P. R. China
| | - Ji Zhang
- West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, P. R. China
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31
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Gu J, Zhao H, Guo X, Sun H, Xu J, Wei Y. A high‐performance SNP panel developed by machine‐learning approaches for characterizing genetic differences of Southern and Northern Han Chinese, Korean, and Japanese individuals. Electrophoresis 2022; 43:1183-1192. [DOI: 10.1002/elps.202100184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 11/21/2021] [Accepted: 01/12/2022] [Indexed: 11/09/2022]
Affiliation(s)
- Jia‐Qi Gu
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics School of Life Sciences Jiangsu Normal University Xuzhou Jiangsu P. R. China
| | - Hui Zhao
- National Engineering Laboratory for Forensic Science Key Laboratory of Forensic Genetics of Ministry of Public Security Beijing Engineering Research Center of Crime Scene Evidence Examination Institute of Forensic Science Beijing P. R. China
| | - Xiao‐Yuan Guo
- Department of Forensic Genetics School of Forensic Science Shanxi Medical University Taiyuan Shanxi P. R. China
| | - Hao‐Yun Sun
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics School of Life Sciences Jiangsu Normal University Xuzhou Jiangsu P. R. China
| | - Jing‐Yi Xu
- Department of Biochemistry and Molecular Biology Tianjin Key Laboratory of Medical Epigenetics School of Basic Medical Sciences Tianjin Medical University Tianjin P. R. China
| | - Yi‐Liang Wei
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics School of Life Sciences Jiangsu Normal University Xuzhou Jiangsu P. R. China
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Alladio E, Poggiali B, Cosenza G, Pilli E. Multivariate statistical approach and machine learning for the evaluation of biogeographical ancestry inference in the forensic field. Sci Rep 2022; 12:8974. [PMID: 35643723 PMCID: PMC9148302 DOI: 10.1038/s41598-022-12903-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 04/13/2022] [Indexed: 11/24/2022] Open
Abstract
The biogeographical ancestry (BGA) of a trace or a person/skeleton refers to the component of ethnicity, constituted of biological and cultural elements, that is biologically determined. Nowadays, many individuals are interested in exploring their genealogy, and the capability to distinguish biogeographic information about population groups and subgroups via DNA analysis plays an essential role in several fields such as in forensics. In fact, for investigative and intelligence purposes, it is beneficial to inference the biogeographical origins of perpetrators of crimes or victims of unsolved cold cases when no reference profile from perpetrators or database hits for comparative purposes are available. Current approaches for biogeographical ancestry estimation using SNPs data are usually based on PCA and Structure software. The present study provides an alternative method that involves multivariate data analysis and machine learning strategies to evaluate BGA discriminating power of unknown samples using different commercial panels. Starting from 1000 Genomes project, Simons Genome Diversity Project and Human Genome Diversity Project datasets involving African, American, Asian, European and Oceania individuals, and moving towards further and more geographically restricted populations, powerful multivariate techniques such as Partial Least Squares-Discriminant Analysis (PLS-DA) and machine learning techniques such as XGBoost were employed, and their discriminating power was compared. PLS-DA method provided more robust classifications than XGBoost method, showing that the adopted approach might be an interesting tool for forensic experts to infer BGA information from the DNA profile of unknown individuals, but also highlighting that the commercial forensic panels could be inadequate to discriminate populations at intra-continental level.
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Affiliation(s)
- Eugenio Alladio
- Department of Chemistry, University of Turin, Turin, Italy.,Centro Regionale Antidoping e di Tossicologia "A. Bertinaria", Orbassano, Torino, Italy
| | - Brando Poggiali
- Department of Biology, Forensic Molecular Anthropology Laboratory, University of Florence, Florence, Italy
| | - Giulia Cosenza
- Department of Biology, Forensic Molecular Anthropology Laboratory, University of Florence, Florence, Italy
| | - Elena Pilli
- Department of Biology, Forensic Molecular Anthropology Laboratory, University of Florence, Florence, Italy.
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33
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Unlocking the potential of forensic traces: Analytical approaches to generate investigative leads. Sci Justice 2022; 62:310-326. [PMID: 35598924 DOI: 10.1016/j.scijus.2022.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 03/17/2022] [Accepted: 03/19/2022] [Indexed: 11/21/2022]
Abstract
Forensic investigation involves gathering the information necessary to understand the criminal events as well as linking objects or individuals to an item, location or other individual(s) for investigative purposes. For years techniques such as presumptive chemical tests, DNA profiling or fingermark analysis have been of great value to this process. However, these techniques have their limitations, whether it is a lack of confidence in the results obtained due to cross-reactivity, subjectivity and low sensitivity; or because they are dependent on holding reference samples in a pre-existing database. There is currently a need to devise new ways to gather as much information as possible from a single trace, particularly from biological traces commonly encountered in forensic casework. This review outlines the most recent advancements in the forensic analysis of biological fluids, fingermarks and hair. Special emphasis is placed on analytical methods that can expand the information obtained from the trace beyond what is achieved in the usual practices. Special attention is paid to those methods that accurately determine the nature of the sample, as well as how long it has been at the crime scene, along with individualising information regarding the donor source of the trace.
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34
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Jobling MA. Forensic genetics through the lens of Lewontin: population structure, ancestry and race. Philos Trans R Soc Lond B Biol Sci 2022; 377:20200422. [PMID: 35430883 PMCID: PMC9014189 DOI: 10.1098/rstb.2020.0422] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
In his famous 1972 paper, Richard Lewontin used ‘classical’ protein-based markers to show that greater than 85% of human genetic diversity was contained within, rather than between, populations. At that time, these same markers also formed the basis of forensic technology aiming to identify individuals. This review describes the evolution of forensic genetic methods into DNA profiling, and how the field has accounted for the apportionment of genetic diversity in considering the weight of forensic evidence. When investigative databases fail to provide a match to a crime-scene profile, specific markers can be used to seek intelligence about a suspect: these include inferences on population of origin (biogeographic ancestry) and externally visible characteristics, chiefly pigmentation of skin, hair and eyes. In this endeavour, ancestry and phenotypic variation are closely entangled. The markers used show patterns of inter- and intrapopulation diversity that are very atypical compared to the genome as a whole, and reinforce an apparent link between ancestry and racial divergence that is not systematically present otherwise. Despite the legacy of Lewontin's result, therefore, in a major area in which genetics coincides with issues of public interest, methods tend to exaggerate human differences and could thereby contribute to the reification of biological race. This article is part of the theme issue ‘Celebrating 50 years since Lewontin's apportionment of human diversity’.
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Affiliation(s)
- Mark A. Jobling
- Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester LE1 7RH, UK
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35
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Zhou Y, Jin X, Wu B, Zhu B. Development and Performance Evaluation of a Novel Ancestry Informative DIP Panel for Continental Origin Inference. Front Genet 2022; 12:801275. [PMID: 35251118 PMCID: PMC8891605 DOI: 10.3389/fgene.2021.801275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 12/01/2021] [Indexed: 11/13/2022] Open
Abstract
Ancestry informative markers (AIMs) are useful to infer individual biogeographical ancestry and to estimate admixture proportions of admixed populations or individuals. Although a growing number of AIM panels for forensic ancestry origin analyses were developed, they may not efficiently infer the ancestry origins of most populations in China. In this study, a set of 52 ancestry informative deletion/insertion polymorphisms (AIDIPs) were selected with the aim of effectively differentiate continental and partial Chinese populations. All of the selected markers were successfully incorporated into a single multiplex PCR panel, which could be conveniently and efficiently detected on capillary electrophoresis platforms. Genetic distributions of the same 50 AIDIPs in different continental populations revealed that most loci showed high genetic differentiations between East Asian populations and other continental populations. Population genetic analyses of different continental populations indicated that these 50 AIDIPs could clearly discriminate East Asian, European, and African populations. In addition, the 52 AIDIPs also exhibited relatively high cumulative discrimination power in the Eastern Han population, which could be used as a supplementary tool for forensic investigation. Furthermore, the Eastern Han population showed close genetic relationships with East Asian populations and high ancestral components from East Asian populations. In the future, we need to investigate genetic distributions of these 52 AIDIPs in Chinese Han populations in different regions and other ethnic groups, and further evaluate the power of these loci to differentiate different Chinese populations.
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Affiliation(s)
- Yongsong Zhou
- Shenzhen Stomatology Hospital (Pingshan), Southern Medical University, Shenzhen, China
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Xiaoye Jin
- School of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Buling Wu
- Shenzhen Stomatology Hospital (Pingshan), Southern Medical University, Shenzhen, China
- *Correspondence: Buling Wu, ; Bofeng Zhu,
| | - Bofeng Zhu
- Shenzhen Stomatology Hospital (Pingshan), Southern Medical University, Shenzhen, China
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi’an Jiaotong University, Xi’an, China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi’an Jiaotong University, Xi’an, China
- *Correspondence: Buling Wu, ; Bofeng Zhu,
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36
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Evaluation of the VISAGE basic tool for appearance and ancestry inference using ForenSeq® chemistry on the MiSeq FGx® system. Forensic Sci Int Genet 2022; 58:102675. [DOI: 10.1016/j.fsigen.2022.102675] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 01/13/2022] [Accepted: 02/01/2022] [Indexed: 11/04/2022]
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37
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Tvedebrink T. Review of the Forensic Applicability of Biostatistical Methods for Inferring Ancestry from Autosomal Genetic Markers. Genes (Basel) 2022; 13:genes13010141. [PMID: 35052480 PMCID: PMC8774801 DOI: 10.3390/genes13010141] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/10/2022] [Accepted: 01/11/2022] [Indexed: 02/01/2023] Open
Abstract
The inference of ancestry has become a part of the services many forensic genetic laboratories provide. Interest in ancestry may be to provide investigative leads or identify the region of origin in cases of unidentified missing persons. There exist many biostatistical methods developed for the study of population structure in the area of population genetics. However, the challenges and questions are slightly different in the context of forensic genetics, where the origin of a specific sample is of interest compared to the understanding of population histories and genealogies. In this paper, the methodologies for modelling population admixture and inferring ancestral populations are reviewed with a focus on their strengths and weaknesses in relation to ancestry inference in the forensic context.
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Affiliation(s)
- Torben Tvedebrink
- Department of Mathematical Sciences, Aalborg University, DK-9220 Aalborg, Denmark;
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, DK-1165 Copenhagen, Denmark
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38
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Pośpiech E, Teisseyre P, Mielniczuk J, Branicki W. Predicting Physical Appearance from DNA Data-Towards Genomic Solutions. Genes (Basel) 2022; 13:genes13010121. [PMID: 35052461 PMCID: PMC8774670 DOI: 10.3390/genes13010121] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 01/03/2022] [Accepted: 01/04/2022] [Indexed: 02/04/2023] Open
Abstract
The idea of forensic DNA intelligence is to extract from genomic data any information that can help guide the investigation. The clues to the externally visible phenotype are of particular practical importance. The high heritability of the physical phenotype suggests that genetic data can be easily predicted, but this has only become possible with less polygenic traits. The forensic community has developed DNA-based predictive tools by employing a limited number of the most important markers analysed with targeted massive parallel sequencing. The complexity of the genetics of many other appearance phenotypes requires big data coupled with sophisticated machine learning methods to develop accurate genomic predictors. A significant challenge in developing universal genomic predictive methods will be the collection of sufficiently large data sets. These should be created using whole-genome sequencing technology to enable the identification of rare DNA variants implicated in phenotype determination. It is worth noting that the correctness of the forensic sketch generated from the DNA data depends on the inclusion of an age factor. This, however, can be predicted by analysing epigenetic data. An important limitation preventing whole-genome approaches from being commonly used in forensics is the slow progress in the development and implementation of high-throughput, low DNA input sequencing technologies. The example of palaeoanthropology suggests that such methods may possibly be developed in forensics.
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Affiliation(s)
- Ewelina Pośpiech
- Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Kraków, Poland;
| | - Paweł Teisseyre
- Institute of Computer Science, Polish Academy of Sciences, 01-248 Warsaw, Poland; (P.T.); (J.M.)
- Faculty of Mathematics and Information Science, Warsaw University of Technology, 00-662 Warsaw, Poland
| | - Jan Mielniczuk
- Institute of Computer Science, Polish Academy of Sciences, 01-248 Warsaw, Poland; (P.T.); (J.M.)
- Faculty of Mathematics and Information Science, Warsaw University of Technology, 00-662 Warsaw, Poland
| | - Wojciech Branicki
- Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Kraków, Poland;
- Central Forensic Laboratory of the Police, 00-583 Warsaw, Poland
- Correspondence: ; Tel.: +48-126-645-024
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39
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Frégeau CJ. A multiple predictive tool approach for phenotypic and biogeographical ancestry inferences. CANADIAN SOCIETY OF FORENSIC SCIENCE JOURNAL 2021. [DOI: 10.1080/00085030.2021.2016206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Chantal J. Frégeau
- Royal Canadian Mounted Police, Forensic Science & Identification Services, Biology Policy & Program Support, Ottawa, ON, Canada
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40
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de Vries JH, Kling D, Vidaki A, Arp P, Kalamara V, Verbiest MMPJ, Piniewska-Róg D, Parsons TJ, Uitterlinden AG, Kayser M. Impact of SNP microarray analysis of compromised DNA on kinship classification success in the context of investigative genetic genealogy. Forensic Sci Int Genet 2021; 56:102625. [PMID: 34753062 DOI: 10.1016/j.fsigen.2021.102625] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 10/25/2021] [Accepted: 10/27/2021] [Indexed: 11/04/2022]
Abstract
Single nucleotide polymorphism (SNP) data generated with microarray technologies have been used to solve murder cases via investigative leads obtained from identifying relatives of the unknown perpetrator included in accessible genomic databases, an approach referred to as investigative genetic genealogy (IGG). However, SNP microarrays were developed for relatively high input DNA quantity and quality, while DNA typically obtainable from crime scene stains is of low DNA quantity and quality, and SNP microarray data obtained from compromised DNA are largely missing. By applying the Illumina Global Screening Array (GSA) to 264 DNA samples with systematically altered quantity and quality, we empirically tested the impact of SNP microarray analysis of compromised DNA on kinship classification success, as relevant in IGG. Reference data from manufacturer-recommended input DNA quality and quantity were used to estimate genotype accuracy in the compromised DNA samples and for simulating data of different degree relatives. Although stepwise decrease of input DNA amount from 200 ng to 6.25 pg led to decreased SNP call rates and increased genotyping errors, kinship classification success did not decrease down to 250 pg for siblings and 1st cousins, 1 ng for 2nd cousins, while at 25 pg and below kinship classification success was zero. Stepwise decrease of input DNA quality via increased DNA fragmentation resulted in the decrease of genotyping accuracy as well as kinship classification success, which went down to zero at the average DNA fragment size of 150 base pairs. Combining decreased DNA quantity and quality in mock casework and skeletal samples further highlighted possibilities and limitations. Overall, GSA analysis achieved maximal kinship classification success from 800 to 200 times lower input DNA quantities than manufacturer-recommended, although DNA quality plays a key role too, while compromised DNA produced false negative kinship classifications rather than false positive ones.
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Affiliation(s)
- Jard H de Vries
- Erasmus MC, University Medical Center Rotterdam, Department of Internal Medicine, Dr. Molewaterplein 40, 3015 GD Rotterdam, the Netherlands
| | - Daniel Kling
- Department of Forensic Genetics and Toxicology, National Board of Forensic Medicine, Artillerigatan 12, 587 58 Linköping, Sweden
| | - Athina Vidaki
- Erasmus MC, University Medical Center Rotterdam, Department of Genetic Identification, Dr. Molewaterplein 40, 3015 GD Rotterdam, the Netherlands
| | - Pascal Arp
- Erasmus MC, University Medical Center Rotterdam, Department of Internal Medicine, Dr. Molewaterplein 40, 3015 GD Rotterdam, the Netherlands
| | - Vivian Kalamara
- Erasmus MC, University Medical Center Rotterdam, Department of Genetic Identification, Dr. Molewaterplein 40, 3015 GD Rotterdam, the Netherlands
| | - Michael M P J Verbiest
- Erasmus MC, University Medical Center Rotterdam, Department of Internal Medicine, Dr. Molewaterplein 40, 3015 GD Rotterdam, the Netherlands
| | - Danuta Piniewska-Róg
- Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Krakow, Poland; Department of Forensic Medicine, Jagiellonian University Medical College, 31-531 Krakow, Poland
| | - Thomas J Parsons
- International Commission on Missing Persons, Koninginnegracht 12a, 2514 AA Den Haag, the Netherlands
| | - André G Uitterlinden
- Erasmus MC, University Medical Center Rotterdam, Department of Internal Medicine, Dr. Molewaterplein 40, 3015 GD Rotterdam, the Netherlands; Erasmus MC, University Medical Center Rotterdam, Department of Epidemiology, Dr. Molewaterplein 40, 3015 GD Rotterdam, the Netherlands
| | - Manfred Kayser
- Erasmus MC, University Medical Center Rotterdam, Department of Genetic Identification, Dr. Molewaterplein 40, 3015 GD Rotterdam, the Netherlands.
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41
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Chen C, Jin X, Zhang X, Zhang W, Guo Y, Tao R, Chen A, Xu Q, Li M, Yang Y, Zhu B. Comprehensive Insights Into Forensic Features and Genetic Background of Chinese Northwest Hui Group Using Six Distinct Categories of 231 Molecular Markers. Front Genet 2021; 12:705753. [PMID: 34721519 PMCID: PMC8555763 DOI: 10.3389/fgene.2021.705753] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 09/07/2021] [Indexed: 11/13/2022] Open
Abstract
The Hui minority is predominantly composed of Chinese-speaking Islamic adherents distributed throughout China, of which the individuals are mainly concentrated in Northwest China. In the present study, we employed the length and sequence polymorphisms-based typing system of 231 molecular markers, i.e., amelogenin, 22 phenotypic-informative single nucleotide polymorphisms (PISNPs), 94 identity-informative single nucleotide polymorphisms (IISNPs), 24 Y-chromosomal short tandem repeats (Y-STRs), 56 ancestry-informative single nucleotide polymorphisms (AISNPs), 7 X-chromosomal short tandem repeats (X-STRs), and 27 autosomal short tandem repeats (A-STRs), into 90 unrelated male individuals from the Chinese Northwest Hui group to comprehensively explore its forensic characteristics and genetic background. Total of 451 length-based and 652 sequence-based distinct alleles were identified from 58 short tandem repeats (STRs) in 90 unrelated Northwest Hui individuals, denoting that the sequence-based genetic markers could pronouncedly provide more genetic information than length-based markers. The forensic characteristics and efficiencies of STRs and IISNPs were estimated, both of which externalized high polymorphisms in the Northwest Hui group and could be further utilized in forensic investigations. No significant departure from the Hardy-Weinberg equilibrium (HWE) expectation was observed after the Bonferroni correction. Additionally, four group sets of reference population data were exploited to dissect the genetic background of the Northwest Hui group separately from different perspectives, which contained 26 populations for 93 IISNPs, 58 populations for 17 Y-STRs, 26 populations for 55 AISNPs (raw data), and 109 populations for 55 AISNPs (allele frequencies). As a result, the analyses based on the Y-STRs indicated that the Northwest Hui group primarily exhibited intimate genetic relationships with reference Hui groups from Chinese different regions except for the Sichuan Hui group and secondarily displayed close genetic relationships with populations from Central and West Asia, as well as several Chinese groups. However, the AISNP analyses demonstrated that the Northwest Hui group shared more intimate relationships with current East Asian populations apart from reference Hui group, harboring the large proportion of ancestral component contributed by East Asia.
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Affiliation(s)
- Chong Chen
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Xiaoye Jin
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China
| | - Xingru Zhang
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Wenqing Zhang
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China
| | - Yuxin Guo
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China
| | - Ruiyang Tao
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, China
| | - Anqi Chen
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, China.,Department of Forensic Medicine, Shanghai Medical College of Fudan University, Shanghai, China
| | - Qiannan Xu
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, China.,Institute of Forensic Medicine, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Min Li
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, China.,Institute of Forensic Medicine, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Yue Yang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, China.,School of Basic Medicine, Inner Mongolia Medical University, Hohhot, China
| | - Bofeng Zhu
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China.,Department of Forensic Genetics, Multi-Omics Innovative Research Center of Forensic Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China
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42
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Truelsen D, Freire-Aradas A, Nazari M, Aliferi A, Ballard D, Phillips C, Morling N, Pereira V, Børsting C. Evaluation of a custom QIAseq targeted DNA panel with 164 ancestry informative markers sequenced with the Illumina MiSeq. Sci Rep 2021; 11:21040. [PMID: 34702940 PMCID: PMC8548529 DOI: 10.1038/s41598-021-99933-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 09/29/2021] [Indexed: 11/08/2022] Open
Abstract
Introduction of new methods requires meticulous evaluation before they can be applied to forensic genetic case work. Here, a custom QIAseq Targeted DNA panel with 164 ancestry informative markers was assessed using the MiSeq sequencing platform. Concordance, sensitivity, and the capability for analysis of mixtures were tested. The assay gave reproducible and nearly concordant results with an input of 10 and 2 ng DNA. Lower DNA input led to an increase in both locus and allele drop-outs, and a higher variation in heterozygote balance. Locus or allele drop-outs in the samples with less than 2 ng DNA input were not necessarily associated with the overall performance of a locus. Thus, the QIAseq assay will be difficult to implement in a forensic genetic setting where the sample material is often scarce and of poor quality. With equal or near equal mixture ratios, the mixture DNA profiles were easily identified by an increased number of imbalanced heterozygotes. For more skewed mixture ratios, the mixture DNA profiles were identified by an increased noise level. Lastly, individuals from Great Britain and the Middle East were investigated. The Middle Eastern individuals showed a greater affinity with South European populations compared to North European populations.
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Affiliation(s)
- D Truelsen
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2100, Copenhagen, Denmark.
| | - A Freire-Aradas
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - M Nazari
- Faculty of Life Sciences and Medicine, King's College, London, UK
| | - A Aliferi
- Faculty of Life Sciences and Medicine, King's College, London, UK
| | - D Ballard
- Faculty of Life Sciences and Medicine, King's College, London, UK
| | - C Phillips
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - N Morling
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2100, Copenhagen, Denmark
- Department of Mathematical Sciences, Aalborg University, 9220, Aalborg, Denmark
| | - V Pereira
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2100, Copenhagen, Denmark
| | - C Børsting
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2100, Copenhagen, Denmark
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43
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Developments in forensic DNA analysis. Emerg Top Life Sci 2021; 5:381-393. [PMID: 33792660 PMCID: PMC8457771 DOI: 10.1042/etls20200304] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 03/12/2021] [Accepted: 03/16/2021] [Indexed: 12/20/2022]
Abstract
The analysis of DNA from biological evidence recovered in the course of criminal investigations can provide very powerful evidence when a recovered profile matches one found on a DNA database or generated from a suspect. However, when no profile match is found, when the amount of DNA in a sample is too low, or the DNA too degraded to be analysed, traditional STR profiling may be of limited value. The rapidly expanding field of forensic genetics has introduced various novel methodologies that enable the analysis of challenging forensic samples, and that can generate intelligence about the donor of a biological sample. This article reviews some of the most important recent advances in the field, including the application of massively parallel sequencing to the analysis of STRs and other marker types, advancements in DNA mixture interpretation, particularly the use of probabilistic genotyping methods, the profiling of different RNA types for the identification of body fluids, the interrogation of SNP markers for predicting forensically relevant phenotypes, epigenetics and the analysis of DNA methylation to determine tissue type and estimate age, and the emerging field of forensic genetic genealogy. A key challenge will be for researchers to consider carefully how these innovations can be implemented into forensic practice to ensure their potential benefits are maximised.
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44
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Truelsen D, Tvedebrink T, Mogensen HS, Farzad MS, Shan MA, Morling N, Pereira V, Børsting C. Assessment of the effectiveness of the EUROFORGEN NAME and Precision ID Ancestry panel markers for ancestry investigations. Sci Rep 2021; 11:18595. [PMID: 34545122 PMCID: PMC8452675 DOI: 10.1038/s41598-021-97654-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 08/11/2021] [Indexed: 11/08/2022] Open
Abstract
The EUROFORGEN NAME panel is a regional ancestry panel designed to differentiate individuals from the Middle East, North Africa, and Europe. The first version of the panel was developed for the MassARRAY system and included 111 SNPs. Here, a custom AmpliSeq EUROFORGEN NAME panel with 102 of the original 111 loci was used to sequence 1098 individuals from 14 populations from Europe, the Middle East, North Africa, North-East Africa, and South-Central Asia. These samples were also sequenced with a global ancestry panel, the Precision ID Ancestry Panel. The GenoGeographer software was used to assign the AIM profiles to reference populations and calculate the weight of the evidence as likelihood ratios. The combination of the EUROFORGEN NAME and Precision ID Ancestry panels led to fewer ambiguous assignments, especially for individuals from the Middle East and South-Central Asia. The likelihood ratios showed that North African individuals could be separated from European and Middle Eastern individuals using the Precision ID Ancestry Panel. The separation improved with the addition of the EUROFORGEN NAME panel. The analyses also showed that the separation of Middle Eastern populations from European and South-Central Asian populations was challenging even when both panels were applied.
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Affiliation(s)
- D Truelsen
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2100, Copenhagen, Denmark.
| | - T Tvedebrink
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2100, Copenhagen, Denmark
- Department of Mathematical Sciences, Aalborg University, 9220, Aalborg, Denmark
| | - H S Mogensen
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2100, Copenhagen, Denmark
| | - M S Farzad
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2100, Copenhagen, Denmark
| | - M A Shan
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2100, Copenhagen, Denmark
| | - N Morling
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2100, Copenhagen, Denmark
- Department of Mathematical Sciences, Aalborg University, 9220, Aalborg, Denmark
| | - V Pereira
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2100, Copenhagen, Denmark
| | - C Børsting
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2100, Copenhagen, Denmark
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45
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de la Puente M, Ruiz-Ramírez J, Ambroa-Conde A, Xavier C, Pardo-Seco J, Álvarez-Dios J, Freire-Aradas A, Mosquera-Miguel A, Gross TE, Cheung EYY, Branicki W, Nothnagel M, Parson W, Schneider PM, Kayser M, Carracedo Á, Lareu MV, Phillips C. Development and Evaluation of the Ancestry Informative Marker Panel of the VISAGE Basic Tool. Genes (Basel) 2021; 12:1284. [PMID: 34440458 PMCID: PMC8391248 DOI: 10.3390/genes12081284] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 08/18/2021] [Accepted: 08/18/2021] [Indexed: 11/29/2022] Open
Abstract
We detail the development of the ancestry informative single nucleotide polymorphisms (SNPs) panel forming part of the VISAGE Basic Tool (BT), which combines 41 appearance predictive SNPs and 112 ancestry predictive SNPs (three SNPs shared between sets) in one massively parallel sequencing (MPS) multiplex, whereas blood-based age analysis using methylation markers is run in a parallel MPS analysis pipeline. The selection of SNPs for the BT ancestry panel focused on established forensic markers that already have a proven track record of good sequencing performance in MPS, and the overall SNP multiplex scale closely matched that of existing forensic MPS assays. SNPs were chosen to differentiate individuals from the five main continental population groups of Africa, Europe, East Asia, America, and Oceania, extended to include differentiation of individuals from South Asia. From analysis of 1000 Genomes and HGDP-CEPH samples from these six population groups, the BT ancestry panel was shown to have no classification error using the Bayes likelihood calculators of the Snipper online analysis portal. The differentiation power of the component ancestry SNPs of BT was balanced as far as possible to avoid bias in the estimation of co-ancestry proportions in individuals with admixed backgrounds. The balancing process led to very similar cumulative population-specific divergence values for Africa, Europe, America, and Oceania, with East Asia being slightly below average, and South Asia an outlier from the other groups. Comparisons were made of the African, European, and Native American estimated co-ancestry proportions in the six admixed 1000 Genomes populations, using the BT ancestry panel SNPs and 572,000 Affymetrix Human Origins array SNPs. Very similar co-ancestry proportions were observed down to a minimum value of 10%, below which, low-level co-ancestry was not always reliably detected by BT SNPs. The Snipper analysis portal provides a comprehensive population dataset for the BT ancestry panel SNPs, comprising a 520-sample standardised reference dataset; 3445 additional samples from 1000 Genomes, HGDP-CEPH, Simons Foundation and Estonian Biocentre genome diversity projects; and 167 samples of six populations from in-house genotyping of individuals from Middle East, North and East African regions complementing those of the sampling regimes of the other diversity projects.
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Affiliation(s)
- María de la Puente
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain; (M.d.l.P.); (J.R.-R.); (A.A.-C.); (A.F.-A.); (A.M.-M.); (Á.C.); (M.V.L.)
| | - Jorge Ruiz-Ramírez
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain; (M.d.l.P.); (J.R.-R.); (A.A.-C.); (A.F.-A.); (A.M.-M.); (Á.C.); (M.V.L.)
| | - Adrián Ambroa-Conde
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain; (M.d.l.P.); (J.R.-R.); (A.A.-C.); (A.F.-A.); (A.M.-M.); (Á.C.); (M.V.L.)
| | - Catarina Xavier
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria; (C.X.); (W.P.)
| | - Jacobo Pardo-Seco
- Genetics, Vaccines, Infectious Diseases and Pediatrics Research Group (GENVIP Group), Instituto de Investigación Sanitaria de Santiago de Compostela, 15706 Santiago de Compostela, Spain;
| | - Jose Álvarez-Dios
- Faculty of Mathematics, University of Santiago de Compostela, 15705 Santiago de Compostela, Spain;
| | - Ana Freire-Aradas
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain; (M.d.l.P.); (J.R.-R.); (A.A.-C.); (A.F.-A.); (A.M.-M.); (Á.C.); (M.V.L.)
| | - Ana Mosquera-Miguel
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain; (M.d.l.P.); (J.R.-R.); (A.A.-C.); (A.F.-A.); (A.M.-M.); (Á.C.); (M.V.L.)
| | - Theresa E. Gross
- Institute of Legal Medicine, Faculty of Medicine and University Clinic, University of Cologne, 50823 Cologne, Germany; (T.E.G.); (E.Y.Y.C.); (P.M.S.)
- Hessisches Landeskriminalamt, 65187 Wiesbaden, Germany
| | - Elaine Y. Y. Cheung
- Institute of Legal Medicine, Faculty of Medicine and University Clinic, University of Cologne, 50823 Cologne, Germany; (T.E.G.); (E.Y.Y.C.); (P.M.S.)
| | - Wojciech Branicki
- Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Kraków, Poland;
| | - Michael Nothnagel
- Cologne Center for Genomics, University of Cologne, 50823 Cologne, Germany;
- University Hospital Cologne, 50937 Cologne, Germany
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria; (C.X.); (W.P.)
- Forensic Science Program, The Pennsylvania State University, University Park, State College, PA 16802, USA
| | - Peter M. Schneider
- Institute of Legal Medicine, Faculty of Medicine and University Clinic, University of Cologne, 50823 Cologne, Germany; (T.E.G.); (E.Y.Y.C.); (P.M.S.)
| | - Manfred Kayser
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, 3015 CN Rotterdam, South Holland, The Netherlands;
| | - Ángel Carracedo
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain; (M.d.l.P.); (J.R.-R.); (A.A.-C.); (A.F.-A.); (A.M.-M.); (Á.C.); (M.V.L.)
- Fundación Pública Galega de Medicina Xenómica (FPGMX), 15706 Santiago de Compostela, Spain
| | - Maria Victoria Lareu
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain; (M.d.l.P.); (J.R.-R.); (A.A.-C.); (A.F.-A.); (A.M.-M.); (Á.C.); (M.V.L.)
| | - Christopher Phillips
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain; (M.d.l.P.); (J.R.-R.); (A.A.-C.); (A.F.-A.); (A.M.-M.); (Á.C.); (M.V.L.)
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Piniewska-Róg D, Heidegger A, Pośpiech E, Xavier C, Pisarek A, Jarosz A, Woźniak A, Wojtas M, Phillips C, Kayser M, Parson W, Branicki W. Impact of excessive alcohol abuse on age prediction using the VISAGE enhanced tool for epigenetic age estimation in blood. Int J Legal Med 2021; 135:2209-2219. [PMID: 34405265 PMCID: PMC8523459 DOI: 10.1007/s00414-021-02665-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 07/06/2021] [Indexed: 12/13/2022]
Abstract
DNA methylation-based clocks provide the most accurate age estimates with practical implications for clinical and forensic genetics. However, the effects of external factors that may influence the estimates are poorly studied. Here, we evaluated the effect of alcohol consumption on epigenetic age prediction in a cohort of extreme alcohol abusers. Blood samples from deceased alcohol abusers and age- and sex-matched controls were analyzed using the VISAGE enhanced tool for age prediction from somatic tissues that enables examination of 44 CpGs within eight age markers. Significantly altered DNA methylation was recorded for alcohol abusers in MIR29B2CHG. This resulted in a mean predicted age of 1.4 years higher compared to the controls and this trend increased in older individuals. The association of alcohol abuse with epigenetic age acceleration, as determined by the prediction analysis performed based on MIR29B2CHG, was small but significant (β = 0.190; P-value = 0.007). However, the observed alteration in DNA methylation of MIR29B2CHG had a non-significant effect on age estimation with the VISAGE age prediction model. The mean absolute error in the alcohol-abusing cohort was 3.1 years, compared to 3.3 years in the control group. At the same time, upregulation of MIR29B2CHG expression may have a biological function, which merits further studies.
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Affiliation(s)
- Danuta Piniewska-Róg
- Jagiellonian University Medical College, Faculty of Medicine, Department of Forensic Medicine, Grzegórzecka 16, 31-531, Krakow, Poland
| | - Antonia Heidegger
- Institute of Legal Medicine, Medical University of Innsbruck, Muellerstrasse 44, 6020, Innsbruck, Austria
| | - Ewelina Pośpiech
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-348, Krakow, Poland
| | - Catarina Xavier
- Institute of Legal Medicine, Medical University of Innsbruck, Muellerstrasse 44, 6020, Innsbruck, Austria
| | - Aleksandra Pisarek
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-348, Krakow, Poland
| | - Agata Jarosz
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-348, Krakow, Poland
| | - Anna Woźniak
- Central Forensic Laboratory of the Police, Aleje Ujazdowskie 7, 00-583, Warsaw, Poland
| | - Marta Wojtas
- Jagiellonian University Medical College, Faculty of Medicine, Department of Forensic Medicine, Grzegórzecka 16, 31-531, Krakow, Poland
| | - Christopher Phillips
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, R/ San Francisco s/n, 15782, Santiago de Compostela, Spain
| | - Manfred Kayser
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, Muellerstrasse 44, 6020, Innsbruck, Austria
- Forensic Science Program, The Pennsylvania State University, 13 Thomas Building, University Park, PA, 16802, USA
| | - Wojciech Branicki
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-348, Krakow, Poland.
- Central Forensic Laboratory of the Police, Aleje Ujazdowskie 7, 00-583, Warsaw, Poland.
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47
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Epigenetic age prediction in semen - marker selection and model development. Aging (Albany NY) 2021; 13:19145-19164. [PMID: 34375949 PMCID: PMC8386575 DOI: 10.18632/aging.203399] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 07/17/2021] [Indexed: 12/12/2022]
Abstract
DNA methylation analysis is becoming increasingly useful in biomedical research and forensic practice. The discovery of differentially methylated sites (DMSs) that continuously change over an individual's lifetime has led to breakthroughs in molecular age estimation. Although semen samples are often used in forensic DNA analysis, previous epigenetic age prediction studies mainly focused on somatic cell types. Here, Infinium MethylationEPIC BeadChip arrays were applied to semen-derived DNA samples, which identified numerous novel DMSs moderately correlated with age. Validation of the ten most age-correlated novel DMSs and three previously known sites in an independent set of semen-derived DNA samples using targeted bisulfite massively parallel sequencing, confirmed age-correlation for nine new and three previously known markers. Prediction modelling revealed the best model for semen, based on 6 CpGs from newly identified genes SH2B2, EXOC3, IFITM2, and GALR2 as well as the previously known FOLH1B gene, which predict age with a mean absolute error of 5.1 years in an independent test set. Further increases in the accuracy of age prediction from semen DNA will require technological progress to allow sensitive, simultaneous analysis of a much larger number of age correlated DMSs from the compromised DNA typical of forensic semen stains.
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48
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Suárez D, Cruz R, Torres M, Mogollón F, Moncada J, Carracedo A, Usaquén W. Ancestry analysis using autosomal SNPs in northern South America, reveals interpretation differences between an AIM panel and an identification panel. Forensic Sci Int 2021; 326:110934. [PMID: 34404021 DOI: 10.1016/j.forsciint.2021.110934] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 07/14/2021] [Accepted: 07/23/2021] [Indexed: 12/20/2022]
Abstract
Current human populations are studied to elucidate their ancestry composition and to obtain reference values for an array of genetic markers for forensic practice. This study compared the 79 ancestry informative markers (AIMs) panel with the SNPforID 52plex set used in forensic identification, using samples belonging to Continental Caribbean populations from Colombia with a high percentage of locals self-determined as Native American descendants. The results show a bias in the individual estimation made with the identification markers, which disregards the Native American ancestry component and overestimates the African ancestry component. Also, the analysis made with the Bayesian Classification Algorithm shows better likelihoods for individual assignment with AIMs than with SNPforID 52plex.
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Affiliation(s)
- Dayana Suárez
- Populations Genetics and Identification Group, Institute of Genetics, National University of Colombia, Bogotá, Colombia.
| | - Raquel Cruz
- CIBERER, Genomic Medicine Group, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - María Torres
- Galician Public Foundation of Genomic Medicine (SERGAS)-CIBERER, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Fernanda Mogollón
- Populations Genetics and Identification Group, Institute of Genetics, National University of Colombia, Bogotá, Colombia
| | - Julie Moncada
- Populations Genetics and Identification Group, Institute of Genetics, National University of Colombia, Bogotá, Colombia
| | - Angel Carracedo
- CIBERER, Genomic Medicine Group, University of Santiago de Compostela, Santiago de Compostela, Spain; Galician Public Foundation of Genomic Medicine (SERGAS)-CIBERER, University of Santiago de Compostela, Santiago de Compostela, Spain; Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Spain
| | - William Usaquén
- Populations Genetics and Identification Group, Institute of Genetics, National University of Colombia, Bogotá, Colombia.
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49
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Investigative DNA analysis of two-person mixed crime scene trace in a murder case. Forensic Sci Int Genet 2021; 54:102557. [PMID: 34175530 DOI: 10.1016/j.fsigen.2021.102557] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 06/17/2021] [Accepted: 06/18/2021] [Indexed: 11/20/2022]
Abstract
It has been advocated before that appearance prediction of unknown suspects from crime scene DNA, in the context of Forensic DNA Phenotyping (FDP), is mostly suitable for single source DNA samples, whereas FDP from DNA mixtures to which more than one person contributed, is viewed challenging. With this report on a murder case, we practically demonstrate the feasibility of appearance DNA prediction of an unknown suspect from a mixed crime scene trace, to which the unknown suspect and the known victim had contributed. From this two-person DNA mixture, we successfully predicted eye, hair and skin color of the unknown suspect with the HIrisPlex-S system by applying targeted massively parallel sequencing (MPS). We argue that at least three factors benefit appearance DNA prediction of unknown suspects from mixed crime scene traces, which were met in this murder case: i) SNP genotype knowledge from reference DNA analysis for one of the two persons in the mixture (here the known victim), ii) about equal DNA contributions by both donors to the mixed crime scene stain, and iii) the use of MPS allowing quantitative SNP analysis. Moreover, we show that additionally analyzing animal DNA in this mixed crime scene trace provides further investigative information. We envision that the investigative DNA strategy that we applied here for analyzing a two-person mixed crime scene trace in a murder case, will be applied in the future to more criminal cases with two-person DNA mixtures, for instance sexual assault cases.
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50
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Zhu Q, Cao Y, Zhang S, Huang Y, Hu Y, Zhou Y, Wang H, Wang Y, Zhang J. A targeted ancestry informative InDels panel on capillary electrophoresis for ancestry inference in Asian populations. Electrophoresis 2021; 42:1605-1613. [PMID: 34081340 DOI: 10.1002/elps.202100016] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 04/12/2021] [Accepted: 05/30/2021] [Indexed: 11/09/2022]
Abstract
CE is the primary methodology used in forensic DNA typing. Alleles of commonly used types of genetic markers could be separated and detected via CE based on dye color and migration time. Insertion/deletion (InDel) is an ideal genetic marker for forensic DNA analysis due to their abundance in the human genome, low mutation rate, availability of their allele types via CE, and elimination of stutter peaks. Moreover, InDels could be used as ancestry informative markers since allele frequencies of InDels is different among geographically separated populations. Several ancestry informative insertion/deletion panels have been established based on CE platform to achieve the intercontinental populations distinction. However, improvements to differentiate intracontinental populations is few. In this study, 21 InDels with fixation index (FST ) > 0.15 were selected and assembled into one ancestry informative insertion/deletion panel. Using well-designed primers, those 21 InDels could be amplified successfully and genotyped on the CE platform accurately and completely. The panel showed a large FST distance distinction among the ten Asian populations. Using clustering analysis, ten Asian populations were classified into three subgroups: East Asian, Southeast Asian, and South Asian subgroups. To evaluate the panel's capability in ancestry inference, a validation experiment was undertaken with 319 individuals from four geographically separated populations in China. Four Chinese populations were classified into different ancestry subgroups and 81.8% test individuals' ancestry could be inferred correctly. Our result showed that development of high ancestry informative InDels panel based on CE platform is a potential for individual ancestry inference among intracontinental populations.
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Affiliation(s)
- Qiang Zhu
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, P. R. China
| | - Yueyan Cao
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, P. R. China
| | - Shu Zhang
- Basic Medicine Colleges, Chengdu University of Traditional Chinese Medicine, Chengdu, P. R. China
| | - Yuguo Huang
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, P. R. China
| | - Yuhan Hu
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, P. R. China
| | - Yijun Zhou
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, P. R. China
| | - Haoyu Wang
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, P. R. China
| | - Yufang Wang
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, P. R. China
| | - Ji Zhang
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, P. R. China
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