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Liu L, Li S, Cui W, Fang Y, Mei S, Chen M, Xu H, Bai X, Zhu B. Ancestry analysis using a self-developed 56 AIM-InDel loci and machine learning methods. Forensic Sci Int 2024; 361:112065. [PMID: 38889603 DOI: 10.1016/j.forsciint.2024.112065] [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: 10/20/2023] [Revised: 12/11/2023] [Accepted: 05/16/2024] [Indexed: 06/20/2024]
Abstract
Insertion/deletion (InDel) polymorphisms can be used as one of the ancestry-informative markers in ancestry analysis. In this study, a self-developed panel consisting of 56 ancestry-informative InDels was used to investigate the genetic structures and genetic relationships between Chinese Inner Mongolia Manchu group and 26 reference populations. The Inner Mongolia Manchu group was closely related in genetic background to East Asian populations, especially the Han Chinese in Beijing. Moreover, populations from northern and southern East Asia displayed obvious variations in ancestral components, suggesting the potential value of this panel in distinguishing the populations from northern and southern East Asia. Subsequently, four machine learning models were performed based on the 56 AIM-InDel loci to evaluate the performance of this panel in ancestry prediction. The random forest model presented better performance in ancestry prediction, with 91.87% and 99.73% accuracy for the five and three continental populations, respectively. The individuals of the Inner Mongolia Manchu group were assigned to the East Asian populations by the random forest model, and they exhibited closer genetic affinities with northern East Asian populations. Furthermore, the random forest model distinguished 87.18% of the Inner Mongolia Manchus from the East Asian populations, suggesting that the random forest model based on the 56 ancestry-informative InDels could be a potential tool for ancestry analysis.
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Affiliation(s)
- Liu Liu
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, 1838 Guangzhou Avenue North, Guangzhou, Guangdong, PR China
| | - Shuanglin Li
- Department of Anatomy and Histology, School of Basic Medical Sciences, Shenzhen University Medical School, Shenzhen University, 1066 Xueyuan Avenue, Shenzhen, Guangdong, China
| | - Wei Cui
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, 1838 Guangzhou Avenue North, Guangzhou, Guangdong, PR China
| | - Yating Fang
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, 1838 Guangzhou Avenue North, Guangzhou, Guangdong, PR China
| | - Shuyan Mei
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, 1838 Guangzhou Avenue North, Guangzhou, Guangdong, PR China
| | - Man Chen
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, 1838 Guangzhou Avenue North, Guangzhou, Guangdong, PR China
| | - Hui Xu
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, 1838 Guangzhou Avenue North, Guangzhou, Guangdong, PR China
| | - Xiaole Bai
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, 1838 Guangzhou Avenue North, Guangzhou, Guangdong, PR China
| | - Bofeng Zhu
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, 1838 Guangzhou Avenue North, Guangzhou, Guangdong, PR China; Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'anJiaotong University, 99 Yanxiang Road, Xi'an, Shaanxi, PR China.
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2
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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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3
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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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4
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Wan W, Zhang H, Ren Z, Wang Q, Liu Y, Ji J, Yang M, Zhang H, Huang J, Jin X. Systematic selection of ancestry informative SNPs for differentiating Han, Japanese, Dai, and Kinh populations. Electrophoresis 2023; 44:1405-1413. [PMID: 37326449 DOI: 10.1002/elps.202200292] [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: 10/10/2022] [Revised: 05/05/2023] [Accepted: 06/03/2023] [Indexed: 06/17/2023]
Abstract
Biogeographical origin inferences of different populations can provide valuable clues in the forensic investigation by narrowing down the detection scope. However, much research mainly focuses on forensic ancestral origin analyses of major continental populations, which may provide limited information in forensic practice. To improve the ancestral resolution of East Asian populations, we systematically selected ancestry informative single-nucleotide polymorphisms (AISNPs) for differentiating Han, Dai, Japanese, and Kinh populations. In addition, we evaluated the performance of the selected AISNPs to differentiate these populations via multiple methods. Totally 116 AISNPs were selected from the genome-wide data to infer the population origins of these four populations. Results of principle component analysis and population genetic structure of these populations indicated that the selected 116 AISNPs could achieve ancestral resolution of most individuals. Furthermore, the machine learning model built by 116 AISNPs unveiled that most individuals from these four populations could be assigned to correct population origins. To sum up, the selected 116 SNPs could be available for ancestral origin predictions of Han, Dai, Japanese, and Kinh populations, which could provide valuable information for forensic research and genome-wide association study in East Asian populations to some extent.
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Affiliation(s)
- Wen Wan
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, P. R. China
| | - Hongling Zhang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, P. R. China
| | - Zheng Ren
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, P. R. China
| | - Qiyan Wang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, P. R. China
| | - Yubo Liu
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, P. R. China
| | - Jingyan Ji
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, P. R. China
| | - Meiqing Yang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, P. R. China
| | - Han Zhang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, P. R. China
| | - Jiang Huang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, P. R. China
| | - Xiaoye Jin
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, P. R. China
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5
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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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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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7
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Watherston J, McNevin D. Skull and long bones – Forensic DNA techniques for historic shipwreck human remains. AUST J FORENSIC SCI 2023. [DOI: 10.1080/00450618.2023.2181395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Affiliation(s)
- J. Watherston
- Centre for Forensic Science, School of Mathematical & Physical Sciences, Faculty of Science, University of Technology Sydney, Ultimo, NSW, Australia
- Biology Unit, Forensic Science Branch, Nt Police, Fire and Emergency Services, Berrimah, NT, Australia
- College of Health & Human Sciences, Faculty of Science, Charles Darwin University, Casuarina, NT, Australia
| | - D. McNevin
- Centre for Forensic Science, School of Mathematical & Physical Sciences, Faculty of Science, University of Technology Sydney, Ultimo, NSW, Australia
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8
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Pilli E, Morelli S, Poggiali B, Alladio E. Biogeographical ancestry, variable selection, and PLS-DA method: a new panel to assess ancestry in forensic samples via MPS technology. Forensic Sci Int Genet 2023; 62:102806. [PMID: 36399972 DOI: 10.1016/j.fsigen.2022.102806] [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: 07/18/2022] [Revised: 11/09/2022] [Accepted: 11/10/2022] [Indexed: 11/14/2022]
Abstract
As evidenced by the large number of articles recently published in the literature, forensic scientists are making great efforts to infer externally visible features and biogeographical ancestry (BGA) from DNA analysis. Just as phenotypic, ancestry information obtained from DNA can provide investigative leads to identify the victims (missing/unidentified persons, crime/armed conflict/mass disaster victims) or trace their perpetrators when no matches were found with the reference profile or in the database. Recently, the advent of Massively Parallel Sequencing technologies associated with the possibility of harnessing high-throughput genetic data allowed us to investigate the associations between phenotypic and genomic variations in worldwide human populations and develop new BGA forensic tools capable of simultaneously analyzing up to millions of markers if for example the ancient DNA approach of hybridization capture was adopted to target SNPs of interest. In the present study, a selection of more than 3000 SNPs was performed to create a new BGA panel and the accuracy of the new panel to infer ancestry from unknown samples was evaluated by the PLS-DA method. Subsequently, the panel created was assessed using three variable selection techniques (Backward variable elimination, Genetic Algorithm and Regularized elimination procedure), and the best SNPs in terms of inferring bio-geographical ancestry at inter- and intra-continental level were selected to obtain panels to predict BGA with a reduced number of selected markers to be applied in routine forensic cases where PCR amplification is the best choice to target SNPs.
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Affiliation(s)
- Elena Pilli
- Department of Biology, Forensic Molecular Anthropology Laboratory, University of Florence, Florence, Italy
| | - Stefania Morelli
- Department of Biology, Forensic Molecular Anthropology Laboratory, University of Florence, Florence, Italy
| | - Brando Poggiali
- Department of Biology, Forensic Molecular Anthropology Laboratory, University of Florence, Florence, Italy
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9
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Xavier C, de la Puente M, Mosquera-Miguel A, Freire-Aradas A, Kalamara V, Ralf A, Revoir A, Gross T, Schneider P, Ames C, Hohoff C, Phillips C, Kayser M, Parson W. Development and inter-laboratory evaluation of the VISAGE Enhanced Tool for Appearance and Ancestry inference from DNA. Forensic Sci Int Genet 2022; 61:102779. [DOI: 10.1016/j.fsigen.2022.102779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 09/14/2022] [Accepted: 09/18/2022] [Indexed: 11/30/2022]
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10
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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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11
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Chen L, Zhou Z, Zhang Y, Xu H, Wang S. EASplex: A panel of 308 AISNPs for East Asian ancestry inference using next generation sequencing. Forensic Sci Int Genet 2022; 60:102739. [PMID: 35709629 DOI: 10.1016/j.fsigen.2022.102739] [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: 01/07/2022] [Revised: 06/02/2022] [Accepted: 06/06/2022] [Indexed: 11/26/2022]
Abstract
Ancestry inference is useful in many scientific fields, such as forensic genetics, medical genetics, and molecular archaeology. Various ancestry inferring methods have been released for major continental populations. However, few reports refer to sub-populations within the East Asian population using hundreds of ancestry informative SNPs (AISNPs). In this study, we developed a 308-AISNP panel (EASplex NGS DNA panel) using multiplex PCR and next generation sequencing (NGS). This panel included 56 SNPs relevant for the continent-level ancestry inference and 252 Japanese-, Korean-, and/or Han Chinese-specific AISNPs to address the ancestry inference of global populations and regional populations among Japanese (JPT), Korean minority (CHK), and Han Chinese (CHH). A total of 87 CHK and 59 CHH samples were used to check the performance of the EASplex NGS DNA panel. By analyzing 146 profiles of samples with JPT and CHH data from Beijing and South China in 1000 genomes project, the following results were obtained: (1) the 146 tested samples were correctly assigned to the East Asian group; (2) the paired population assignment rate was 99.73% for JPT and CHH, 95% for JPT and CHK, and 90.11% for CHK and CHH; and (3) the whole population assignment was 92.14% for the JPT, CHK, and CHH data. Overall, the EASplex NGS DNA panel displayed informativeness for continental ancestry inference and regional ancestry inference among JPT, CHH, and CHK and has the potential for use in forensic and genetic population studies.
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Affiliation(s)
- Lu Chen
- Beijing Institute of Microbiology and Epidemiology, 27 Taiping Road, Beijing 100850, PR China
| | - Zhe Zhou
- Beijing Institute of Microbiology and Epidemiology, 27 Taiping Road, Beijing 100850, PR China.
| | - Yongji Zhang
- Department of Pathology and Forensic Medicine, College of Medicine, Yanbian University, No. 977 Park Road, Jilin 133002, PR China
| | - Hao Xu
- Beijing Institute of Microbiology and Epidemiology, 27 Taiping Road, Beijing 100850, PR China
| | - Shengqi Wang
- Beijing Institute of Microbiology and Epidemiology, 27 Taiping Road, Beijing 100850, PR China.
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12
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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] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 01/28/2022] [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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13
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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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14
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Zou X, He G, Liu J, Jiang L, Wang M, Chen P, Hou Y, Wang Z. Screening and selection of 21 novel microhaplotype markers for ancestry inference in ten Chinese subpopulations. Forensic Sci Int Genet 2022; 58:102687. [DOI: 10.1016/j.fsigen.2022.102687] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 02/20/2022] [Accepted: 03/11/2022] [Indexed: 11/04/2022]
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15
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Rauf S, Austin JJ, Higgins D, Khan MR. Unveiling forensically relevant biogeographic, phenotype and Y-chromosome SNP variation in Pakistani ethnic groups using a customized hybridisation enrichment forensic intelligence panel. PLoS One 2022; 17:e0264125. [PMID: 35176104 PMCID: PMC8853543 DOI: 10.1371/journal.pone.0264125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 02/03/2022] [Indexed: 11/19/2022] Open
Abstract
Massively parallel sequencing following hybridisation enrichment provides new opportunities to obtain genetic data for various types of forensic testing and has proven successful on modern as well as degraded and ancient DNA. A customisable forensic intelligence panel that targeted 124 SNP markers (67 ancestry informative markers, 23 phenotype markers from the HIrisplex panel, and 35 Y-chromosome SNPs) was used to examine biogeographic ancestry, phenotype and sex and Y-lineage in samples from different ethnic populations of Pakistan including Pothwari, Gilgit, Baloach, Pathan, Kashmiri and Siraiki. Targeted sequencing and computational data analysis pipeline allowed filtering of variants across the targeted loci. Study samples showed an admixture between East Asian and European ancestry. Eye colour was predicted accurately based on the highest p-value giving overall prediction accuracy of 92.8%. Predictions were consistent with reported hair colour for all samples, using the combined highest p-value approach and step-wise model incorporating probability thresholds for light or dark shade. Y-SNPs were successfully recovered only from male samples which indicates the ability of this method to identify biological sex and allow inference of Y-haplogroup. Our results demonstrate practicality of using hybridisation enrichment and MPS to aid in human intelligence gathering and will open many insights into forensic research in South Asia.
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Affiliation(s)
- Sobiah Rauf
- Genome Editing & Sequencing Lab, National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan
| | - Jeremy J. Austin
- Australian Centre for Ancient DNA (ACAD), School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Denice Higgins
- Australian Centre for Ancient DNA (ACAD), School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
- School of Dentistry, Health and Medical Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Muhammad Ramzan Khan
- Genome Editing & Sequencing Lab, National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan
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16
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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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17
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Pakstis AJ, Gandotra N, Speed WC, Murtha M, Scharfe C, Kidd KK. The population genetics characteristics of a 90 locus panel of microhaplotypes. Hum Genet 2021; 140:1753-1773. [PMID: 34643790 PMCID: PMC8553733 DOI: 10.1007/s00439-021-02382-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 09/30/2021] [Indexed: 12/26/2022]
Abstract
Single-nucleotide polymorphisms (SNPs) and small genomic regions with multiple SNPs (microhaplotypes, MHs) are rapidly emerging as novel forensic investigative tools to assist in individual identification, kinship analyses, ancestry inference, and deconvolution of DNA mixtures. Here, we analyzed information for 90 microhaplotype loci in 4009 individuals from 79 world populations in 6 major biogeographic regions. The study included multiplex microhaplotype sequencing (mMHseq) data analyzed for 524 individuals from 16 populations and genotype data for 3485 individuals from 63 populations curated from public repositories. Analyses of the 79 populations revealed excellent characteristics for this 90-plex MH panel for various forensic applications achieving an overall average effective number of allele values (Ae) of 4.55 (range 1.04–19.27) for individualization and mixture deconvolution. Population-specific random match probabilities ranged from a low of 10–115 to a maximum of 10–66. Mean informativeness (In) for ancestry inference was 0.355 (range 0.117–0.883). 65 novel SNPs were detected in 39 of the MHs using mMHseq. Of the 3018 different microhaplotype alleles identified, 1337 occurred at frequencies > 5% in at least one of the populations studied. The 90-plex MH panel enables effective differentiation of population groupings for major biogeographic regions as well as delineation of distinct subgroupings within regions. Open-source, web-based software is available to support validation of this technology for forensic case work analysis and to tailor MH analysis for specific geographical regions.
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Affiliation(s)
- Andrew J Pakstis
- Department of Genetics, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Neeru Gandotra
- Department of Genetics, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - William C Speed
- Department of Genetics, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Michael Murtha
- Department of Genetics, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Curt Scharfe
- Department of Genetics, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Kenneth K Kidd
- Department of Genetics, Yale University School of Medicine, New Haven, CT, 06520, USA.
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18
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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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19
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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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20
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Bolarín JM, Pérez-Cárceles M, Luna A, Minguela A, Muro M, Legaz I. Killer cell immunoglobulin-like receptors (KIR) genes can be an adequate tool in forensic anthropological studies: evaluation in a wide Caucasian Spanish population. AUST J FORENSIC SCI 2021. [DOI: 10.1080/00450618.2021.1930156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- J. M. Bolarín
- Department of Legal and Forensic Medicine, Biomedical Research Institute (IMIB), Regional Campus of International Excellence “Campus Mare Nostrum”, Faculty of Medicine, University of Murcia, Murcia, Spain
| | - M.D. Pérez-Cárceles
- Department of Legal and Forensic Medicine, Biomedical Research Institute (IMIB), Regional Campus of International Excellence “Campus Mare Nostrum”, Faculty of Medicine, University of Murcia, Murcia, Spain
| | - A. Luna
- Department of Legal and Forensic Medicine, Biomedical Research Institute (IMIB), Regional Campus of International Excellence “Campus Mare Nostrum”, Faculty of Medicine, University of Murcia, Murcia, Spain
| | - A. Minguela
- Immunology Service, Instituto Murciano de investigación biosanitaria (IMIB) and Centro de Investigación Biomédica en Red de enfermedades hepáticas y digestivas (CIBERehd), Hospital Clínico Universitario Virgen de la Arrixaca (HCUVA), Murcia, Spain
| | - M. Muro
- Immunology Service, Instituto Murciano de investigación biosanitaria (IMIB) and Centro de Investigación Biomédica en Red de enfermedades hepáticas y digestivas (CIBERehd), Hospital Clínico Universitario Virgen de la Arrixaca (HCUVA), Murcia, Spain
| | - I. Legaz
- Department of Legal and Forensic Medicine, Biomedical Research Institute (IMIB), Regional Campus of International Excellence “Campus Mare Nostrum”, Faculty of Medicine, University of Murcia, Murcia, Spain
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21
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Developmental validations of a self-developed 39 AIM-InDel panel and its forensic efficiency evaluations in the Shaanxi Han population. Int J Legal Med 2021; 135:1359-1367. [PMID: 33907868 DOI: 10.1007/s00414-021-02600-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Accepted: 04/06/2021] [Indexed: 11/27/2022]
Abstract
Most of insertion/deletion polymorphisms are diallelic molecular markers characterized as small amplicon sizes, high inter-population diversities, and low mutation rates, which make them the promising genetic markers in biogeographic ancestor inference field. The developmental validations of a 39 ancestry informative marker-insertion/deletion (AIM-InDel) panel and the genetic polymorphic investigations of this panel were performed in the Shaanxi Han population of China. The developmental validation included the optimizations of PCR-related indicators, repeatability, reproducibility, precision, accuracy, sensitivity, species specificity, stability of the panel, and the abilities in analyzing degraded, casework, and mixture samples, and the present results demonstrated that this 39 AIM-InDel panel was robust, sensitive, and accurate. For the population diversity analyses, the combined discrimination power value of 38 AIM-InDel loci except for rs36038238 locus was 0.999999999931257, indicating that this novel panel was highly polymorphic, biogeographic informative, and could be also used in individual identifications in the Shaanxi Han population.
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22
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Mizuno F, Naka I, Ueda S, Ohashi J, Kurosaki K. The number of SNPs required for distinguishing Japanese from other East Asians. Leg Med (Tokyo) 2021; 49:101849. [PMID: 33485062 DOI: 10.1016/j.legalmed.2021.101849] [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: 03/05/2020] [Revised: 09/16/2020] [Accepted: 01/10/2021] [Indexed: 11/25/2022]
Abstract
In some cases, it is necessary to estimate the national origin of an unknown subject in forensic medicine. The use of single nucleotide polymorphism (SNP) markers appears to be very effective for this purpose, since genome-wide SNP genotype data of many human populations are publicly available. In this study, we examined the number of SNPs that could objectively and accurately distinguish Japanese subjects (1KG-JPT) from the other East Asians (1KG-CDX, -CHB, -CHS, and -KHV) using the combination of principal component analysis and hierarchical cluster analysis. A computer simulation showed that approximately 3000 randomly selected SNPs were enough for the discrimination. Our results suggest that at least a 0.024% coverage is needed in the next generation sequencing experiment to objectively determine whether an unknown person is Japanese or not if the amount of DNA sample from him/her is insufficient or the quality is low.
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Affiliation(s)
- Fuzuki Mizuno
- Department of Legal Medicine, Toho University School of Medicine, Japan
| | - Izumi Naka
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Japan
| | - Shintaroh Ueda
- Department of Legal Medicine, Toho University School of Medicine, Japan; Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Japan
| | - Jun Ohashi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Japan.
| | - Kunihiko Kurosaki
- Department of Legal Medicine, Toho University School of Medicine, Japan.
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Evaluation of the Ion AmpliSeq™ PhenoTrivium Panel: MPS-Based Assay for Ancestry and Phenotype Predictions Challenged by Casework Samples. Genes (Basel) 2020; 11:genes11121398. [PMID: 33255693 PMCID: PMC7760956 DOI: 10.3390/genes11121398] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 11/19/2020] [Accepted: 11/22/2020] [Indexed: 12/21/2022] Open
Abstract
As the field of forensic DNA analysis has started to transition from genetics to genomics, new methods to aid in crime scene investigations have arisen. The development of informative single nucleotide polymorphism (SNP) markers has led the forensic community to question if DNA can be a reliable "eye-witness" and whether the data it provides can shed light on unknown perpetrators. We have developed an assay called the Ion AmpliSeq™ PhenoTrivium Panel, which combines three groups of markers: 41 phenotype- and 163 ancestry-informative autosomal SNPs together with 120 lineage-specific Y-SNPs. Here, we report the results of testing the assay's sensitivity and the predictions obtained for known reference samples. Moreover, we present the outcome of a blind study performed on real casework samples in order to understand the value and reliability of the information that would be provided to police investigators. Furthermore, we evaluated the accuracy of admixture prediction in Converge™ Software. The results show the panel to be a robust and sensitive assay which can be used to analyze casework samples. We conclude that the combination of the obtained predictions of phenotype, biogeographical ancestry, and male lineage can serve as a potential lead in challenging police investigations such as cold cases or cases with no suspect.
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Garafutdinov RR, Sakhabutdinova AR, Slominsky PA, Aminev FG, Chemeris AV. A new digital approach to SNP encoding for DNA identification. Forensic Sci Int 2020; 317:110520. [PMID: 33031982 DOI: 10.1016/j.forsciint.2020.110520] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 08/21/2020] [Accepted: 09/11/2020] [Indexed: 10/23/2022]
Abstract
Identification of individuals has become an urgent problem for mankind. In the last three decades, STR-based DNA identification has actively evolved along with traditional biometric methods. Nonetheless, single-nucleotide polymorphisms (SNPs) are now of great interest and a number of relevant SNP panels have been proposed for DNA identification. Here, a simple approach to SNP data digitization that can provide assigning a unique genetic identification number (GIN) to each person is proposed. The key points of this approach are as follows: 1) SNP data are digitized as whole 4-bit boxes in the most convenient binary format, where character "1" (YES) is assigned to revealed nucleotides, and character "0" (NO) to missing nucleotides after SNP-typing; 2) all SNPs should be considered tetra-allelic. Calculations showed that a 72-plex SNP panel is enough to provide the population with unique GINs, which can be represented in digital (binary or hexadecimal) or graphic (linear or two-dimensional) formats. Simple software for SNP data processing and GINs creation in any format was written. It is likely that the national and global GIN databases will facilitate the solution of problems related to identification of individuals or human biological materials. The proposed approach may be extended to other living organisms as well.
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Affiliation(s)
- Ravil R Garafutdinov
- Institute of Biochemistry and Genetics, Ufa Federal Research Centre, Russian Academy of Sciences, 450054, prosp. Oktyabrya, 71, Ufa, Bashkortostan, Russia.
| | - Assol R Sakhabutdinova
- Institute of Biochemistry and Genetics, Ufa Federal Research Centre, Russian Academy of Sciences, 450054, prosp. Oktyabrya, 71, Ufa, Bashkortostan, Russia
| | - Petr A Slominsky
- Institute of Molecular Genetics, Russian Academy of Sciences, 123182, Kurchatov sq. 2, Moscow, Russia
| | - Farit G Aminev
- Bashkir State University, 450076, Zaki Validi str., 32, Ufa, Bashkortostan, Russia
| | - Alexey V Chemeris
- Institute of Biochemistry and Genetics, Ufa Federal Research Centre, Russian Academy of Sciences, 450054, prosp. Oktyabrya, 71, Ufa, Bashkortostan, Russia
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Ryan L, Mathieson M, Dwyer T, Edwards M, Harris L, Krosch M, Power D, Brisotto P, Allen C, Taylor E. Massively parallel sequencing as an investigative tool. AUST J FORENSIC SCI 2020. [DOI: 10.1080/00450618.2020.1781251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Luke Ryan
- Police Services Stream, Forensic & Scientific Services, Queensland Health, Brisbane, Australia
| | - Megan Mathieson
- Police Services Stream, Forensic & Scientific Services, Queensland Health, Brisbane, Australia
| | - Tegan Dwyer
- Police Services Stream, Forensic & Scientific Services, Queensland Health, Brisbane, Australia
| | - Marcus Edwards
- Homicide Group, State Crime Command, Queensland Police Service, Brisbane, Australia
| | - Libby Harris
- DNA Management Section, Forensic Services Group, Queensland Police Service, Brisbane, Australia
| | - Matt Krosch
- , Quality Management Section, Forensic Services Group, Queensland Police Service, Brisbane, Australia
| | - Daniel Power
- Life Science Solutions, Thermo Fisher Scientific, Scoresby, Australia
| | - Paula Brisotto
- Police Services Stream, Forensic & Scientific Services, Queensland Health, Brisbane, Australia
| | - Cathie Allen
- Police Services Stream, Forensic & Scientific Services, Queensland Health, Brisbane, Australia
| | - Ewen Taylor
- Hendra Scenes of Crime, Forensic Services Group, Queensland Police Service, Brisbane, Australia
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Next generation sequencing of a set of ancestry-informative SNPs: ancestry assignment of three continental populations and estimating ancestry composition for Mongolians. Mol Genet Genomics 2020; 295:1027-1038. [PMID: 32206883 DOI: 10.1007/s00438-020-01660-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 02/27/2020] [Indexed: 12/31/2022]
Abstract
When traditional short tandem repeat profiling fails to provide valuable information to arrest the criminal, forensic ancestry inference of the biological samples left at the crime scene will probably offer investigative leads and facilitate the investigation process of the case. That is why there are consistent efforts in developing panels for ancestry inference in forensic science. Presently, a 30-plex next generation sequencing-based assay was exploited in this study by assembling well-differentiated single nucleotide polymorphisms for ancestry assignment of unknown individuals from three continental populations (African, European and East Asian). And meanwhile, relatively balanced population-specific differentiation values were maintained to avoid the over-estimation or under-estimation of co-ancestry proportions in individuals with admixed ancestry. The principal component analysis and STRUCTURE analysis of reference populations, test populations and the studied Mongolian group indicated that the novel assay was efficient enough to determine the ancestry origin of an unknown individual from the three continental populations. Besides, ancestry membership proportion estimations for the Mongolian group revealed that a large fraction of the ancestry was contributed by East Asian genetic component (approximately 83.9%), followed by European (approximately 12.6%) and African genetic components (approximately 3.5%), respectively. And next generation sequencing technology applied in this study offers possibility to incorporate more single nucleotide polymorphisms for individual identification and phenotype prediction into the same assay to provide as many as possible investigative clues in the future.
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Characterization of ancestry informative markers in the Tigray population of Ethiopia: A contribution to the identification process of dead migrants in the Mediterranean Sea. Forensic Sci Int Genet 2020; 45:102207. [DOI: 10.1016/j.fsigen.2019.102207] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 11/16/2019] [Accepted: 11/19/2019] [Indexed: 01/16/2023]
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Pfaffelhuber P, Grundner-Culemann F, Lipphardt V, Baumdicker F. How to choose sets of ancestry informative markers: A supervised feature selection approach. Forensic Sci Int Genet 2020; 46:102259. [PMID: 32105949 DOI: 10.1016/j.fsigen.2020.102259] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 12/23/2019] [Accepted: 02/01/2020] [Indexed: 01/06/2023]
Abstract
Inference of the Biogeographical Ancestry (BGA) of a person or trace relies on three ingredients: (1) a reference database of DNA samples including BGA information; (2) a statistical clustering method; (3) a set of loci which segregate dependent on geographical location, i.e. a set of so-called Ancestry Informative Markers (AIMs). We used the theory of feature selection from statistical learning in order to obtain AIMsets for BGA inference. Using simulations, we show that this learning procedure works in various cases, and outperforms ad hoc methods, based on statistics like FST or informativeness for the choice of AIMs. Applying our method to data from the 1000 genomes project (excluding Admixed Americans) we identified an AIMset of 12 SNPs, which gives a vanishing misclassification error on a continental scale, as do other published AIMsets. In fact, cross validation shows that there exists a multitude of sets with comparable performance to the optimal AIMset. On a sub-continental scale, we find a set of 55 SNPs for distinguishing the five European populations. The misclassification error is reduced by a factor of two relative to published AIMsets, but is still 30% and therefore too large in order to be useful in forensic applications.
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Affiliation(s)
- Peter Pfaffelhuber
- University of Freiburg, Department of Mathematical Stochastics, Ernst-Zermelo-Straße 1, D-79104 Freiburg, Germany.
| | | | - Veronika Lipphardt
- University College Freiburg, Bertoldstraße 17, D-79098 Freiburg, Germany
| | - Franz Baumdicker
- University of Freiburg, Department of Mathematical Stochastics, Ernst-Zermelo-Straße 1, D-79104 Freiburg, Germany
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29
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Evaluation of 12 Multi-InDel markers for forensic ancestry prediction in Asian populations. Forensic Sci Int Genet 2019; 43:102155. [DOI: 10.1016/j.fsigen.2019.102155] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 06/27/2019] [Accepted: 08/24/2019] [Indexed: 11/21/2022]
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30
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Phillips C, McNevin D, Kidd K, Lagacé R, Wootton S, de la Puente M, Freire-Aradas A, Mosquera-Miguel A, Eduardoff M, Gross T, Dagostino L, Power D, Olson S, Hashiyada M, Oz C, Parson W, Schneider P, Lareu M, Daniel R. MAPlex - A massively parallel sequencing ancestry analysis multiplex for Asia-Pacific populations. Forensic Sci Int Genet 2019; 42:213-226. [DOI: 10.1016/j.fsigen.2019.06.022] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Revised: 06/04/2019] [Accepted: 06/26/2019] [Indexed: 11/25/2022]
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Transcriptome variation in human populations and its potential application in forensics. J Appl Genet 2019; 60:319-328. [PMID: 31401728 PMCID: PMC6803616 DOI: 10.1007/s13353-019-00510-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Revised: 07/22/2019] [Accepted: 07/24/2019] [Indexed: 12/04/2022]
Abstract
This review presents the state-of-the-art in the forensic application of genetic methods driven by the research in population transcriptomics. In the first part of the review, the constraints of using classical genomic markers are shortly reviewed. In the second part, the developments in the field of inter-population diversity at the transcriptomic level are presented. Subsequently, a potential of population-specific transcriptomic markers in forensic science applications, including ascertaining population affiliation of human samples and cell mixtures separation, are presented.
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32
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Ancestry informative markers (AIMs) for Korean and other East Asian and South East Asian populations. Int J Legal Med 2019; 133:1711-1719. [DOI: 10.1007/s00414-019-02129-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Accepted: 07/26/2019] [Indexed: 01/28/2023]
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33
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Qu S, Zhu J, Wang Y, Yin L, Lv M, Wang L, Jian H, Tan Y, Zhang R, Liu Y, Li F, Huang S, Liang W, Zhang L. Establishing a second-tier panel of 18 ancestry informative markers to improve ancestry distinctions among Asian populations. Forensic Sci Int Genet 2019; 41:159-167. [DOI: 10.1016/j.fsigen.2019.05.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 05/08/2019] [Accepted: 05/09/2019] [Indexed: 11/16/2022]
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34
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Shi C, Liu Q, Zhao S, Chen H. Ancestry informative SNP panels for discriminating the major East Asian populations: Han Chinese, Japanese and Korean. Ann Hum Genet 2019; 83:348-354. [DOI: 10.1111/ahg.12320] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 03/21/2019] [Accepted: 04/02/2019] [Indexed: 01/01/2023]
Affiliation(s)
- Cheng‐Min Shi
- CAS Key Laboratory of Genomic and Precision Medicine Beijing Institute of Genomics, Chinese Academy of Sciences Beijing China
| | - Qi Liu
- CAS Key Laboratory of Genomic and Precision Medicine Beijing Institute of Genomics, Chinese Academy of Sciences Beijing China
- University of Chinese Academy of Sciences Beijing China
| | - Shilei Zhao
- CAS Key Laboratory of Genomic and Precision Medicine Beijing Institute of Genomics, Chinese Academy of Sciences Beijing China
- University of Chinese Academy of Sciences Beijing China
| | - Hua Chen
- CAS Key Laboratory of Genomic and Precision Medicine Beijing Institute of Genomics, Chinese Academy of Sciences Beijing China
- CAS Center for Excellence in Animal Evolution and Genetics Chinese Academy of Sciences Kunming China
- University of Chinese Academy of Sciences Beijing China
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35
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Zhao S, Shi CM, Ma L, Liu Q, Liu Y, Wu F, Chi L, Chen H. AIM-SNPtag: A computationally efficient approach for developing ancestry-informative SNP panels. Forensic Sci Int Genet 2019; 38:245-253. [DOI: 10.1016/j.fsigen.2018.10.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 10/03/2018] [Accepted: 10/23/2018] [Indexed: 01/13/2023]
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36
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Gao Z, Chen X, Zhao Y, Zhao X, Zhang S, Yang Y, Wang Y, Zhang J. Forensic genetic informativeness of an SNP panel consisting of 19 multi-allelic SNPs. Forensic Sci Int Genet 2018; 34:49-56. [DOI: 10.1016/j.fsigen.2018.01.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 01/07/2018] [Accepted: 01/26/2018] [Indexed: 11/28/2022]
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37
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Bardan F, Higgins D, Austin JJ. A mini-multiplex SNaPshot assay for the triage of degraded human DNA. Forensic Sci Int Genet 2018; 34:62-70. [DOI: 10.1016/j.fsigen.2018.02.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 01/03/2018] [Accepted: 02/05/2018] [Indexed: 12/01/2022]
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Affiliation(s)
- Elaine Y. Y. Cheung
- National Centre for Forensic Studies, Faculty of Science and Technology, University of Canberra, Bruce, Australia
| | - Michelle Elizabeth Gahan
- National Centre for Forensic Studies, Faculty of Science and Technology, University of Canberra, Bruce, Australia
| | - Dennis McNevin
- National Centre for Forensic Studies, Faculty of Science and Technology, University of Canberra, Bruce, Australia
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A review of bioinformatic methods for forensic DNA analyses. Forensic Sci Int Genet 2017; 33:117-128. [PMID: 29247928 DOI: 10.1016/j.fsigen.2017.12.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 11/30/2017] [Accepted: 12/10/2017] [Indexed: 12/20/2022]
Abstract
Short tandem repeats, single nucleotide polymorphisms, and whole mitochondrial analyses are three classes of markers which will play an important role in the future of forensic DNA typing. The arrival of massively parallel sequencing platforms in forensic science reveals new information such as insights into the complexity and variability of the markers that were previously unseen, along with amounts of data too immense for analyses by manual means. Along with the sequencing chemistries employed, bioinformatic methods are required to process and interpret this new and extensive data. As more is learnt about the use of these new technologies for forensic applications, development and standardization of efficient, favourable tools for each stage of data processing is being carried out, and faster, more accurate methods that improve on the original approaches have been developed. As forensic laboratories search for the optimal pipeline of tools, sequencer manufacturers have incorporated pipelines into sequencer software to make analyses convenient. This review explores the current state of bioinformatic methods and tools used for the analyses of forensic markers sequenced on the massively parallel sequencing (MPS) platforms currently most widely used.
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40
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Nakanishi H, Pereira V, Børsting C, Yamamoto T, Tvedebrink T, Hara M, Takada A, Saito K, Morling N. Analysis of mainland Japanese and Okinawan Japanese populations using the precision ID Ancestry Panel. Forensic Sci Int Genet 2017; 33:106-109. [PMID: 29223883 DOI: 10.1016/j.fsigen.2017.12.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2017] [Revised: 11/18/2017] [Accepted: 12/05/2017] [Indexed: 01/28/2023]
Abstract
We typed 165 AIMs in 49 mainland Japanese and 47 Okinawa Japanese using the Precision ID Ancestry Panel (Thermo Fisher Scientific). None of the 165 SNPs showed significant deviation from Hardy-Weinberg equilibrium in the mainland Japanese. One SNP (rs3943253) showed significant deviation from Hardy-Weinberg equilibrium in Okinawa Japanese. Fisher's exact tests showed that the genotype frequencies of 14 loci were significantly different (p<0.05) between the two populations before correction for multiple testing. After Bonferroni correction, only rs671 remained statistically significant (p<0.0003). This SNP is located in the ALDH2 gene. The mutant A allele is associated with increased side effects after alcohol intake. The frequency of the GG genotype (wild type) was higher in the Okinawa Japanese (78.7%) than in mainland Japanese (34.7%; Bonferroni corrected P<0.001). For 31 (63.3%) of the mainland Japanese and 42 (89.4%) of Okinawa Japanese, the highest population likelihood was obtained with the Japanese reference population. However, only in a few individuals, the likelihoods were significantly different from those calculated using reference data from neighboring populations. The likelihoods for mainland Japanese and Okinawa Japanese were not significantly different from each other for any of the investigated individuals. STRUCTURE and PCA analyses showed that mainland Japanese, Okinawa Japanese, and East Asians could not be differentiated with the Precision ID Ancestry Panel.
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Affiliation(s)
- Hiroaki Nakanishi
- Department of Forensic Medicine, Juntendo University School of Medicine, 2-1-1, Hongo, Bunkyo-Ku, Tokyo, Japan; Department of Forensic Medicine, Saitama Medical University, Morohongo, Moroyama, Saitama, Japan
| | - Vania Pereira
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark.
| | - Claus Børsting
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Toshimichi Yamamoto
- Department of Legal Medicine and Bioethics, Graduate School of Medicine, Nagoya University, Nagoya, Japan
| | | | - Masaaki Hara
- Department of Forensic Medicine, Saitama Medical University, Morohongo, Moroyama, Saitama, Japan
| | - Aya Takada
- Department of Forensic Medicine, Saitama Medical University, Morohongo, Moroyama, Saitama, Japan
| | - Kazuyuki Saito
- Department of Forensic Medicine, Juntendo University School of Medicine, 2-1-1, Hongo, Bunkyo-Ku, Tokyo, Japan; Department of Forensic Medicine, Saitama Medical University, Morohongo, Moroyama, Saitama, Japan
| | - Niels Morling
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
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41
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Ramani A, Wong Y, Tan SZ, Shue BH, Syn C. Ancestry prediction in Singapore population samples using the Illumina ForenSeq kit. Forensic Sci Int Genet 2017; 31:171-179. [DOI: 10.1016/j.fsigen.2017.08.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 07/18/2017] [Accepted: 08/11/2017] [Indexed: 11/24/2022]
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Mehta B, Daniel R, Phillips C, Doyle S, Elvidge G, McNevin D. Massively parallel sequencing of customised forensically informative SNP panels on the MiSeq. Electrophoresis 2017; 37:2832-2840. [PMID: 27605155 DOI: 10.1002/elps.201600190] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Revised: 08/20/2016] [Accepted: 08/23/2016] [Indexed: 02/04/2023]
Abstract
Forensic DNA-based intelligence, or forensic DNA phenotyping, utilises SNPs to infer the biogeographical ancestry and externally visible characteristics of the donor of evidential material. SNaPshot® is a commonly employed forensic SNP genotyping technique, which is limited to multiplexes of 30-40 SNPs in a single reaction and prone to PCR contamination. Massively parallel sequencing has the ability to genotype hundreds of SNPs in multiple samples simultaneously by employing an oligonucleotide sample barcoding strategy. This study of the Illumina MiSeq massively parallel sequencing platform analysed 136 unique SNPs in 48 samples from SNaPshot PCR amplicons generated by five established forensic DNA phenotyping assays comprising the SNPforID 52-plex, SNPforID 34-plex, Eurasiaplex, Pacifiplex and IrisPlex. Approximately 3 GB of sequence data were generated from two MiSeq flow cells and profiles were obtained from just 0.25 ng of DNA. Compared with SNaPshot, an average 98% genotyping concordance was achieved. Our customised approach was successful in attaining SNP profiles from extremely degraded, inhibited, and compromised casework samples. Heterozygote imbalance and sequence coverage in negative controls highlight the need to establish baseline sequence coverage thresholds and refine allele frequency thresholds. This study demonstrates the potential of the MiSeq for forensic SNP analysis.
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Affiliation(s)
- Bhavik Mehta
- National Centre for Forensic Studies, Faculty of ESTeM, University of Canberra, Canberra, Australia.
| | - Runa Daniel
- Office of the Chief Forensic Scientist, Victoria Police Forensic Services Department, Melbourne, Australia
| | - Chris Phillips
- Forensic Genetics Unit, Institute of Legal Medicine, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Stephen Doyle
- Department of Animal, Plant and Soil Sciences, La Trobe University, Melbourne, Australia
| | | | - Dennis McNevin
- National Centre for Forensic Studies, Faculty of ESTeM, University of Canberra, Canberra, Australia
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DNA methylation in ELOVL2 and C1orf132 correctly predicted chronological age of individuals from three disease groups. Int J Legal Med 2017; 132:1-11. [PMID: 28725932 PMCID: PMC5748441 DOI: 10.1007/s00414-017-1636-0] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 07/04/2017] [Indexed: 12/21/2022]
Abstract
Improving accuracy of the available predictive DNA methods is important for their wider use in routine forensic work. Information on age in the process of identification of an unknown individual may provide important hints that can speed up the process of investigation. DNA methylation markers have been demonstrated to provide accurate age estimation in forensics, but there is growing evidence that DNA methylation can be modified by various factors including diseases. We analyzed DNA methylation profile in five markers from five different genes (ELOVL2, C1orf132, KLF14, FHL2, and TRIM59) used for forensic age prediction in three groups of individuals with diagnosed medical conditions. The obtained results showed that the selected age-related CpG sites have unchanged age prediction capacity in the group of late onset Alzheimer’s disease patients. Aberrant hypermethylation and decreased prediction accuracy were found for TRIM59 and KLF14 markers in the group of early onset Alzheimer’s disease suggesting accelerated aging of patients. In the Graves’ disease patients, altered DNA methylation profile and modified age prediction accuracy were noted for TRIM59 and FHL2 with aberrant hypermethylation observed for the former and aberrant hypomethylation for the latter. Our work emphasizes high utility of the ELOVL2 and C1orf132 markers for prediction of chronological age in forensics by showing unchanged prediction accuracy in individuals affected by three diseases. The study also demonstrates that artificial neural networks could be a convenient alternative for the forensic predictive DNA analyses.
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44
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Sun K, Ye Y, Luo T, Hou Y. Multi-InDel Analysis for Ancestry Inference of Sub-Populations in China. Sci Rep 2016; 6:39797. [PMID: 28004788 PMCID: PMC5177877 DOI: 10.1038/srep39797] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 11/29/2016] [Indexed: 01/03/2023] Open
Abstract
Ancestry inference is of great interest in diverse areas of scientific researches, including the forensic biology, medical genetics and anthropology. Various methods have been published for distinguishing populations. However, few reports refer to sub-populations (like ethnic groups) within Asian populations for the limitation of markers. Several InDel loci located very tightly in physical positions were treated as one marker by us, which is multi-InDel. The multi-InDel shows potential as Ancestry Inference Marker (AIM). In this study, we performed a genome-wide scan for multi-InDels as AIM. After examining the FST distributions in the 1000 Genomes Database, 12 candidates were selected and validated for eastern Asian populations. A multiplexed assay was developed as a panel to genotype 12 multi-InDel markers simultaneously. Ancestry component analysis with STRUCTURE and principal component analysis (PCA) were employed to estimate its capability for ancestry inference. Furthermore, ancestry assignments of trial individuals were conducted. It proved to be very effective when 210 samples from Han and Tibetan individuals in China were tested. The panel consisting of multi-InDel markers exhibited considerable potency in ancestry inference, and was suggested to be applied in forensic practices and genetic population studies.
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Affiliation(s)
- Kuan Sun
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, P.R. China
| | - Yi Ye
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, P.R. China
| | - Tao Luo
- Laboratory of Infection and Immunity, School of Basic Medical Sciences, West China Center of Medical Science, Sichuan University, Chengdu P.R. China
| | - Yiping Hou
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, P.R. China
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45
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Prediction of biogeographical ancestry from genotype: a comparison of classifiers. Int J Legal Med 2016; 131:901-912. [DOI: 10.1007/s00414-016-1504-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 11/21/2016] [Indexed: 12/19/2022]
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Frequency of TNFA, INFG, and IL10 Gene Polymorphisms and Their Association with Malaria Vivax and Genomic Ancestry. Mediators Inflamm 2016; 2016:5168363. [PMID: 27999453 PMCID: PMC5143728 DOI: 10.1155/2016/5168363] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 07/14/2016] [Accepted: 09/27/2016] [Indexed: 02/08/2023] Open
Abstract
Polymorphisms in cytokine genes can alter the production of these proteins and consequently affect the immune response. The trihybrid heterogeneity of the Brazilian population is characterized as a condition for the use of ancestry informative markers. The objective of this study was to evaluate the frequency of -1031T>C, -308G>A and -238G>A TNFA, +874 A>T IFNG and -819C>T, and -592C>A IL10 gene polymorphisms and their association with malaria vivax and genomic ancestry. Samples from 90 vivax malaria-infected individuals and 51 noninfected individuals from northern Brazil were evaluated. Genotyping was carried out by using ASO-PCR or PCR/RFLP. The genomic ancestry of the individuals was classified using 48 insertion/deletion polymorphism biallelic markers. There were no differences in the proportions of African, European, and Native American ancestry between men and women. No significant association was observed for the allele and genotype frequencies of the 6 SNPs between malaria-infected and noninfected individuals. However, there was a trend toward decreasing the frequency of individuals carrying the TNF-308A allele with the increasing proportion of European ancestry. No ethnic-specific SNPs were identified, and there was no allelic or genotype association with susceptibility or resistance to vivax malaria. Understanding the genomic mechanisms by which ancestry influences this association is critical and requires further study.
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Forensically relevant SNaPshot® assays for human DNA SNP analysis: a review. Int J Legal Med 2016; 131:21-37. [DOI: 10.1007/s00414-016-1490-5] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 10/31/2016] [Indexed: 10/20/2022]
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Eduardoff M, Gross TE, Santos C, de la Puente M, Ballard D, Strobl C, Børsting C, Morling N, Fusco L, Hussing C, Egyed B, Souto L, Uacyisrael J, Syndercombe Court D, Carracedo Á, Lareu MV, Schneider PM, Parson W, Phillips C, Parson W, Phillips C. Inter-laboratory evaluation of the EUROFORGEN Global ancestry-informative SNP panel by massively parallel sequencing using the Ion PGM™. Forensic Sci Int Genet 2016; 23:178-189. [PMID: 27208666 DOI: 10.1016/j.fsigen.2016.04.008] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Revised: 04/14/2016] [Accepted: 04/15/2016] [Indexed: 10/21/2022]
Abstract
The EUROFORGEN Global ancestry-informative SNP (AIM-SNPs) panel is a forensic multiplex of 128 markers designed to differentiate an individual's ancestry from amongst the five continental population groups of Africa, Europe, East Asia, Native America, and Oceania. A custom multiplex of AmpliSeq™ PCR primers was designed for the Global AIM-SNPs to perform massively parallel sequencing using the Ion PGM™ system. This study assessed individual SNP genotyping precision using the Ion PGM™, the forensic sensitivity of the multiplex using dilution series, degraded DNA plus simple mixtures, and the ancestry differentiation power of the final panel design, which required substitution of three original ancestry-informative SNPs with alternatives. Fourteen populations that had not been previously analyzed were genotyped using the custom multiplex and these studies allowed assessment of genotyping performance by comparison of data across five laboratories. Results indicate a low level of genotyping error can still occur from sequence misalignment caused by homopolymeric tracts close to the target SNP, despite careful scrutiny of candidate SNPs at the design stage. Such sequence misalignment required the exclusion of component SNP rs2080161 from the Global AIM-SNPs panel. However, the overall genotyping precision and sensitivity of this custom multiplex indicates the Ion PGM™ assay for the Global AIM-SNPs is highly suitable for forensic ancestry analysis with massively parallel sequencing.
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Affiliation(s)
- M Eduardoff
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - T E Gross
- Institute of Legal Medicine, Faculty of Medicine, University of Cologne, Cologne, Germany
| | - C Santos
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - M de la Puente
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - D Ballard
- Faculty of Life Sciences and Medicine, King's College, London, UK
| | - C Strobl
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - C Børsting
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - N Morling
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - L Fusco
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - C Hussing
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - B Egyed
- Department of Genetics, Faculty of Science, Eötvös Loránd University Budapest, Hungary
| | - L Souto
- Department of Biology, University of Aveiro, Aveiro, Portugal
| | - J Uacyisrael
- Fiji Police Forensic Biology and DNA Laboratory, Nasova, Suva, Fiji
| | | | - Á Carracedo
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Santiago de Compostela, Spain; Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
| | - M V Lareu
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - P M Schneider
- Institute of Legal Medicine, Faculty of Medicine, University of Cologne, Cologne, Germany
| | - W Parson
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria; Forensic Science Program, The Pennsylvania State University, PA, USA
| | - C Phillips
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Santiago de Compostela, Spain.
| | | | - W Parson
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria; Forensic Science Program, The Pennsylvania State University, PA, USA
| | - C Phillips
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Santiago de Compostela, Spain.
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