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Huang Y, Wang M, Liu C, He G. Comprehensive landscape of non-CODIS STRs in global populations provides new insights into challenging DNA profiles. Forensic Sci Int Genet 2024; 70:103010. [PMID: 38271830 DOI: 10.1016/j.fsigen.2024.103010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 01/13/2024] [Accepted: 01/14/2024] [Indexed: 01/27/2024]
Abstract
The worldwide implementation of short tandem repeats (STR) profiles in forensic genetics necessitated establishing and expanding the CODIS core loci set to facilitated efficient data management and exchange. Currently, the mainstay CODIS STRs are adopted in most general-purpose forensic kits. However, relying solely on these loci failed to yield satisfactory results for challenging tasks, such as bio-geographical ancestry inference, complex DNA mixture profile interpretation, and distant kinship analysis. In this context, non-CODIS STRs are potent supplements to enhance the systematic discriminating power, particularly when combined with the high-throughput next-generation sequencing (NGS) technique. Nevertheless, comprehensive evaluation on non-CODIS STRs in diverse populations was scarce, hindering their further application in routine caseworks. To address this gap, we investigated genetic variations of 178 historically available non-CODIS STRs from ethnolinguistically different worldwide populations and studied their characteristics and forensic potentials via high-coverage whole genome sequencing (WGS) data. Initially, we delineated the genomic properties of these non-CODIS markers through sequence searching, repeat structure scanning, and manual inspection. Subsequent population genetics analysis suggested that these non-CODIS STRs had comparable polymorphism levels and forensic utility to CODIS STRs. Furthermore, we constructed a theoretical next-generation sequencing (NGS) panel comprising 108 STRs (20 CODIS STRs and 88 non-CODIS STRs), and evaluated its performance in inferring bio-geographical ancestry origins, deconvoluting complex DNA mixtures, and differentiating distant kinships using real and simulated datasets. Our findings demonstrated that incorporating supplementary non-CODIS STRs enabled the extrapolation of multidimensional information from a single STR profile, thereby facilitating the analysis of challenging forensic tasks. In conclusion, this study presents an extensive genomic landscape of forensic non-CODIS STRs among global populations, and emphasized the imperative inclusion of additional polymorphic non-CODIS STRs in future NGS-based forensic systems.
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Affiliation(s)
- Yuguo Huang
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu 610041, China.
| | - Mengge Wang
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu 610041, China
| | - Chao Liu
- Anti-Drug Technology Center of Guangdong Province, Guangzhou 510230, China; Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China.
| | - Guanglin He
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu 610041, China; Center for Archaeological Science, Sichuan University, Chengdu 610000, China.
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2
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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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3
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Budowle B, Sajantila A. Revisiting informed consent in forensic genomics in light of current technologies and the times. Int J Legal Med 2023; 137:551-565. [PMID: 36642749 PMCID: PMC9902322 DOI: 10.1007/s00414-023-02947-w] [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: 08/10/2022] [Accepted: 12/14/2022] [Indexed: 01/17/2023]
Abstract
Informed consent is based on basic ethical principles that should be considered when conducting biomedical and behavioral research involving human subjects. These principles-respect, beneficence, and justice-form the foundations of informed consent which in itself is grounded on three fundamental elements: information, comprehension, and voluntary participation. While informed consent has focused on human subjects and research, the practice has been adopted willingly in the forensic science arena primarily to acquire reference samples from family members to assist in identifying missing persons. With advances in molecular biology technologies, data mining, and access to metadata, it is important to assess whether the past informed consent process and in particular associated risks are concomitant with these increased capabilities. Given the state-of-the-art, areas in which informed consent may need to be modified and augmented are as follows: reference samples from family members in missing persons or unidentified human remains cases; targeted analysis of an individual(s) during forensic genetic genealogy cases to reduce an investigative burden; donors who provide their samples for validation studies (to include population studies and entry into databases that would be applied to forensic statistical calculations) to support implementation of procedures and operations of the forensic laboratory; family members that may contribute samples or obtain genetic information from a molecular autopsy; and use of medical and other acquired samples that could be informative for identification purposes. The informed consent process should cover (1) purpose for collection of samples; (2) process to analyze the samples (to include type of data); (3) benefits (to donor, target, family, community, etc. as applicable); (4) risks (to donor, target, family, community, etc. as applicable); (5) access to data/reports by the donor; (6) sample disposition; (7) removal of data process (i.e., expungement); (8) process to ask questions/assessment of comprehension; (9) follow-up processes; and (10) voluntary, signed, and dated consent. Issues surrounding these topics are discussed with an emphasis on addressing risk factors. Addressing informed consent will allow human subjects to make decisions voluntarily and with autonomy as well as secure the use of samples for intended use.
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Affiliation(s)
- Bruce Budowle
- Department of Forensic Medicine, University of Helsinki, Helsinki, Finland.
| | - Antti Sajantila
- Department of Forensic Medicine, University of Helsinki, Helsinki, Finland
- Forensic Medicine Unit, Finnish Institute for Health and Welfare, Helsinki, Finland
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4
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A reference database of forensic autosomal and gonosomal STR markers in the Tigray population of Ethiopia. Forensic Sci Int Genet 2021; 56:102618. [PMID: 34735940 DOI: 10.1016/j.fsigen.2021.102618] [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: 04/27/2021] [Revised: 08/31/2021] [Accepted: 10/20/2021] [Indexed: 11/20/2022]
Abstract
Allele frequencies of 21 autosomal STR markers (AmpF/STR GlobalFiler) and haplotype frequencies of 27 Y- and 12 X-STR markers (AmpF/STR YFiler Plus and Investigator Argus X-12, respectively) were investigated in the Tigray population of Ethiopia, representing the main population group in the Tigray regional state of Ethiopia and neighboring Eritrea. For autosomal STR allele frequencies, the average random match probability in the Tigray sample was 2.1 × 10-27. The average locus by locus FST distance calculated comparing autosomal STR allele frequencies from Tigray and from a broad regional reference dataset currently available for the Horn of Africa was 0.003. The Tigray male sample displayed high Y-STR diversity, with complete individualization of haplotypes using the AmpF/STR YFiler Plus panel. Analysis of molecular variance did not detect significant heterogeneity between Y-STR haplotypes observed in the present study and those previously reported in the literature for other Tigray population samples from Ethiopia and Eritrea. Study of the X-STR landscape in Tigray evidenced several distinctive features including: the molecular characterization of a novel null allele at locus DXS10146 with frequency > 1%; allele dependency between loci within linkage groups I and III; significant differences in haplotype distribution compared to other Horn of Africa populations, that should be taken into account in kinship analysis. The collected data can be used as a reference STR database by local forensic genetics services and in genetic identification procedures of victims of human trafficking in the Mediterranean Sea, which frequently involve individuals originating from the Horn of Africa.
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Jeong SJ, Lee HJ, Lee JW. Statistical considerations in forensic science: a review. J Korean Stat Soc 2021. [DOI: 10.1007/s42952-021-00123-7] [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]
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6
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The analysis of ancestry with small-scale forensic panels of genetic markers. Emerg Top Life Sci 2021; 5:443-453. [PMID: 33949669 DOI: 10.1042/etls20200327] [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: 02/03/2021] [Revised: 04/07/2021] [Accepted: 04/19/2021] [Indexed: 11/17/2022]
Abstract
In the last 10 years, forensic genetic analysis has been extended beyond identification tests that link a suspect to crime scene evidence using standard DNA profiling, to new supplementary tests that can provide information to investigators about a suspect in the absence of a database hit or eyewitness testimony. These tests now encompass the prediction of physical appearance, ancestry and age. In this review, we give a comprehensive overview of the full range of DNA-based ancestry inference tests designed to work with forensic contact traces, when the level of DNA is often very low or highly degraded. We outline recent developments in the design of ancestry-informative marker sets, forensic assays that use capillary electrophoresis or massively parallel sequencing, and the statistical analysis frameworks that examine the test profile and compares it to reference population variation. Three casework ancestry analysis examples are described which were successfully accomplished in the authors' laboratory, where the ancestry information obtained was critical to the outcome of the DNA analyses made.
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Wyner N, Barash M, McNevin D. Forensic Autosomal Short Tandem Repeats and Their Potential Association With Phenotype. Front Genet 2020; 11:884. [PMID: 32849844 PMCID: PMC7425049 DOI: 10.3389/fgene.2020.00884] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 07/17/2020] [Indexed: 12/11/2022] Open
Abstract
Forensic DNA profiling utilizes autosomal short tandem repeat (STR) markers to establish identity of missing persons, confirm familial relations, and link persons of interest to crime scenes. It is a widely accepted notion that genetic markers used in forensic applications are not predictive of phenotype. At present, there has been no demonstration of forensic STR variants directly causing or predicting disease. Such a demonstration would have many legal and ethical implications. For example, is there a duty to inform a DNA donor if a medical condition is discovered during routine analysis of their sample? In this review, we evaluate the possibility that forensic STRs could provide information beyond mere identity. An extensive search of the literature returned 107 articles associating a forensic STR with a trait. A total of 57 of these studies met our inclusion criteria: a reported link between a STR-inclusive gene and a phenotype and a statistical analysis reporting a p-value less than 0.05. A total of 50 unique traits were associated with the 24 markers included in the 57 studies. TH01 had the greatest number of associations with 27 traits reportedly linked to 40 different genotypes. Five of the articles associated TH01 with schizophrenia. None of the associations found were independently causative or predictive of disease. Regardless, the likelihood of identifying significant associations is increasing as the function of non-coding STRs in gene expression is steadily revealed. It is recommended that regular reviews take place in order to remain aware of future studies that identify a functional role for any forensic STRs.
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Affiliation(s)
- Nicole Wyner
- Centre for Forensic Science, School of Mathematical and Physical Sciences, Faculty of Science, University of Technology Sydney, Sydney, NSW, Australia
| | - Mark Barash
- Centre for Forensic Science, School of Mathematical and Physical Sciences, Faculty of Science, University of Technology Sydney, Sydney, NSW, Australia.,Department of Justice Studies, San José State University, San Jose, CA, United States
| | - Dennis McNevin
- Centre for Forensic Science, School of Mathematical and Physical Sciences, Faculty of Science, University of Technology Sydney, Sydney, NSW, Australia
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8
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Evaluation of the classification method using ancestry SNP markers for ethnic group. COMMUNICATIONS FOR STATISTICAL APPLICATIONS AND METHODS 2019. [DOI: 10.29220/csam.2019.26.1.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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9
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10
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Cheung EY, Gahan ME, McNevin D. Prediction of biogeographical ancestry in admixed individuals. Forensic Sci Int Genet 2018; 36:104-111. [DOI: 10.1016/j.fsigen.2018.06.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 05/09/2018] [Accepted: 06/20/2018] [Indexed: 12/14/2022]
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Gaussian Fuzzy Number for STR-DNA Similarity Calculation Involving Familial and Tribal Relationships. Adv Bioinformatics 2018; 2018:8602513. [PMID: 30151007 PMCID: PMC6087604 DOI: 10.1155/2018/8602513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Accepted: 07/09/2018] [Indexed: 11/27/2022] Open
Abstract
We performed locus similarity calculation by measuring fuzzy intersection between individual locus and reference locus and then performed CODIS STR-DNA similarity calculation. The fuzzy intersection calculation enables a more robust CODIS STR-DNA similarity calculation due to imprecision caused by noise produced by PCR machine. We also proposed shifted convoluted Gaussian fuzzy number (SCGFN) and Gaussian fuzzy number (GFN) to represent each locus value as improvement of triangular fuzzy number (TFN) as used in previous research. Compared to triangular fuzzy number (TFN), GFN is more realistic to represent uncertainty of locus information because the distribution is assumed to be Gaussian. Then, the original Gaussian fuzzy number (GFN) is convoluted with distribution of certain ethnic locus information to produce the new SCGFN which more represents ethnic information compared to original GFN. Experiments were done for the following cases: people with family relationships, people of the same tribe, and certain tribal populations. The statistical test with analysis of variance (ANOVA) shows the difference in similarity between SCGFN, GFN, and TFN with a significant level of 95%. The Tukey method in ANOVA shows that SCGFN yields a higher similarity which means being better than the GFN and TFN methods. The proposed method enables CODIS STR-DNA similarity calculation which is more robust to noise and performed better CODIS similarity calculation involving familial and tribal relationships.
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12
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Benvisto A, Messina F, Finocchio A, Popa L, Stefan M, Stefanescu G, Mironeanu C, Novelletto A, Rapone C, Berti A. A genetic portrait of the South-Eastern Carpathians based on autosomal short tandem repeats loci used in forensics. Am J Hum Biol 2018; 30:e23139. [PMID: 30099799 DOI: 10.1002/ajhb.23139] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 04/02/2018] [Accepted: 05/17/2018] [Indexed: 11/09/2022] Open
Abstract
OBJECTIVES This work aimed to describe the genetic landscape of the Balkan Peninsula, as revealed by STR markers commonly used in forensics and spatial methods specifically developed for genetic data. METHODS We generated and analyzed 16 short tandem repeats (STRs) autosomal genotypes in 287 subjects from ten administrative/geographical regions of Eastern Europe (Romania and the Republic of Moldova). We report estimates of the allele frequencies in these sub-populations, their fixation indexes, and use these results to complement previous spatial analyses of Southern Europe. RESULTS In seven out of ten analyzed regional samples the heterozygosity, averaged across loci, was lower than expected. The average Fis was 0.011. Among the 16 loci, five returned a significant fixation index Fst. The composite Fst across the 16 loci, among the 10 regional samples, was 0.00417, a figure twice as large as that obtained with the same markers across the entire Northern Mediterranean. The first spatial principal component (sPC1) returned the picture of a Central-European pattern of frequencies for the Carpathians, which extended to the Southern boundary of the Balkan Peninsula. However, the 8 alleles extracted by sPC1 returned a picture of a strong reduction of the migration rate in the Carpathian region, mostly between the inner locations. CONCLUSIONS Our results revealed an unexpected heterogeneity in the area. We believe that populations from some regions will require treatment as distinct entities when considered in forensic applications.
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Affiliation(s)
- Alessandro Benvisto
- Reparto Carabinieri Investigazioni Scientifiche - Sezione di Biologia, Rome, 00191, Italy
| | - Francesco Messina
- Department of Biology, University of Rome Tor Vergata, Rome, 00133, Italy
| | - Andrea Finocchio
- Department of Biology, University of Rome Tor Vergata, Rome, 00133, Italy
| | - Luis Popa
- "Grigore Antipa" National Museum of Natural History, Bucharest, 011341, Romania
| | - Mihaela Stefan
- Department of Genetics, University of Bucharest, Bucharest, 76258, Romania
| | | | | | - Andrea Novelletto
- Department of Biology, University of Rome Tor Vergata, Rome, 00133, Italy
| | - Cesare Rapone
- Reparto Carabinieri Investigazioni Scientifiche - Sezione di Biologia, Rome, 00191, Italy
| | - Andrea Berti
- Reparto Carabinieri Investigazioni Scientifiche - Sezione di Biologia, Rome, 00191, Italy
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Hessab T, Aranha RS, Moura-Neto RS, Balding DJ, Schrago CG. Evaluating DNA evidence in a genetically complex population. Forensic Sci Int Genet 2018; 36:141-147. [PMID: 29990826 DOI: 10.1016/j.fsigen.2018.06.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 06/27/2018] [Accepted: 06/28/2018] [Indexed: 11/28/2022]
Abstract
In forensic genetics, the likelihood ratio (LR), measuring the value of DNA profile evidence, is computed from a database of allele frequencies. Here, we address the choice of database and adjustments for population structure and sample size in the context of Brazil. The Brazilian population underwent a complex process of colonization, migration and mating, which created an admixed genetic composition that makes it difficult to obtain an appropriate database for a given case. National databases are now available, as well as databases for many Brazilian states. However, those databases are not statistically random samples, and state boundaries may not accurately reflect the sub-structuring of genetic diversity. We compared the LR calculated using the relevant state-specific database with the statistics calculated when a national database and when international databases were used. We evaluated two methods of adjustment for population structure, due to Wright [13] and Balding and Nichols [14]. We also considered two adjustments for database sample size: the Balding size bias correction [15] and a minimum allele frequency [16]. Our results show that the use of a national database with the Balding and Nichols adjustment and θ = 0.002 generated lower LR values than did the state-specific database in more than 50% of the profiles simulated using the state-based allele frequencies, while θ = 0.01 produced lower LRs for more than 90% of the profiles. We conclude that the utilization of a national database for Brazilian cases can be justified in association with the appropriate adjustment for population structure.
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Affiliation(s)
- T Hessab
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil; Instituto de Pesquisa e Perícias em Genética Forense, DGPTC/PCERJ, Rio de Janeiro, RJ, Brazil.
| | - R S Aranha
- Escola de Matemática Aplicada, Fundação Getúlio Vargas, Rio de Janeiro, RJ, Brazil
| | - R S Moura-Neto
- Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - D J Balding
- Melbourne Integrative Genomics, School of BioSciences and School of Mathematics & Statistics, The University of Melbourne, Melbourne, Australia
| | - C G Schrago
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
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Autosomal and Y-STR: A combinatory approach to ethnicity inference in Singapore. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2017. [DOI: 10.1016/j.fsigss.2017.09.086] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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15
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Tau T, Wally A, Fanie TP, Ngono GL, Mpoloka SW, Davison S, D'Amato ME. Genetic variation and population structure of Botswana populations as identified with AmpFLSTR Identifiler short tandem repeat (STR) loci. Sci Rep 2017; 7:6768. [PMID: 28754995 PMCID: PMC5533702 DOI: 10.1038/s41598-017-06365-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 06/14/2017] [Indexed: 11/09/2022] Open
Abstract
Population structure was investigated in 990 Botswana individuals according to ethno-linguistics, Bantu and Khoisan, and geography (the nine administrative districts) using the Identifiler autosomal microsatellite markers. Genetic diversity and forensic parameters were calculated for the overall population, and according to ethno-linguistics and geography. The overall combined power of exclusion (CPE) was 0.9999965412 and the combined match probability 6,28 × 10-19. CPE was highest for the Khoisan Tuu ethnolinguistic group and the Northeast District at 0.9999582029 and 0.9999922652 respectively. CMP ranged from 6.28 × 10-19 (Khoisan Tuu) to 1,02 × 10-18 (Northwest district). Using pairwise genetic distances (FST), analysis of molecular variance (AMOVA), factorial correspondence analysis (FCA), and the unsupervised Bayesian clustering method found in STRUCTURE and TESS, ethno-linguistics were found to have a greater influence on population structure than geography. FCA showed clustering between Bantu and Khoisan, and within the Bantu. This Bantu sub-structuring was not seen with STRUCTURE and TESS, which detected clustering only between Bantu and Khoisan. The patterns of population structure revealed highlight the need for regional reference databases that include ethno-linguistic and geographic location information. These markers have important potential for bio-anthropological studies as well as for forensic applications.
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Affiliation(s)
- Tiroyamodimo Tau
- University of the Western Cape, Department of Biotechnology, Forensic DNA Laboratory, Private Bag X17, 7535, Bellville, Cape Town, South Africa
| | - Anthony Wally
- Botswana Police Service, Forensic Science Laboratory, Private Bag 0400, Gaborone, Botswana
| | | | - Goitseone Lorato Ngono
- Botswana Police Service, Forensic Science Laboratory, Private Bag 0400, Gaborone, Botswana
| | - Sununguko Wata Mpoloka
- University of Botswana, Biological Sciences Department, Private Bag 00704, Gaborone, Botswana
| | - Sean Davison
- University of the Western Cape, Department of Biotechnology, Forensic DNA Laboratory, Private Bag X17, 7535, Bellville, Cape Town, South Africa
| | - María Eugenia D'Amato
- University of the Western Cape, Department of Biotechnology, Forensic DNA Laboratory, Private Bag X17, 7535, Bellville, Cape Town, South Africa.
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Ehler E, Vanek D. Forensic genetic analyses in isolated populations with examples of central European Valachs and Roma. J Forensic Leg Med 2017; 48:46-52. [PMID: 28454050 DOI: 10.1016/j.jflm.2017.04.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 03/22/2017] [Accepted: 04/09/2017] [Indexed: 01/27/2023]
Abstract
Isolated populations present a constant threat to the correctness of forensic genetic casework. In this review article we present several examples of how analyzing samples from isolated populations can bias the results of the forensic statistics and analyses. We select our examples from isolated populations from central and southeastern Europe, namely the Valachs and the European Roma. We also provide the reader with general strategies and principles to improve the laboratory practice (best practice) and reporting of samples from supposedly isolated populations. These include reporting the precise population data used for computing the forensic statistics, using the appropriate θ correction factor for calculating allele frequencies, typing ancestry informative markers in samples of unknown or uncertain ethnicity and establishing ethnic-specific forensic databases.
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Affiliation(s)
- Edvard Ehler
- Department of Biology and Environmental Studies, Charles University in Prague, Faculty of Education, Magdaleny Rettigove 4, Prague, 116 39, Czech Republic; Institute of Anthropology, Faculty of Biology, Adam Mickiewicz University, ul. Umultowska 89, 61-614, Poznan, Poland.
| | - Daniel Vanek
- Forensic DNA Service, Janovskeho 18, Prague 7, 170 00, Czech Republic; Charles University in Prague, 2nd Faculty of Medicine, V Uvalu 84, Prague, 150 06, Czech Republic; Nemocnice Na Bulovce, Institute of Legal Medicine, Budinova 2, Prague, 180 81, Czech Republic.
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17
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Kruijver M. Characterizing the genetic structure of a forensic DNA database using a latent variable approach. Forensic Sci Int Genet 2016; 23:130-149. [DOI: 10.1016/j.fsigen.2016.03.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Revised: 02/24/2016] [Accepted: 03/21/2016] [Indexed: 12/11/2022]
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18
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Algee-Hewitt B, Edge M, Kim J, Li J, Rosenberg N. Individual Identifiability Predicts Population Identifiability in Forensic Microsatellite Markers. Curr Biol 2016; 26:935-42. [DOI: 10.1016/j.cub.2016.01.065] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Revised: 12/10/2015] [Accepted: 01/26/2016] [Indexed: 10/22/2022]
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Phillips C, Santos C, Fondevila M, Carracedo Á, Lareu MV. Inference of Ancestry in Forensic Analysis I: Autosomal Ancestry-Informative Marker Sets. Methods Mol Biol 2016; 1420:233-53. [PMID: 27259744 DOI: 10.1007/978-1-4939-3597-0_18] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
An expanding choice of ancestry-informative marker single nucleotide polymorphisms (AIM-SNPs) is becoming available for the forensic user in the form of sensitive SNaPshot-based tests or in alternative single-base extension genotyping systems (e.g., Sequenom iPLEX) that can be adapted for analysis with SNaPshot. In addition, alternative ancestry-informative variation: Indels and STRs can be analyzed using direct PCR-to-CE techniques that offer the possibility to detect mixed profiles. We review the current forensically viable AIM panels, their optimized PCR multiplexes, and the population differentiation power they offer. We also describe how improved population divergence balance can be achieved with the enlarged multiplex scales of next-generation sequencing approaches to enable analysis of admixed individuals without biased estimation of co-ancestry proportions.
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Affiliation(s)
- Chris Phillips
- Forensic Genetics Unit, Luis Concheiro Institute of Forensic Sciences, Genomic Medicine Group, University of Santiago de Compostela, Galicia, 15782, Spain.
| | - Carla Santos
- Forensic Genetics Unit, Luis Concheiro Institute of Forensic Sciences, Genomic Medicine Group, University of Santiago de Compostela, Galicia, 15782, Spain
| | - Manuel Fondevila
- Forensic Genetics Unit, Luis Concheiro Institute of Forensic Sciences, Genomic Medicine Group, University of Santiago de Compostela, Galicia, 15782, Spain
| | - Ángel Carracedo
- Forensic Genetics Unit, Luis Concheiro Institute of Forensic Sciences, Genomic Medicine Group, University of Santiago de Compostela, Galicia, 15782, Spain
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Maria Victoria Lareu
- Forensic Genetics Unit, Luis Concheiro Institute of Forensic Sciences, Genomic Medicine Group, University of Santiago de Compostela, Galicia, 15782, Spain
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Forensic genetic analysis of bio-geographical ancestry. Forensic Sci Int Genet 2015; 18:49-65. [DOI: 10.1016/j.fsigen.2015.05.012] [Citation(s) in RCA: 151] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Revised: 05/02/2015] [Accepted: 05/14/2015] [Indexed: 01/20/2023]
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Phillips C, Gelabert-Besada M, Fernandez-Formoso L, García-Magariños M, Santos C, Fondevila M, Ballard D, Syndercombe Court D, Carracedo Á, Victoria Lareu M. “New turns from old STaRs”: Enhancing the capabilities of forensic short tandem repeat analysis. Electrophoresis 2014; 35:3173-87. [DOI: 10.1002/elps.201400095] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Revised: 04/25/2014] [Accepted: 05/15/2014] [Indexed: 02/01/2023]
Affiliation(s)
- Christopher Phillips
- Forensic Genetics Unit, Institute of Legal Medicine; University of Santiago de Compostela; Santiago de Compostela Spain
| | - Miguel Gelabert-Besada
- Forensic Genetics Unit, Institute of Legal Medicine; University of Santiago de Compostela; Santiago de Compostela Spain
| | - Luis Fernandez-Formoso
- Forensic Genetics Unit, Institute of Legal Medicine; University of Santiago de Compostela; Santiago de Compostela Spain
| | | | - Carla Santos
- Forensic Genetics Unit, Institute of Legal Medicine; University of Santiago de Compostela; Santiago de Compostela Spain
| | - Manuel Fondevila
- Forensic Genetics Unit, Institute of Legal Medicine; University of Santiago de Compostela; Santiago de Compostela Spain
| | - David Ballard
- Department of Forensic and Analytical Science; King's College London; London UK
| | | | - Ángel Carracedo
- Forensic Genetics Unit, Institute of Legal Medicine; University of Santiago de Compostela; Santiago de Compostela Spain
- Center of Excellence in Genomic Medicine Research; King Abdulaziz University; Jeddah Saudi Arabia
| | - Maria Victoria Lareu
- Forensic Genetics Unit, Institute of Legal Medicine; University of Santiago de Compostela; Santiago de Compostela Spain
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Cortellini V, Verzeletti A, Cerri N, Marino A, De Ferrari F. Y-chromosome polymorphisms and ethnic group - a combined STR and SNP approach in a population sample from northern Italy. Croat Med J 2013; 54:279-85. [PMID: 23771759 PMCID: PMC3692336 DOI: 10.3325/cmj.2013.54.279] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Accepted: 06/01/2013] [Indexed: 11/16/2022] Open
Abstract
AIM To find an association between Y chromosome polymorphisms and some ethnic groups. METHODS Short tandem repeats (STR) and single-nucleotide polymorphisms (SNP) on the Y chromosome were typed in 311 unrelated men from four different ethnic groups - Italians from northern Italy, Albanians, Africans from the Maghreb region, and Indo-Pakistanis, using the AmpFlSTR® Yfiler PCR Amplification Kit and the SNaPshot Multiplex Kit. RESULTS STRs analysis found 299 different haplotypes and SNPs analysis 11 different haplogroups. Haplotypes and haplogroups were analyzed and compared between different ethnic groups. Significant differences were found among all the population groups, except between Italians and Indo-Pakistanis and between Albanians and Indo-Pakistanis. CONCLUSIONS Typing both STRs and SNPs on the Y chromosome could become useful in determining ethnic origin of a potential suspect.
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Porras-Hurtado L, Ruiz Y, Santos C, Phillips C, Carracedo A, Lareu MV. An overview of STRUCTURE: applications, parameter settings, and supporting software. Front Genet 2013; 4:98. [PMID: 23755071 PMCID: PMC3665925 DOI: 10.3389/fgene.2013.00098] [Citation(s) in RCA: 257] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Accepted: 05/14/2013] [Indexed: 12/22/2022] Open
Abstract
Objectives: We present an up-to-date review of STRUCTURE software: one of the most widely used population analysis tools that allows researchers to assess patterns of genetic structure in a set of samples. STRUCTURE can identify subsets of the whole sample by detecting allele frequency differences within the data and can assign individuals to those sub-populations based on analysis of likelihoods. The review covers STRUCTURE's most commonly used ancestry and frequency models, plus an overview of the main applications of the software in human genetics including case-control association studies (CCAS), population genetics, and forensic analysis. The review is accompanied by supplementary material providing a step-by-step guide to running STRUCTURE. Methods: With reference to a worked example, we explore the effects of changing the principal analysis parameters on STRUCTURE results when analyzing a uniform set of human genetic data. Use of the supporting software: CLUMPP and distruct is detailed and we provide an overview and worked example of STRAT software, applicable to CCAS. Conclusion: The guide offers a simplified view of how STRUCTURE, CLUMPP, distruct, and STRAT can be applied to provide researchers with an informed choice of parameter settings and supporting software when analyzing their own genetic data.
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Affiliation(s)
- Liliana Porras-Hurtado
- Universidad Tecnológica de Pereira Pereira, Colombia ; Forensic Genetics Unit, Institute of Legal Medicine, University of Santiago de Compostela Santiago de Compostela, Spain
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Phillips C, Fernandez-Formoso L, Gelabert-Besada M, Garcia-Magariños M, Santos C, Fondevila M, Carracedo Á, Lareu MV. Development of a novel forensic STR multiplex for ancestry analysis and extended identity testing. Electrophoresis 2013; 34:1151-62. [DOI: 10.1002/elps.201200621] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2012] [Revised: 12/13/2012] [Accepted: 12/17/2012] [Indexed: 11/11/2022]
Affiliation(s)
- Chris Phillips
- Forensic Genetics Unit; Institute of Legal Medicine; University of Santiago de Compostela; Santiago de Compostela; Spain
| | - Luis Fernandez-Formoso
- Forensic Genetics Unit; Institute of Legal Medicine; University of Santiago de Compostela; Santiago de Compostela; Spain
| | - Miguel Gelabert-Besada
- Forensic Genetics Unit; Institute of Legal Medicine; University of Santiago de Compostela; Santiago de Compostela; Spain
| | | | - Carla Santos
- Forensic Genetics Unit; Institute of Legal Medicine; University of Santiago de Compostela; Santiago de Compostela; Spain
| | - Manuel Fondevila
- Forensic Genetics Unit; Institute of Legal Medicine; University of Santiago de Compostela; Santiago de Compostela; Spain
| | | | - Maria Victoria Lareu
- Forensic Genetics Unit; Institute of Legal Medicine; University of Santiago de Compostela; Santiago de Compostela; Spain
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Abstract
An individual's genotypes at a group of single-nucleotide polymorphisms (SNPs) can be used to predict that individual's ethnicity or ancestry. In medical studies, knowledge of a subject's ancestry can minimize possible confounding, and in forensic applications, such knowledge can help direct investigations. Our goal is to select a small subset of SNPs, from the millions already identified in the human genome, that can predict ancestry with a minimal error rate. The general form for this variable selection procedure is to estimate the expected error rates for sets of SNPs using a training dataset and consider those sets with the lowest error rates given their size. The quality of the estimate for the error rate determines the quality of the resulting SNPs. As the apparent error rate performs poorly when either the number of SNPs or the number of populations is large; we propose a new estimate, the Improved Bayesian Estimate. We demonstrate that selection procedures based on this estimate produce small sets of SNPs that can accurately predict ancestry. We also provide a list of the 100 optimal SNPs for identifying ancestry.
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Tucker VC, Baumgartner C, Stead GR, Hopwood AJ. UK population data generated with the PowerPlex® ESI 16 system. Forensic Sci Int Genet 2011; 6:e112-8. [PMID: 21944937 DOI: 10.1016/j.fsigen.2011.08.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2011] [Revised: 08/09/2011] [Accepted: 08/16/2011] [Indexed: 11/17/2022]
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27
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Giardina E, Pietrangeli I, Martínez-Labarga C, Martone C, de Angelis F, Spinella A, De Stefano G, Rickards O, Novelli G. Haplotypes in SLC24A5 Gene as Ancestry Informative Markers in Different Populations. Curr Genomics 2011; 9:110-4. [PMID: 19440451 PMCID: PMC2674805 DOI: 10.2174/138920208784139528] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2008] [Revised: 02/26/2008] [Accepted: 02/27/2008] [Indexed: 11/22/2022] Open
Abstract
Ancestry informative markers (AIMs) are human polymorphisms that exhibit substantially allele frequency differences among populations. These markers can be useful to provide information about ancestry of samples which may be useful in predicting a perpetrator’s ethnic origin to aid criminal investigations. Variations in human pigmentation are the most obvious phenotypes to distinguish individuals. It has been recently shown that the variation of a G in an A allele of the coding single-nucleotide polymorphism (SNP) rs1426654 within SLC24A5 gene varies in frequency among several population samples according to skin pigmentation. Because of these observations, the SLC24A5 locus has been evaluated as Ancestry Informative Region (AIR) by typing rs1426654 together with two additional intragenic markers (rs2555364 and rs16960620) in 471 unrelated individuals originating from three different continents (Africa, Asia and Europe). This study further supports the role of human SLC24A5 gene in skin pigmentation suggesting that variations in SLC24A5 haplotypes can correlate with human migration and ancestry. Furthermore, our data do reveal the utility of haplotype and combined unphased genotype analysis of SLC24A5 in predicting ancestry and provide a good example of usefulness of genetic characterization of larger regions, in addition to single polymorphisms, as candidates for population-specific sweeps in the ancestral population.
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Affiliation(s)
- Emiliano Giardina
- Centre of Excellence for Genomic Risk Assessment in Multifactorial and Complex Diseases, School of Medicine, Tor Vergata University of Rome, Italy
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PopAffiliator: online calculator for individual affiliation to a major population group based on 17 autosomal short tandem repeat genotype profile. Int J Legal Med 2010; 125:629-36. [DOI: 10.1007/s00414-010-0472-2] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2010] [Accepted: 05/17/2010] [Indexed: 11/25/2022]
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Analysis of global variability in 15 established and 5 new European Standard Set (ESS) STRs using the CEPH human genome diversity panel. Forensic Sci Int Genet 2010; 5:155-69. [PMID: 20457091 DOI: 10.1016/j.fsigen.2010.02.003] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2009] [Revised: 02/02/2010] [Accepted: 02/06/2010] [Indexed: 11/22/2022]
Abstract
The CEPH human genome diversity cell line panel (CEPH-HGDP) of 51 globally distributed populations was used to analyze patterns of variability in 20 core human identification STRs. The markers typed comprised the 15 STRs of Identifiler, one of the most widely used forensic STR multiplexes, plus five recently introduced European Standard Set (ESS) STRs: D1S1656, D2S441, D10S1248, D12S391 and D22S1045. From the genotypes obtained for the ESS STRs we identified rare, intermediate or off-ladder alleles that had not been previously reported for these loci. Examples of novel ESS STR alleles found were characterized by sequence analysis. This revealed extensive repeat structure variation in three ESS STRs, with D12S391 showing particularly high variability for tandem runs of AGAT and AGAC repeat units. The global geographic distribution of the CEPH panel samples gave an opportunity to study in detail the extent of substructure shown by the 20 STRs amongst populations and between their parent population groups. An assessment was made of the forensic informativeness of the new ESS STRs compared to the loci they will replace: CSF1PO, D5S818, D7S820, D13S317 and TPOX, with results showing a clear enhancement of discrimination power using multiplexes that genotype the new ESS loci. We also measured the ability of Identifiler and ESS STRs to infer the ancestry of the CEPH-HGDP samples and demonstrate that forensic STRs in large multiplexes have the potential to differentiate the major population groups but only with sufficient reliability when used with other ancestry-informative markers such as single nucleotide polymorphisms. Finally we checked for possible association by linkage between the two ESS multiplex STRs closely positioned on chromosome-12: vWA and D12S391 by examining paired genotypes from the complete CEPH data set.
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Koen C, D’Amato M. Simulation of Y-chromosomal haplotype data. Math Biosci 2010; 224:24-8. [DOI: 10.1016/j.mbs.2009.12.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2009] [Revised: 10/07/2009] [Accepted: 12/01/2009] [Indexed: 10/20/2022]
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31
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Graydon M, Cholette F, Ng LK. Inferring ethnicity using 15 autosomal STR loci—Comparisons among populations of similar and distinctly different physical traits. Forensic Sci Int Genet 2009; 3:251-4. [DOI: 10.1016/j.fsigen.2009.03.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2008] [Revised: 01/07/2009] [Accepted: 03/27/2009] [Indexed: 11/16/2022]
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32
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Ancestry analysis in the 11-M Madrid bomb attack investigation. PLoS One 2009; 4:e6583. [PMID: 19668368 PMCID: PMC2719087 DOI: 10.1371/journal.pone.0006583] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2008] [Accepted: 07/08/2009] [Indexed: 11/26/2022] Open
Abstract
The 11-M Madrid commuter train bombings of 2004 constituted the second biggest terrorist attack to occur in Europe after Lockerbie, while the subsequent investigation became the most complex and wide-ranging forensic case in Spain. Standard short tandem repeat (STR) profiling of 600 exhibits left certain key incriminatory samples unmatched to any of the apprehended suspects. A judicial order to perform analyses of unmatched samples to differentiate European and North African ancestry became a critical part of the investigation and was instigated to help refine the search for further suspects. Although mitochondrial DNA (mtDNA) and Y-chromosome markers routinely demonstrate informative geographic differentiation, the populations compared in this analysis were known to show a proportion of shared mtDNA and Y haplotypes as a result of recent gene-flow across the western Mediterranean, while any two loci can be unrepresentative of the ancestry of an individual as a whole. We based our principal analysis on a validated 34plex autosomal ancestry-informative-marker single nucleotide polymorphism (AIM-SNP) assay to make an assignment of ancestry for DNA from seven unmatched case samples including a handprint from a bag containing undetonated explosives together with personal items recovered from various locations in Madrid associated with the suspects. To assess marker informativeness before genotyping, we predicted the probable classification success for the 34plex assay with standard error estimators for a naïve Bayesian classifier using Moroccan and Spanish training sets (each n = 48). Once misclassification error was found to be sufficiently low, genotyping yielded seven near-complete profiles (33 of 34 AIM-SNPs) that in four cases gave probabilities providing a clear assignment of ancestry. One of the suspects predicted to be North African by AIM-SNP analysis of DNA from a toothbrush was identified late in the investigation as Algerian in origin. The results achieved illustrate the benefit of adding specialized marker sets to provide enhanced scope and power to an already highly effective system of DNA analysis for forensic identification.
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34
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Amorim A. A cautionary note on the evaluation of genetic evidence from uniparentally transmitted markers. Forensic Sci Int Genet 2008; 2:376-8. [PMID: 19083851 DOI: 10.1016/j.fsigen.2008.04.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2008] [Revised: 03/30/2008] [Accepted: 04/01/2008] [Indexed: 10/22/2022]
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35
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The SNPforID browser: an online tool for query and display of frequency data from the SNPforID project. Int J Legal Med 2008; 122:435-40. [DOI: 10.1007/s00414-008-0233-7] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2007] [Accepted: 03/13/2008] [Indexed: 11/26/2022]
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36
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Phillips C, Salas A, Sánchez J, Fondevila M, Gómez-Tato A, Álvarez-Dios J, Calaza M, de Cal MC, Ballard D, Lareu M, Carracedo Á. Inferring ancestral origin using a single multiplex assay of ancestry-informative marker SNPs. Forensic Sci Int Genet 2007; 1:273-80. [DOI: 10.1016/j.fsigen.2007.06.008] [Citation(s) in RCA: 218] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2007] [Revised: 06/25/2007] [Accepted: 06/27/2007] [Indexed: 10/22/2022]
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37
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Genotype versus phenotype: Human pigmentation. Forensic Sci Int Genet 2007; 1:105-10. [DOI: 10.1016/j.fsigen.2007.01.005] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2007] [Accepted: 01/27/2007] [Indexed: 11/24/2022]
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39
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Daniel R, Walsh SJ. The Continuing Evolution of Forensic DNA Profiling - From STRS to SNPS. AUST J FORENSIC SCI 2006. [DOI: 10.1080/00450610609410633] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Wallace H. The UK National DNA Database. Balancing crime detection, human rights and privacy. EMBO Rep 2006; 7 Spec No:S26-30. [PMID: 16819445 PMCID: PMC1490298 DOI: 10.1038/sj.embor.7400727] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
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41
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Abstract
Over the past decade, the human identity testing community has settled on a set of core short tandem repeat (STR) loci that are widely used for DNA typing applications. A variety of commercial kits enable robust amplification of these core STR loci. A brief history is presented regarding the selection of core autosomal and Y-chromosomal STR markers. The physical location of each STR locus in the human genome is delineated and allele ranges and variants observed in human populations are summarized as are mutation rates observed from parentage testing. Internet resources for additional information on core STR loci are reviewed. Additional topics are also discussed, including potential linkage of STR loci to genetic disease-causing genes, probabilistic predictions of sample ethnicity, and desirable characteristics for additional STR loci that may be added in the future to the current core loci. These core STR loci, which form the basis for DNA databases worldwide, will continue to play an important role in forensic science for many years to come.
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Affiliation(s)
- John M Butler
- National Institute of Standards and Technology, Gaithersburg, MD 20899-8311, USA.
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42
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Cho MK. Racial and ethnic categories in biomedical research: there is no baby in the bathwater. THE JOURNAL OF LAW, MEDICINE & ETHICS : A JOURNAL OF THE AMERICAN SOCIETY OF LAW, MEDICINE & ETHICS 2006; 34:497-9, 479. [PMID: 17144171 PMCID: PMC2271137 DOI: 10.1111/j.1748-720x.2006.00061.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The use of racial categories in biomedicine has had a long history in the United States. However, social hierarchy and discrimination, justified by purported scientific differences, has also plagued the history of racial categories. Because "race" has some correlation with biological and genetic characteristics, there has been a call not to "throw the baby out with the bathwater" by eliminating race as a research or clinical category. I argue that race is too undefined and fluid to be useful as a proxy for biology or genetics.
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43
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Wetton JH, Tsang KW, Khan H. Inferring the population of origin of DNA evidence within the UK by allele-specific hybridization of Y-SNPs. Forensic Sci Int 2005; 152:45-53. [PMID: 15878814 DOI: 10.1016/j.forsciint.2005.03.009] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2004] [Accepted: 03/04/2005] [Indexed: 11/30/2022]
Abstract
Marked differences in Y-SNP allele frequencies between continental populations can be used to predict the biogeographic origin of a man's ancestral paternal lineage. Using 627 samples collected from individuals within the UK with pale-skinned Caucasian, dark-skinned Caucasian, African/Caribbean, South Asian, East Asian or Middle Eastern appearance we demonstrate that an individual's Y-SNP haplogroup is also strongly correlated with their physical appearance. Furthermore, experimental evaluation of the Marligen Signet Y-SNP kit in conjunction with the Luminex 100 detection instrument indicates that reliable and reproducible haplogrouping results can be obtained from 1 ng or more of target template derived from a variety of forensic evidence types including, blood, saliva and post-coital vaginal swabs. The test proved highly male-specific with reliable results being generated in the presence of a 1000-fold excess of female DNA, and no anomalous results were observed during degradation studies despite a gradual loss of typable loci. Hence, Y-SNP haplogrouping has considerable potential forensic utility in predicting likely ethnic appearance.
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Affiliation(s)
- Jon H Wetton
- The Forensic Science Service, R&D, Trident Court 2960, Solihull Parkway, Birmingham Business Park, Solihull B37 7YN, UK.
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44
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Shriver M, Frudakis T, Budowle B. Getting the science and the ethics right in forensic genetics. Nat Genet 2005; 37:449-50; author reply 450-1. [PMID: 15858585 DOI: 10.1038/ng0505-449] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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45
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Affiliation(s)
- Troy Duster
- Institute for the History of the Production of Knowledge, New York University, 269 Mercer Street, New York, NY 10003-6687, USA.
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46
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Egeland T, Bøvelstad HM, Storvik GO, Salas A. Inferring the most likely geographical origin of mtDNA sequence profiles. Ann Hum Genet 2005; 68:461-71. [PMID: 15469423 DOI: 10.1046/j.1529-8817.2004.00109.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
In a number of practical cases it is important to determine the likely geographical origin of an individual or a biological sample. A dead body, old bones or a sample of semen may be available. Information on where the sample might come from can assist investigation or research. The first part of this paper is independent of specific data structure. We formulate the problem as a classification problem. Bayes' theorem allows different sources of information or data to be reconciled conveniently. The main part of the paper involves high dimensional data for which simple, standard methods are not likely to work properly. Mitochondrial DNA (mtDNA) data is a typical example of such data. We propose a procedure involving essentially two steps. First, principal component analysis is used to reduce the dimension of the data. Next, quadratic discriminant analysis performs the actual classification. A cross validation procedure is implemented to select the optimal number of principal components. The importance of using separate data sets for model fitting and testing is emphasized. This method distinguishes well between individuals with a self reported European (Icelandic or German) origin and SE Africans. In this case the error rate is 2.0%.
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Affiliation(s)
- T Egeland
- Biostatistics, Rikshospitalet, 0027 Oslo, Norway.
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47
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Ossorio P, Duster T. Race and genetics: Controversies in biomedical, behavioral, and forensic sciences. AMERICAN PSYCHOLOGIST 2005; 60:115-28. [PMID: 15641926 DOI: 10.1037/0003-066x.60.1.115] [Citation(s) in RCA: 112] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Among biomedical scientists, there is a great deal of controversy over the nature of race, the relevance of racial categories for research, and the proper methods of using racial variables. This article argues that researchers and scholars should avoid a binary-type argument, in which the question is whether to use race always or never. Researchers should instead focus on developing standards for when and how to use racial variables. The article then discusses 1 context, criminology, in which the use of racial variables in behavioral genetics research could be particularly problematic. If genetic studies of criminalized behavior use forensic DNA databanks or forensic genetic profiles, they will be confounded by the many racial biases of the law enforcement and penal system.
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Affiliation(s)
- Pilar Ossorio
- Department of Medical History and Bioethics, University of Wisconsin--Madison, Madison, WI 53706-1399, USA.
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Forensic genetics and ethical, legal and social implications beyond the clinic. Nat Genet 2004; 36:S8-12. [DOI: 10.1038/ng1594] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2004] [Accepted: 09/09/2004] [Indexed: 11/08/2022]
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Abstract
Sherlock Holmes said "it has long been an axiom of mine that the little things are infinitely the most important", but never imagined that such a little thing, the DNA molecule, could become perhaps the most powerful single tool in the multifaceted fight against crime. Twenty years after the development of DNA fingerprinting, forensic DNA analysis is key to the conviction or exoneration of suspects and the identification of victims of crimes, accidents and disasters, driving the development of innovative methods in molecular genetics, statistics and the use of massive intelligence databases.
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Affiliation(s)
- Mark A Jobling
- Department of Genetics, University of Leicester, University Road, Leicester LE1 7RH, United Kingdom.
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Yuasa I, Umetsu K, Watanabe G, Nakamura H, Endoh M, Irizawa Y. MATP polymorphisms in Germans and Japanese: the L374F mutation as a population marker for Caucasoids. Int J Legal Med 2004; 118:364-6. [PMID: 15455243 DOI: 10.1007/s00414-004-0490-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2004] [Accepted: 09/09/2004] [Indexed: 10/26/2022]
Abstract
Inference of the population and ancestry to which an individual belongs is important in forensic individualization and personal identification. In this study, five polymorphisms of the membrane-associated transporter protein (MATP) gene were investigated in German and Japanese populations. The L374F mutation was present at an allele frequency as high as 0.96 in the German population, whereas it was completely absent in the Japanese population. This extreme difference in allele frequency suggests that the L374F mutation is valuable as a population and ancestry informative marker for Caucasoids.
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Affiliation(s)
- Isao Yuasa
- Division of Legal Medicine Faculty of Medicine, Tottori University, 683-8503 Yonago, Japan.
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