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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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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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Satam H, Joshi K, Mangrolia U, Waghoo S, Zaidi G, Rawool S, Thakare RP, Banday S, Mishra AK, Das G, Malonia SK. Next-Generation Sequencing Technology: Current Trends and Advancements. BIOLOGY 2023; 12:997. [PMID: 37508427 PMCID: PMC10376292 DOI: 10.3390/biology12070997] [Citation(s) in RCA: 82] [Impact Index Per Article: 82.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 07/09/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023]
Abstract
The advent of next-generation sequencing (NGS) has brought about a paradigm shift in genomics research, offering unparalleled capabilities for analyzing DNA and RNA molecules in a high-throughput and cost-effective manner. This transformative technology has swiftly propelled genomics advancements across diverse domains. NGS allows for the rapid sequencing of millions of DNA fragments simultaneously, providing comprehensive insights into genome structure, genetic variations, gene expression profiles, and epigenetic modifications. The versatility of NGS platforms has expanded the scope of genomics research, facilitating studies on rare genetic diseases, cancer genomics, microbiome analysis, infectious diseases, and population genetics. Moreover, NGS has enabled the development of targeted therapies, precision medicine approaches, and improved diagnostic methods. This review provides an insightful overview of the current trends and recent advancements in NGS technology, highlighting its potential impact on diverse areas of genomic research. Moreover, the review delves into the challenges encountered and future directions of NGS technology, including endeavors to enhance the accuracy and sensitivity of sequencing data, the development of novel algorithms for data analysis, and the pursuit of more efficient, scalable, and cost-effective solutions that lie ahead.
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Affiliation(s)
- Heena Satam
- miBiome Therapeutics, Mumbai 400102, India; (H.S.); (K.J.); (U.M.); (S.W.); (G.Z.); (S.R.)
| | - Kandarp Joshi
- miBiome Therapeutics, Mumbai 400102, India; (H.S.); (K.J.); (U.M.); (S.W.); (G.Z.); (S.R.)
| | - Upasana Mangrolia
- miBiome Therapeutics, Mumbai 400102, India; (H.S.); (K.J.); (U.M.); (S.W.); (G.Z.); (S.R.)
| | - Sanober Waghoo
- miBiome Therapeutics, Mumbai 400102, India; (H.S.); (K.J.); (U.M.); (S.W.); (G.Z.); (S.R.)
| | - Gulnaz Zaidi
- miBiome Therapeutics, Mumbai 400102, India; (H.S.); (K.J.); (U.M.); (S.W.); (G.Z.); (S.R.)
| | - Shravani Rawool
- miBiome Therapeutics, Mumbai 400102, India; (H.S.); (K.J.); (U.M.); (S.W.); (G.Z.); (S.R.)
| | - Ritesh P. Thakare
- Department of Molecular Cell and Cancer Biology, UMass Chan Medical School, Worcester, MA 01605, USA; (R.P.T.); (S.B.); (A.K.M.)
| | - Shahid Banday
- Department of Molecular Cell and Cancer Biology, UMass Chan Medical School, Worcester, MA 01605, USA; (R.P.T.); (S.B.); (A.K.M.)
| | - Alok K. Mishra
- Department of Molecular Cell and Cancer Biology, UMass Chan Medical School, Worcester, MA 01605, USA; (R.P.T.); (S.B.); (A.K.M.)
| | - Gautam Das
- miBiome Therapeutics, Mumbai 400102, India; (H.S.); (K.J.); (U.M.); (S.W.); (G.Z.); (S.R.)
| | - Sunil K. Malonia
- Department of Molecular Cell and Cancer Biology, UMass Chan Medical School, Worcester, MA 01605, USA; (R.P.T.); (S.B.); (A.K.M.)
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Hołub K, Malyarchuk BA, Derenko MV, Kovačević-Grujičić N, Stevanović M, Drakulić D, Davidović TG, Grzybowski T. Verification of insertion-deletion markers (InDels) and microsatellites (STRs) as subsidiary tools for inferring Slavic population ancestry. ARCHIVES OF FORENSIC MEDICINE AND CRIMINOLOGY 2023. [DOI: 10.4467/16891716amsik.22.015.17393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023] Open
Abstract
Genetic markers for the prediction of biogeographical ancestry have proved to be effective tools for law enforcement agencies for many years now. In this study, we attempted to assess the potential of insertion-deletion markers (InDel) and microsatellites (STRs) as subsidiary polymorphisms for inference of Slavic population ancestry. For that purpose, we genotyped Slavic-speaking populations samples from Belarus, the Czech Republic, Poland, Serbia, Ukraine and Russia in 46 InDels and 15 STRs by PCR and capillary electrophoresis and analyzed for between-population differentiation with the use of distance-based methods (FST, principal component analysis and multidimensional scaling). Additionally, we studied a sample from a Polish individual of well-documented genealogy whose biogeographic ancestry had previously been inferred by commercial genomic services using autosomal single nucleotide polymorphisms (SNPs), mitochondrial DNA and Y-SNP markers. For comparative purposes, we used genotype data collected in the “forInDel” browser and allele frequencies from previously published papers. The results obtained for InDels and STRs show that the Slavic populations constitute a genetically homogeneous group, with the exception of the Czechs differing clearly from the other tested populations. The analysis of the known Polish sample in the Snipper application proves the usefulness of the InDel markers on the continental level only. Conversely, microsatellites not only improve prediction, but are also informative if considered as an independent set of ancestry markers.
Weryfikacja markerów insercyjno-delecyjnych (InDels) i mikrosatelitarnych (STR) jako narzędzi pomocniczych do wnioskowania o pochodzeniu populacji słowiańskiej
Markery genetyczne do przewidywania pochodzenia biogeograficznego od wielu lat okazują się skutecznymi narzędziami dla organów ścigania. W tym badaniu podjęliśmy próbę oceny potencjału markerów insercyjno-delecyjnych (InDel) i mikrosatelitarnych (STR) jako pomocniczych polimorfizmów do wnioskowania o pochodzeniu populacji słowiańskiej. W tym celu genotypowaliśmy próbki populacji słowiańskojęzycznych z Białorusi, Czech, Polski, Serbii, Ukrainy i Rosji w w zakresie 46 markerów InDel oraz 15 loci STR za pomocą PCR i elektroforezy kapilarnej oraz analizowaliśmy pod kątem różnicowania między populacjami za pomocą metod bazujących na dystansach genetycznych (FST, analiza głównych składowych i skalowanie wielowymiarowe). Dodatkowo zbadaliśmy próbkę mężczyzny z populacji polskiej o dobrze udokumentowanej genealogii, którego pochodzenie biogeograficzne zostało wcześniej ustalone przez komercyjne usługi genomiczne przy użyciu autosomalnych polimorfizmów pojedynczych nukleotydów (SNP), mitochondrialnego DNA i markerów Y-SNP. Do celów porównawczych wykorzystaliśmy dane genotypowe zebrane w przeglądarce „forInDel” i częstości alleli z wcześniej opublikowanych artykułów. Uzyskane wyniki dla InDels i STR wskazują, że populacje słowiańskie stanowią grupę genetycznie jednorodną, z wyjątkiem Czechów wyraźnie różniących się od pozostałych badanych populacji. Analiza znanej polskiej próbki w aplikacji Snipper dowodzi przydatności markerów InDel jedynie na poziomie kontynentalnym. Z kolei, mikrosatelity nie tylko poprawiają wyniki predykcji, ale są informatywne jako niezależny zestaw markerów pochodzenia biogeograficznego.
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Affiliation(s)
- Karolina Hołub
- Department of Forensic Medicine, The Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Bydgoszcz, Poland
| | - Boris A. Malyarchuk
- Institute of Biological Problems of the North, Far-East Branch of the Russian Academy of Sciences, Magadan, Russia
| | - Miroslava V. Derenko
- Institute of Biological Problems of the North, Far-East Branch of the Russian Academy of Sciences, Magadan, Russia
| | | | - Milena Stevanović
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia; Serbian Academy of Sciences and Arts, Belgrade, Serbia; Faculty of Biology, University of Belgrade, Belgrade, Serbia
| | | | - Tomasz Grzybowski Davidović
- Institute for Biological Research “Siniša Stanković”, National Institute of Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Tomasz Grzybowski
- Department of Forensic Medicine, Division of Molecular & Forensic Genetics, Faculty of Medicine, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Poland
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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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Barbarić L, Horjan-Zanki I. Challenges in the recovery of the genetic data from human remains found on the Western Balkan migration route. Int J Legal Med 2023; 137:181-193. [PMID: 35449468 DOI: 10.1007/s00414-022-02829-7] [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: 07/30/2021] [Accepted: 04/13/2022] [Indexed: 01/11/2023]
Abstract
Traditional DNA-based identification of human remains relies on the system of matching STR profile of the deceased with the family references or antemortem samples. In forensic cases without any available samples for the comparison, the body remains unidentified. The aim of this study was to assess the applicability of massively parallel sequencing (MPS) approach in the forensic cases of five drowned individuals recovered on the Western Balkan migration route. Besides capillary electrophoresis (CE)-based genetic profiling (aSTR, Y STR, and mitochondrial control region sequencing) of postmortem samples, we applied ForenSeq DNA Signature Prep Kit/Primer Mix B on MiSeqFGx platform and concomitant ForenSeq Universal Analysis (UAS) software. The assay showed high reproducibility and complete concordance with CE-based data except in locus DYF387S1. Allele and locus drop was evident in 2.9% of total SNPs that slightly reduced the completeness of the data. We endeavored to predict the phenotype of the tested samples and accurate biogeographical ancestry of European individual. UAS was less informative for the remaining samples assigned to Admixed American cluster. Nevertheless, the application of FROG-kb and Snipper tools along with admixture analysis in STRUCTURE and lineage markers revealed likely Middle Eastern and North African ancestry. We conclude that the combination of the phenotype and biogeographical ancestry predictions, including paternal and maternal genetic ancestry, represent a promising tool for humanitarian identification of dead migrants. Nevertheless, the data interpretation remains a challenging task.
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Affiliation(s)
- Lucija Barbarić
- Forensic Science Centre "Ivan Vučetić, " Ministry of the Interior, Ilica 335, 10000, Zagreb, Croatia.
| | - Ivana Horjan-Zanki
- Forensic Science Centre "Ivan Vučetić, " Ministry of the Interior, Ilica 335, 10000, Zagreb, Croatia
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Carratto TMT, Moraes VMS, Recalde TSF, Oliveira MLGD, Teixeira Mendes-Junior C. Applications of massively parallel sequencing in forensic genetics. Genet Mol Biol 2022; 45:e20220077. [PMID: 36121926 PMCID: PMC9514793 DOI: 10.1590/1678-4685-gmb-2022-0077] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 07/15/2022] [Indexed: 11/22/2022] Open
Abstract
Massively parallel sequencing, also referred to as next-generation sequencing, has positively changed DNA analysis, allowing further advances in genetics. Its capability of dealing with low quantity/damaged samples makes it an interesting instrument for forensics. The main advantage of MPS is the possibility of analyzing simultaneously thousands of genetic markers, generating high-resolution data. Its detailed sequence information allowed the discovery of variations in core forensic short tandem repeat loci, as well as the identification of previous unknown polymorphisms. Furthermore, different types of markers can be sequenced in a single run, enabling the emergence of DIP-STRs, SNP-STR haplotypes, and microhaplotypes, which can be very useful in mixture deconvolution cases. In addition, the multiplex analysis of different single nucleotide polymorphisms can provide valuable information about identity, biogeographic ancestry, paternity, or phenotype. DNA methylation patterns, mitochondrial DNA, mRNA, and microRNA profiling can also be analyzed for different purposes, such as age inference, maternal lineage analysis, body-fluid identification, and monozygotic twin discrimination. MPS technology also empowers the study of metagenomics, which analyzes genetic material from a microbial community to obtain information about individual identification, post-mortem interval estimation, geolocation inference, and substrate analysis. This review aims to discuss the main applications of MPS in forensic genetics.
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Affiliation(s)
- Thássia Mayra Telles Carratto
- Universidade de São Paulo, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Departamento de Química, Laboratório de Pesquisas Forenses e Genômicas, Ribeirão Preto, SP, Brazil
| | - Vitor Matheus Soares Moraes
- Universidade de São Paulo, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Departamento de Química, Laboratório de Pesquisas Forenses e Genômicas, Ribeirão Preto, SP, Brazil
| | | | | | - Celso Teixeira Mendes-Junior
- Universidade de São Paulo, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Departamento de Química, Laboratório de Pesquisas Forenses e Genômicas, Ribeirão Preto, SP, Brazil
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Urtiaga GO, Domingues WB, Komninou ER, Martins AWS, Blödorn EB, Dellagostin EN, Woloski RDS, Pinto LS, Brum CB, Tovo-Rodrigues L, Campos VF. DNA microarray for forensic intelligence purposes: High-density SNP profiles obtained directly from casework-like samples with and without a DNA purification step. Forensic Sci Int 2022; 332:111181. [PMID: 35042181 DOI: 10.1016/j.forsciint.2022.111181] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 12/16/2021] [Accepted: 01/08/2022] [Indexed: 12/14/2022]
Abstract
SNP analyses from a forensic intelligence perspective have proven to be an important tool to restrict the number of suspected offenders and find missing persons. DNA microarray assays have been demonstrated as a potential feature in forensic analysis, like such as forensic genetic genealogy. The objective of this study was to describe the results from DNA microarray assay from saliva samples deposited on a glass surface collected from by a double swab technique, commonly applied in crime scenes. Eighteen samples from the same person were subjected to Infinium® Global Screening Array-24 v1.0 (~642.824 SNP markers) in two different protocols - with or without the DNA purification procedure. The measured genotype was compared with a Consensus Genotype, obtained from standard control samples, and the parameters such as Call Rate and GenCall Scores were evaluated. Results showed that the Call Rate parameter is enough to estimate the probability of obtaining a correct genotype in the SNP assay. Reliable genotypes with a confidence level of more than 90% (at least 90.15%) were observed in Call Rates above 69.41%, regardless of the experimental condition. Our data demonstrate that DNA Microarray from samples collected under conditions such as those found at crime scenes can generate high-density SNP genetic profiles with a confidence level greater than 90%. Enzymatic adjustments and protocol changes may enable DNA microarray assays for crime analysis and investigation purposes eliminating the purification step in the future. Our data suggest that DNA microarray can support criminal investigation teams from a forensic intelligence perspective.
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Affiliation(s)
- Gabriel O Urtiaga
- Laboratório de Genômica Estrutural, Programa de Pós-Graduação em Biotecnologia, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, RS, Brazil; Núcleo de Identificação, Superintendência da Polícia Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - William B Domingues
- Laboratório de Genômica Estrutural, Programa de Pós-Graduação em Biotecnologia, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Eliza R Komninou
- Laboratório de Genômica Estrutural, Programa de Pós-Graduação em Biotecnologia, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Amanda W S Martins
- Laboratório de Genômica Estrutural, Programa de Pós-Graduação em Biotecnologia, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Eduardo B Blödorn
- Laboratório de Genômica Estrutural, Programa de Pós-Graduação em Biotecnologia, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Eduardo N Dellagostin
- Laboratório de Genômica Estrutural, Programa de Pós-Graduação em Biotecnologia, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Rafael Dos S Woloski
- Laboratório de Bioinformática e Proteômica, Programa de Pós-Graduação em Biotecnologia, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Luciano S Pinto
- Laboratório de Bioinformática e Proteômica, Programa de Pós-Graduação em Biotecnologia, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Clarice B Brum
- Programa de Pós-Graduação em Epidemiologia, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Luciana Tovo-Rodrigues
- Programa de Pós-Graduação em Epidemiologia, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Vinicius F Campos
- Laboratório de Genômica Estrutural, Programa de Pós-Graduação em Biotecnologia, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, RS, Brazil.
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Tvedebrink T. Review of the Forensic Applicability of Biostatistical Methods for Inferring Ancestry from Autosomal Genetic Markers. Genes (Basel) 2022; 13:genes13010141. [PMID: 35052480 PMCID: PMC8774801 DOI: 10.3390/genes13010141] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/10/2022] [Accepted: 01/11/2022] [Indexed: 02/01/2023] Open
Abstract
The inference of ancestry has become a part of the services many forensic genetic laboratories provide. Interest in ancestry may be to provide investigative leads or identify the region of origin in cases of unidentified missing persons. There exist many biostatistical methods developed for the study of population structure in the area of population genetics. However, the challenges and questions are slightly different in the context of forensic genetics, where the origin of a specific sample is of interest compared to the understanding of population histories and genealogies. In this paper, the methodologies for modelling population admixture and inferring ancestral populations are reviewed with a focus on their strengths and weaknesses in relation to ancestry inference in the forensic context.
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Affiliation(s)
- Torben Tvedebrink
- Department of Mathematical Sciences, Aalborg University, DK-9220 Aalborg, Denmark;
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, DK-1165 Copenhagen, Denmark
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10
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Frégeau CJ. A multiple predictive tool approach for phenotypic and biogeographical ancestry inferences. CANADIAN SOCIETY OF FORENSIC SCIENCE JOURNAL 2021. [DOI: 10.1080/00085030.2021.2016206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Chantal J. Frégeau
- Royal Canadian Mounted Police, Forensic Science & Identification Services, Biology Policy & Program Support, Ottawa, ON, Canada
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11
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Wienroth M, Granja R, Lipphardt V, Nsiah Amoako E, McCartney C. Ethics as Lived Practice. Anticipatory Capacity and Ethical Decision-Making in Forensic Genetics. Genes (Basel) 2021; 12:1868. [PMID: 34946816 PMCID: PMC8701090 DOI: 10.3390/genes12121868] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 11/19/2021] [Accepted: 11/23/2021] [Indexed: 01/12/2023] Open
Abstract
Greater scrutiny and demands for innovation and increased productivity place pressures on scientists. Forensic genetics is advancing at a rapid pace but can only do so responsibly, usefully, and acceptably within ethical and legal boundaries. We argue that such boundaries require that forensic scientists embrace 'ethics as lived practice'. As a starting point, we critically discuss 'thin' ethics in forensic genetics, which lead to a myopic focus on procedures, and to seeing 'privacy' as the sole ethical concern and technology as a mere tool. To overcome 'thin' ethics in forensic genetics, we instead propose understanding ethics as an intrinsic part of the lived practice of a scientist. Therefore, we explore, within the context of three case studies of emerging forensic genetics technologies, ethical aspects of decision-making in forensic genetics research and in technology use. We discuss the creation, curation, and use of databases, and the need to engage with societal and policing contexts of forensic practice. We argue that open communication is a vital ethical aspect. Adoption of 'ethics as lived practice' supports the development of anticipatory capacity-empowering scientists to understand, and act within ethical and legal boundaries, incorporating the operational and societal impacts of their daily decisions, and making visible ethical decision making in scientific practice.
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Affiliation(s)
- Matthias Wienroth
- Centre for Crime and Policing, Department of Social Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK
| | - Rafaela Granja
- Communication and Society Research Centre, University of Minho, 4710-057 Braga, Portugal
| | - Veronika Lipphardt
- University College Freiburg, Albert-Ludwigs-Universität, 79098 Freiburg, Germany
| | - Emmanuel Nsiah Amoako
- Department of Applied Sciences, University of the West of England, Bristol BS16 1QY, UK
| | - Carole McCartney
- Science & Justice Research Interest Group, Law School, Northumbria University, Newcastle upon Tyne NE1 8ST, UK
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12
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A novel computational strategy to predict the value of the evidence in the SNP-based forensic mixtures. PLoS One 2021; 16:e0247344. [PMID: 34653182 PMCID: PMC8519470 DOI: 10.1371/journal.pone.0247344] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 09/30/2021] [Indexed: 11/24/2022] Open
Abstract
This study introduces a methodology for inferring the weight of the evidence (WoE) in the single nucleotide polymorphism (SNP)-typed DNA mixtures of forensic interest. First, we redefined some algebraic formulae to approach the semi-continuous calculation of likelihoods and likelihood ratios (LRs). To address the allelic dropouts, a peak height ratio index (“h,” an index of heterozygous state plausibility) was incorporated into semi-continuous formulae to act as a proxy for the “split-drop” model of calculation. Second, the original ratio at which a person of interest (POI) has entered into the mixture was inferred by evaluating the DNA amounts conferred by unique genotypes to any possible permutation of any locus of the typing protocol (unique genotypes are genotypes that appear just once in the relevant permutation). We compared this expected ratio (MRex) to all the mixing ratios emerging at all other permutations of the mixture (MRobs) using several (1 - χ2) tests to evaluate the probability of each permutation to exist in the mixture according to quantitative criteria. At the level of each permutation state, we multiplied the (1 - χ2) value to the genotype frequencies and the h index. All the products of all the permutation states were finally summed to give a likelihood value that accounts for three independent properties of the mixtures. Owing to the (1 - χ2) index and the h index, this approach qualifies as a fully continuous methodology of LR calculation. We compared the MRs and LRs emerging from our methodology to those generated by the EuroForMix software ver. 3.0.3. When the true contributors were tested as POIs, our procedure generated highly discriminant LRs that, unlike EuroForMix, never overcame the corresponding single-source LRs. When false contributors were tested as POIs, we obtained a much lower LR value than that from EuroForMix. These two findings indicate that our computational method is more reliable and realistic than EuroForMix.
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13
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Suárez D, Cruz R, Torres M, Mogollón F, Moncada J, Carracedo A, Usaquén W. Ancestry analysis using autosomal SNPs in northern South America, reveals interpretation differences between an AIM panel and an identification panel. Forensic Sci Int 2021; 326:110934. [PMID: 34404021 DOI: 10.1016/j.forsciint.2021.110934] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 07/14/2021] [Accepted: 07/23/2021] [Indexed: 12/20/2022]
Abstract
Current human populations are studied to elucidate their ancestry composition and to obtain reference values for an array of genetic markers for forensic practice. This study compared the 79 ancestry informative markers (AIMs) panel with the SNPforID 52plex set used in forensic identification, using samples belonging to Continental Caribbean populations from Colombia with a high percentage of locals self-determined as Native American descendants. The results show a bias in the individual estimation made with the identification markers, which disregards the Native American ancestry component and overestimates the African ancestry component. Also, the analysis made with the Bayesian Classification Algorithm shows better likelihoods for individual assignment with AIMs than with SNPforID 52plex.
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Affiliation(s)
- Dayana Suárez
- Populations Genetics and Identification Group, Institute of Genetics, National University of Colombia, Bogotá, Colombia.
| | - Raquel Cruz
- CIBERER, Genomic Medicine Group, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - María Torres
- Galician Public Foundation of Genomic Medicine (SERGAS)-CIBERER, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Fernanda Mogollón
- Populations Genetics and Identification Group, Institute of Genetics, National University of Colombia, Bogotá, Colombia
| | - Julie Moncada
- Populations Genetics and Identification Group, Institute of Genetics, National University of Colombia, Bogotá, Colombia
| | - Angel Carracedo
- CIBERER, Genomic Medicine Group, University of Santiago de Compostela, Santiago de Compostela, Spain; Galician Public Foundation of Genomic Medicine (SERGAS)-CIBERER, University of Santiago de Compostela, Santiago de Compostela, Spain; Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Spain
| | - William Usaquén
- Populations Genetics and Identification Group, Institute of Genetics, National University of Colombia, Bogotá, Colombia.
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14
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Kukla-Bartoszek M, Teisseyre P, Pośpiech E, Karłowska-Pik J, Zieliński P, Woźniak A, Boroń M, Dąbrowski M, Zubańska M, Jarosz A, Płoski R, Grzybowski T, Spólnicka M, Mielniczuk J, Branicki W. Searching for improvements in predicting human eye colour from DNA. Int J Legal Med 2021; 135:2175-2187. [PMID: 34259936 PMCID: PMC8523394 DOI: 10.1007/s00414-021-02645-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 06/17/2021] [Indexed: 01/29/2023]
Abstract
Increasing understanding of human genome variability allows for better use of the predictive potential of DNA. An obvious direct application is the prediction of the physical phenotypes. Significant success has been achieved, especially in predicting pigmentation characteristics, but the inference of some phenotypes is still challenging. In search of further improvements in predicting human eye colour, we conducted whole-exome (enriched in regulome) sequencing of 150 Polish samples to discover new markers. For this, we adopted quantitative characterization of eye colour phenotypes using high-resolution photographic images of the iris in combination with DIAT software analysis. An independent set of 849 samples was used for subsequent predictive modelling. Newly identified candidates and 114 additional literature-based selected SNPs, previously associated with pigmentation, and advanced machine learning algorithms were used. Whole-exome sequencing analysis found 27 previously unreported candidate SNP markers for eye colour. The highest overall prediction accuracies were achieved with LASSO-regularized and BIC-based selected regression models. A new candidate variant, rs2253104, located in the ARFIP2 gene and identified with the HyperLasso method, revealed predictive potential and was included in the best-performing regression models. Advanced machine learning approaches showed a significant increase in sensitivity of intermediate eye colour prediction (up to 39%) compared to 0% obtained for the original IrisPlex model. We identified a new potential predictor of eye colour and evaluated several widely used advanced machine learning algorithms in predictive analysis of this trait. Our results provide useful hints for developing future predictive models for eye colour in forensic and anthropological studies.
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Affiliation(s)
- Magdalena Kukla-Bartoszek
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland. .,Malopolska Centre of Biotechnology of the Jagiellonian University, Kraków, Poland.
| | - Paweł Teisseyre
- Institute of Computer Science, Polish Academy of Sciences, Warsaw, Poland.,Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland
| | - Ewelina Pośpiech
- Malopolska Centre of Biotechnology of the Jagiellonian University, Kraków, Poland
| | - Joanna Karłowska-Pik
- Faculty of Mathematics and Computer Science, Nicolaus Copernicus University in Toruń, Toruń, Poland
| | - Piotr Zieliński
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
| | - Anna Woźniak
- Central Forensic Laboratory of the Police, Warsaw, Poland
| | - Michał Boroń
- Central Forensic Laboratory of the Police, Warsaw, Poland
| | - Michał Dąbrowski
- Laboratory of Bioinformatics, Neurobiology Centre, Nencki Institute of Experimental Biology of Polish Academy of Sciences, Warsaw, Poland
| | - Magdalena Zubańska
- Faculty of Law and Administration, Department of Criminology and Forensic Sciences, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland.,Unit of Forensic Sciences, Faculty of Internal Security, Police Academy, Szczytno, Poland
| | - Agata Jarosz
- Malopolska Centre of Biotechnology of the Jagiellonian University, Kraków, Poland
| | - Rafał Płoski
- Department of Medical Genetics, Warsaw Medical University, Warsaw, Poland
| | - Tomasz Grzybowski
- Division of Molecular and Forensic Genetics, Department of Forensic Medicine, Nicolaus Copernicus University in Toruń, Collegium Medicum in Bydgoszcz, Bydgoszcz, Poland
| | | | - Jan Mielniczuk
- Institute of Computer Science, Polish Academy of Sciences, Warsaw, Poland.,Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland
| | - Wojciech Branicki
- Malopolska Centre of Biotechnology of the Jagiellonian University, Kraków, Poland. .,Central Forensic Laboratory of the Police, Warsaw, Poland.
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15
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Frégeau CJ. Validation of the Verogen ForenSeq™ DNA Signature Prep kit/Primer Mix B for phenotypic and biogeographical ancestry predictions using the Micro MiSeq® Flow Cells. Forensic Sci Int Genet 2021; 53:102533. [PMID: 34058534 DOI: 10.1016/j.fsigen.2021.102533] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 03/17/2021] [Accepted: 05/10/2021] [Indexed: 10/21/2022]
Abstract
In anticipation of offering phenotypic and biogeographical ancestry predictions to help resolve cases, the Verogen ForenSeq™ DNA Signature Prep kit/Primer Mix B was evaluated in the context of Micro MiSeq® Flow Cells. These flow cells were determined as the best format for a quick turnaround time response and cost effective approach compared to standard flow cells. The phenotype informative SNPs (piSNPs) and ancestry informative SNPs (aiSNPs) were thoroughly examined through sensitivity, reproducibility and repeatability, concordance, robustness (mock casework) and low level DNA mixture studies purposely selecting individuals with different phenotypes (hair and eye color) when possible and different biogeographical ancestry. SNP locus-specific interpretation thresholds were established for the Universal Analysis Software (UAS) based on surviving alleles and SNP predictor rank to minimize false homozygous genotypes and maximize the information that can be derived from an unknown sample. Dropin alleles' intensity determined an appropriate threshold to minimize false heterozygous SNP genotypes. The selection of inappropriate interpretation thresholds was shown to have major consequences on phenotypic predictions. A 3.2% and 4.8% minor DNA component contribution to a DNA mixture had no impact on ancestry predictions whereas a 9.1% contribution did. The multi-locus SNP genotypes generated using the ForenSeq™ DNA Signature Prep kit/Primer Mix B were shown to be reliable, reproducible, concordant and resulted in predictions that were also reliable, reproducible and concordant based on the limited number of donors (N = 19) used in this study.
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Affiliation(s)
- Chantal J Frégeau
- Royal Canadian Mounted Police, Forensic Science & Identification Services, Biology Policy & Program Support, 1200 Vanier Parkway, Ottawa, Ontario K1A 0R2, Canada.
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16
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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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17
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Atwood L, Raymond J, Sears A, Bell M, Daniel R. From Identification to Intelligence: An Assessment of the Suitability of Forensic DNA Phenotyping Service Providers for Use in Australian Law Enforcement Casework. Front Genet 2021; 11:568701. [PMID: 33510767 PMCID: PMC7835938 DOI: 10.3389/fgene.2020.568701] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 11/20/2020] [Indexed: 12/29/2022] Open
Abstract
Forensic DNA Phenotyping (FDP) is an established but evolving field of DNA testing. It provides intelligence regarding the appearance (externally visible characteristics), biogeographical ancestry and age of an unknown donor and, although not necessarily a requirement for its casework application, has been previously used as a method of last resort in New South Wales (NSW) Police Force investigations. FDP can further assist law enforcement agencies by re-prioritising an existing pool of suspects or generating a new pool of suspects. In recent years, this capability has become ubiquitous with a wide range of service providers offering their expertise to law enforcement and the public. With the increase in the number of providers offering FDP and its potential to direct and target law enforcement resources, a thorough assessment of the applicability of these services was undertaken. Six service providers of FDP were assessed for suitability for NSW Police Force casework based on prediction accuracy, clarity of reporting, limitations of testing, cost and turnaround times. From these assessment criteria, a service provider for the prediction of biogeographical ancestry, hair and eye colour was deemed suitable for use in NSW Police Force casework. Importantly, the study highlighted the need for standardisation of terminology and reporting in this evolving field, and the requirement for interpretation by biologists with specialist expertise to translate the scientific data to intelligence for police investigators.
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Affiliation(s)
- Lauren Atwood
- Science and Research Unit, Forensic Evidence and Technical Services Command, New South Wales Police Force, Sydney, NSW, Australia
| | - Jennifer Raymond
- Science and Research Unit, Forensic Evidence and Technical Services Command, New South Wales Police Force, Sydney, NSW, Australia
| | - Alison Sears
- Science and Research Unit, Forensic Evidence and Technical Services Command, New South Wales Police Force, Sydney, NSW, Australia.,Forensic Analytical and Science Service, New South Wales Health Pathology, Sydney, NSW, Australia
| | - Michael Bell
- Science and Research Unit, Forensic Evidence and Technical Services Command, New South Wales Police Force, Sydney, NSW, Australia
| | - Runa Daniel
- Office of the Chief Forensic Scientist, Victoria Police Forensic Services Department, Melbourne, VIC, Australia
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18
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Ghaiyed AP, Chaseling J, Lea RA, Bernie A, Haupt LM, Griffiths LR, Wright KM. Development of an accurate genomic ancestry prediction strategy to enable the accounting of Australian and Japanese historical military remains. AUST J FORENSIC SCI 2020. [DOI: 10.1080/00450618.2020.1853233] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- A. P. Ghaiyed
- Centre for Genomics and Personalised Health, Genomics Research Centre, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology (QUT), Kelvin Grove, Australia
| | - J. Chaseling
- School of Environment and Science, Griffith University, Nathan, Australia
| | - R. A. Lea
- Centre for Genomics and Personalised Health, Genomics Research Centre, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology (QUT), Kelvin Grove, Australia
| | - A. Bernie
- Unrecovered War Casualties-Army, Australian Defence Force, Russell Offices, Canberra, Australia
| | - L. M. Haupt
- Centre for Genomics and Personalised Health, Genomics Research Centre, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology (QUT), Kelvin Grove, Australia
| | - L. R. Griffiths
- Centre for Genomics and Personalised Health, Genomics Research Centre, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology (QUT), Kelvin Grove, Australia
| | - K. M. Wright
- Unrecovered War Casualties-Army, Australian Defence Force, Russell Offices, Canberra, Australia
- Royal Australian Air Force (RAAF) No 2 Expeditionary Health Squadron, Williamtown, Australia
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19
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Mogensen HS, Tvedebrink T, Børsting C, Pereira V, Morling N. Ancestry prediction efficiency of the software GenoGeographer using a z-score method and the ancestry informative markers in the Precision ID Ancestry Panel. Forensic Sci Int Genet 2020; 44:102154. [DOI: 10.1016/j.fsigen.2019.102154] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 07/25/2019] [Accepted: 08/24/2019] [Indexed: 10/25/2022]
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20
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Queirós F. The visibilities and invisibilities of race entangled with forensic DNA phenotyping technology. J Forensic Leg Med 2019; 68:101858. [DOI: 10.1016/j.jflm.2019.08.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 07/25/2019] [Accepted: 08/10/2019] [Indexed: 11/30/2022]
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21
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Pardo-Seco J, Gómez-Carballa A, Bello X, Martinón-Torres F, Salas A. Biogeographical informativeness of Y-STR haplotypes. Sci Bull (Beijing) 2019; 64:1381-1384. [PMID: 36659691 DOI: 10.1016/j.scib.2019.07.025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Jacobo Pardo-Seco
- Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), Galicia, Spain; Grupo de Investigación en Genética, Vacunas, Infecciones y Pediatría (GENVIP), Universidade de Santiago de Compostela, and Hospital Clínico Universitario de Santiago (SERGAS), Galicia, Spain
| | - Alberto Gómez-Carballa
- Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), Galicia, Spain; Grupo de Investigación en Genética, Vacunas, Infecciones y Pediatría (GENVIP), Universidade de Santiago de Compostela, and Hospital Clínico Universitario de Santiago (SERGAS), Galicia, Spain
| | - Xabier Bello
- Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), Galicia, Spain; Grupo de Investigación en Genética, Vacunas, Infecciones y Pediatría (GENVIP), Universidade de Santiago de Compostela, and Hospital Clínico Universitario de Santiago (SERGAS), Galicia, Spain
| | - Federico Martinón-Torres
- Grupo de Investigación en Genética, Vacunas, Infecciones y Pediatría (GENVIP), Universidade de Santiago de Compostela, and Hospital Clínico Universitario de Santiago (SERGAS), Galicia, Spain
| | - Antonio Salas
- Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), Galicia, Spain; Grupo de Investigación en Genética, Vacunas, Infecciones y Pediatría (GENVIP), Universidade de Santiago de Compostela, and Hospital Clínico Universitario de Santiago (SERGAS), Galicia, Spain.
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22
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Perego UA, Bodner M, Raveane A, Woodward SR, Montinaro F, Parson W, Achilli A. Resolving a 150-year-old paternity case in Mormon history using DTC autosomal DNA testing of distant relatives. Forensic Sci Int Genet 2019; 42:1-7. [DOI: 10.1016/j.fsigen.2019.05.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 05/31/2019] [Accepted: 05/31/2019] [Indexed: 01/01/2023]
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23
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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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24
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Lang M, Liu H, Song F, Qiao X, Ye Y, Ren H, Li J, Huang J, Xie M, Chen S, Song M, Zhang Y, Qian X, Yuan T, Wang Z, Liu Y, Wang M, Liu Y, Liu J, Hou Y. Forensic characteristics and genetic analysis of both 27 Y-STRs and 143 Y-SNPs in Eastern Han Chinese population. Forensic Sci Int Genet 2019; 42:e13-e20. [PMID: 31353318 DOI: 10.1016/j.fsigen.2019.07.011] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 07/20/2019] [Accepted: 07/20/2019] [Indexed: 12/11/2022]
Abstract
Y-chromosome short tandem repeat (Y-STR) and Y-chromosome single nucleotide polymorphism (Y-SNP) frequency distributions provide resources for assessment of male population stratification among world-wide populations. Currently, the Y-STR Haplotype Reference Database (YHRD) contains numerous Y-chromosome haplotype profiles from various populations and countries around the world. However, for many of the recently discovered and already phylogenetically mapped Y-SNPs, the population data are scarce. Herein, the typing of 27 Y-STRs (Yfiler Plus) and 143 Y-SNPs (self-designed Y-SNP panel) was performed on 1269 unrelated males from 11 Han Chinese populations. Haplogroup O-M175 was the most predominant haplogroup in our Han Chinese data, ranging from 67.34% (Henan Han) to 93.16% (Guangdong Han). The highest haplogroup diversity (0.967056) was observed in Heilongjiang Han, with a discrimination capacity (DC) value of 0.3723. The number of alleles at single-copy loci varied from 2 for DYS391 (Guangdong Han) to 16 for DYS518 (Henan Han). For the majority of the populations (8/11), both the haplotype diversity and DC values are 1.0000. Furthermore, genetic differentiations were observed between Northern and Southern Han Chinese. These genetic differences were mainly reflected in haplogroup distribution and frequency, and they were confirmed by statistical analysis.
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Affiliation(s)
- Min Lang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Hai Liu
- The Institute of Forensic Science and Technology, Henan Provincial Public Security Bureau, Zhengzhou 450003, China
| | - Feng Song
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Xianhua Qiao
- The Institute of Forensic Science and Technology, Henan Provincial Public Security Bureau, Zhengzhou 450003, China
| | - Yi Ye
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - He Ren
- Beijing Police College, Beijing 102202, China
| | - Jienan Li
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Jian Huang
- Department of Forensic genetics, Brain Hospital of Hunan Province, Hunan University of Chinese Medicine, Changsha 410007, China
| | - Mingkun Xie
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Shengjie Chen
- Criminal Detection Unit of Qingxiu District Public Security Sub-bureau in Nanning, Nanning 530000, China
| | - Mengyuan Song
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Youfang Zhang
- Department of Forensic Science, Zhejiang Police College, Hangzhou 310053, China
| | - Xiaoqin Qian
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Taoxiu Yuan
- Forensic Science Institute of Zhejiang Di'an Diagnosis Technology Co., Ltd, Hangzhou 310012, China
| | - Zheng Wang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Yuming Liu
- Forensic Science Center Zhongding Guangdong, Zhanjiang 524000, China
| | - Mengge Wang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Yacheng Liu
- Beijing Tongda Shoucheng Institute of Forensic Science, Beijing 100085, China
| | - Jing Liu
- 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.
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25
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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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26
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Barral-Arca R, Pardo-Seco J, Bello X, Martinón-Torres F, Salas A. Ancestry patterns inferred from massive RNA-seq data. RNA (NEW YORK, N.Y.) 2019; 25:857-868. [PMID: 31010885 PMCID: PMC6573782 DOI: 10.1261/rna.070052.118] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 04/16/2019] [Indexed: 05/24/2023]
Abstract
There is a growing body of evidence suggesting that patterns of gene expression vary within and between human populations. However, the impact of this variation in human diseases has been poorly explored, in part owing to the lack of a standardized protocol to estimate biogeographical ancestry from gene expression studies. Here we examine several studies that provide new solid evidence indicating that the ancestral background of individuals impacts gene expression patterns. Next, we test a procedure to infer genetic ancestry from RNA-seq data in 25 data sets where information on ethnicity was reported. Genome data of reference continental populations retrieved from The 1000 Genomes Project were used for comparisons. Remarkably, only eight out of 25 data sets passed FastQC default filters. We demonstrate that, for these eight population sets, the ancestral background of donors could be inferred very efficiently, even in data sets including samples with complex patterns of admixture (e.g., American-admixed populations). For most of the gene expression data sets of suboptimal quality, ancestral inference yielded odd patterns. The present study thus brings a cautionary note for gene expression studies highlighting the importance to control for the potential confounding effect of ancestral genetic background.
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Affiliation(s)
- Ruth Barral-Arca
- Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, of the Instituto de Investigación Sanitaria de Santiago (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), 15706 Galicia, Spain
- Translational Pediatrics and Infectious Diseases Unit, and GENVIP Research Group (www.genvip.org) of the Instituto de Investigación Sanitaria de Santiago (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), 15706 Galicia, Spain
| | - Jacobo Pardo-Seco
- Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, of the Instituto de Investigación Sanitaria de Santiago (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), 15706 Galicia, Spain
- Translational Pediatrics and Infectious Diseases Unit, and GENVIP Research Group (www.genvip.org) of the Instituto de Investigación Sanitaria de Santiago (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), 15706 Galicia, Spain
| | - Xabi Bello
- Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, of the Instituto de Investigación Sanitaria de Santiago (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), 15706 Galicia, Spain
- Translational Pediatrics and Infectious Diseases Unit, and GENVIP Research Group (www.genvip.org) of the Instituto de Investigación Sanitaria de Santiago (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), 15706 Galicia, Spain
| | - Federico Martinón-Torres
- Translational Pediatrics and Infectious Diseases Unit, and GENVIP Research Group (www.genvip.org) of the Instituto de Investigación Sanitaria de Santiago (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), 15706 Galicia, Spain
| | - Antonio Salas
- Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, of the Instituto de Investigación Sanitaria de Santiago (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), 15706 Galicia, Spain
- Translational Pediatrics and Infectious Diseases Unit, and GENVIP Research Group (www.genvip.org) of the Instituto de Investigación Sanitaria de Santiago (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), 15706 Galicia, Spain
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27
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Socio-technical disagreements as ethical fora: Parabon NanoLab’s forensic DNA Snapshot™ service at the intersection of discourses around robust science, technology validation, and commerce. BIOSOCIETIES 2018. [DOI: 10.1057/s41292-018-0138-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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28
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Moriot A, Santos C, Freire-Aradas A, Phillips C, Hall D. Inferring biogeographic ancestry with compound markers of slow and fast evolving polymorphisms. Eur J Hum Genet 2018; 26:1697-1707. [PMID: 29995845 PMCID: PMC6189140 DOI: 10.1038/s41431-018-0215-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 04/23/2018] [Accepted: 06/12/2018] [Indexed: 11/09/2022] Open
Abstract
Bio-geographic ancestry is an area of considerable interest in the medical genetics, anthropology and forensics. Although genome-wide panels are ideal as they provide dense genotyping data, small sets of ancestry informative marker provide a cost-effective way to investigate genetic ancestry and population structure. Here, we investigate the performance of a reduced marker set that combine different types of autosomal markers through haplotype analysis. In particular, recently described DIP-STR markers should offer the advantage of comprising both, low mutation rate Indels (DIPs), to study human history over longer time scale; and high mutation rate STRs, to trace relatively recent demographic events. In this study, we assessed the ability of an initial set of 23 DIP-STRs to distinguish major population groups using the HGDP-CEPH reference samples. The results obtained applying the STRUCTURE algorithm show that the discrimination capacity of the DIP-STRs is comparable to currently used small-scale ancestry informative markers by approaching seven major demographic groups. Yet, the DIP-STRs show an improved success rate in assigning individuals to populations of Europe and Middle East. These data show a remarkable ability of a preliminary set of 23 DIP-STR markers to infer major biogeographic origins. A novel set of DIP-STRs preselected to contain ancestry information should lead to further improvements.
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Affiliation(s)
- Amandine Moriot
- Unité de Génétique Forensique, Centre Universitaire Romand de Médecine Légale, Centre Hospitalier Universitaire Vaudois et Université de Lausanne, Lausanne, Switzerland
| | - Carla Santos
- Forensic Genetics Unit, Institute of Forensic Science, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Ana Freire-Aradas
- Forensic Genetics Unit, Institute of Forensic Science, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Christopher Phillips
- Forensic Genetics Unit, Institute of Forensic Science, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Diana Hall
- Unité de Génétique Forensique, Centre Universitaire Romand de Médecine Légale, Centre Hospitalier Universitaire Vaudois et Université de Lausanne, Lausanne, Switzerland.
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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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Assessment of the Precision ID Ancestry panel. Int J Legal Med 2018; 132:1581-1594. [DOI: 10.1007/s00414-018-1785-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 01/17/2018] [Indexed: 01/28/2023]
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31
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Weight of the evidence of genetic investigations of ancestry informative markers. Theor Popul Biol 2018; 120:1-10. [DOI: 10.1016/j.tpb.2017.12.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 12/11/2017] [Accepted: 12/14/2017] [Indexed: 01/03/2023]
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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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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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34
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Kling D, Egeland T, Piñero MH, Vigeland MD. Evaluating the statistical power of DNA-based identification, exemplified by ‘The missing grandchildren of Argentina’. Forensic Sci Int Genet 2017; 31:57-66. [DOI: 10.1016/j.fsigen.2017.08.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 08/01/2017] [Accepted: 08/04/2017] [Indexed: 11/16/2022]
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35
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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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36
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Ristow PG, Barnes N, Murphy GP, Brown H, Cloete KW, D'Amato ME. Evaluation of the InnoTyper ® 21 genotyping kit in multi-ethnic populations. Forensic Sci Int Genet 2017. [PMID: 28628900 DOI: 10.1016/j.fsigen.2017.06.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
We report the findings of the evaluation of the InnoTyper® 21 genotyping kit for the use of human identification (HID) and paternity testing in South Africa. This novel forensic kit evaluates 20 retrotransposable elements (AC4027, MLS26, ALU79712, NBC216, NBC106, RG148, NBC13, AC2265, MLS09, AC1141, TARBP, AC2305, HS4.69, NBC51, ACA1766, NBC120, NBC10, NBC102, SB19.12 and NBC148) and the Amelogenin locus for sex determination. The evaluation of the genotyping performance showed no significant spectral pull-up for peak heights between 100 and 30,000 RFUs. All loci presented biallelic patterns except the triallelic RG148 locus resulting from a variant insertion allele, named RG148I-1, observed exclusively in the Bantu. The InnoTyper® 21 kit was found to be highly discriminatory between the 507 unrelated individuals of the Afrikaaner, Asian Indian, Coloured, amaXhosa and amaZulu groups. The HID parameters: the CPD ranged between 0.99999987 and 0.9999999845, and the CMP between 1.0335×10-7 and 1.5506×10-8. The paternity parameters: the CPI ranged between 0.0202 and 0.3177, and the CPE between 0.9161 and 0.9749. There were no significant signs of deviations from HWE or linkage disequilibrium (LD) after applying a Bonferroni correction. This kit also showed minor levels of population structure which could differentiate between the African and non-African population groups. Finally, in challenging casework with severely degraded biological material, the InnoTyper® 21 genotyping kit was compatible with GlobalFiler® and Investigator DIPplex® to increase the HID parameters.
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Affiliation(s)
- Peter Gustav Ristow
- Forensic DNA Laboratory, Department of Biotechnology, University of the Western Cape, Bellville, 7535, South Africa; Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen, Denmark
| | - Nicole Barnes
- Forensic DNA Laboratory, Department of Biotechnology, University of the Western Cape, Bellville, 7535, South Africa
| | - Gina Pineda Murphy
- InnoGenomics Technologies, 1441 Canal Street, Suite 307, New Orleans, LA, 70112, United States of America
| | - Hiromi Brown
- InnoGenomics Technologies, 1441 Canal Street, Suite 307, New Orleans, LA, 70112, United States of America
| | - Kevin Wesley Cloete
- Forensic DNA Laboratory, Department of Biotechnology, University of the Western Cape, Bellville, 7535, South Africa
| | - Maria Eugenia D'Amato
- Forensic DNA Laboratory, Department of Biotechnology, University of the Western Cape, Bellville, 7535, South Africa.
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37
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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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38
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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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39
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GlobalFiler ® Express DNA amplification kit in South Africa: Extracting the past from the present. Forensic Sci Int Genet 2016; 24:194-201. [DOI: 10.1016/j.fsigen.2016.07.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Revised: 06/10/2016] [Accepted: 07/11/2016] [Indexed: 01/23/2023]
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40
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Cherni L, Pakstis AJ, Boussetta S, Elkamel S, Frigi S, Khodjet-El-Khil H, Barton A, Haigh E, Speed WC, Ben Ammar Elgaaied A, Kidd JR, Kidd KK. Genetic variation in Tunisia in the context of human diversity worldwide. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2016; 161:62-71. [PMID: 27192181 PMCID: PMC5084816 DOI: 10.1002/ajpa.23008] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 04/22/2016] [Indexed: 11/09/2022]
Abstract
OBJECTIVES North Africa has a complex demographic history of migrations from within Africa, Europe, and the Middle East. However, population genetic studies, especially for autosomal genetic markers, are few relative to other world regions. We examined autosomal markers for eight Tunisian and Libyan populations in order to place them in a global context. MATERIALS AND METHODS Data were collected by TaqMan on 399 autosomal single nucleotide polymorphisms on 331 individuals from Tunisia and Libya. These data were combined with data on the same SNPs previously typed on 2585 individuals from 57 populations from around the world. Where meaningful, close by SNPs were combined into multiallelic haplotypes. Data were evaluated by clustering, principal components, and population tree analyses. For a subset of 102 SNPs, data from the literature on seven additional North African populations were included in analyses. RESULTS Average heterozygosity of the North African populations is high relative to our global samples, consistent with a complex demographic history. The Tunisian and Libyan samples form a discrete cluster in the global and regional views and can be separated from sub-Sahara, Middle East, and Europe. Within Tunisia the Nebeur and Smar are outlier groups. Across North Africa, pervasive East-West geographical patterns were not found. DISCUSSION Known historical migrations and invasions did not displace or homogenize the genetic variation in the region but rather enriched it. Even a small region like Tunisia contains considerable genetic diversity. Future studies across North Africa have the potential to increase our understanding of the historical demographic factors influencing the region. Am J Phys Anthropol 161:62-71, 2016. © 2016 The Authors American Journal of Physical Anthropology Published by Wiley Periodicals, Inc.
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Affiliation(s)
- Lotfi Cherni
- Laboratory of Genetics, Immunology and Human Pathology, Science Faculty of Tunis, University of Tunis El Manar, 2092, Tunis, Tunisia.,High Institute of Biotechnology, University of Monastir, Monastir, 5000, Tunisia
| | - Andrew J Pakstis
- Department of Genetics, Yale University School of Medicine, New Haven, CT, 06520
| | - Sami Boussetta
- Laboratory of Genetics, Immunology and Human Pathology, Science Faculty of Tunis, University of Tunis El Manar, 2092, Tunis, Tunisia
| | - Sarra Elkamel
- Laboratory of Genetics, Immunology and Human Pathology, Science Faculty of Tunis, University of Tunis El Manar, 2092, Tunis, Tunisia
| | - Sabeh Frigi
- Laboratory of Genetics, Immunology and Human Pathology, Science Faculty of Tunis, University of Tunis El Manar, 2092, Tunis, Tunisia
| | - Houssein Khodjet-El-Khil
- Laboratory of Genetics, Immunology and Human Pathology, Science Faculty of Tunis, University of Tunis El Manar, 2092, Tunis, Tunisia
| | - Alison Barton
- Department of Genetics, Yale University School of Medicine, New Haven, CT, 06520
| | - Eva Haigh
- Department of Genetics, Yale University School of Medicine, New Haven, CT, 06520
| | - William C Speed
- Department of Genetics, Yale University School of Medicine, New Haven, CT, 06520
| | - Amel Ben Ammar Elgaaied
- Laboratory of Genetics, Immunology and Human Pathology, Science Faculty of Tunis, University of Tunis El Manar, 2092, Tunis, Tunisia
| | - Judith R Kidd
- Department of Genetics, Yale University School of Medicine, New Haven, CT, 06520
| | - Kenneth K Kidd
- Department of Genetics, Yale University School of Medicine, New Haven, CT, 06520
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41
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Approaching ethical, legal and social issues of emerging forensic DNA phenotyping (FDP) technologies comprehensively: Reply to ‘Forensic DNA phenotyping: Predicting human appearance from crime scene material for investigative purposes’ by Manfred Kayser. Forensic Sci Int Genet 2016; 22:e1-e4. [DOI: 10.1016/j.fsigen.2016.01.010] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Revised: 12/07/2015] [Accepted: 01/16/2016] [Indexed: 11/20/2022]
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Abstract
The author's thoughts and opinions on where the field of forensic DNA testing is headed for the next decade are provided in the context of where the field has come over the past 30 years. Similar to the Olympic motto of 'faster, higher, stronger', forensic DNA protocols can be expected to become more rapid and sensitive and provide stronger investigative potential. New short tandem repeat (STR) loci have expanded the core set of genetic markers used for human identification in Europe and the USA. Rapid DNA testing is on the verge of enabling new applications. Next-generation sequencing has the potential to provide greater depth of coverage for information on STR alleles. Familial DNA searching has expanded capabilities of DNA databases in parts of the world where it is allowed. Challenges and opportunities that will impact the future of forensic DNA are explored including the need for education and training to improve interpretation of complex DNA profiles.
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Affiliation(s)
- John M Butler
- National Institute of Standards and Technology, Gaithersburg, MD, USA
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43
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Brooks A, Creighton EK, Gandolfi B, Khan R, Grahn RA, Lyons LA. SNP Miniplexes for Individual Identification of Random-Bred Domestic Cats. J Forensic Sci 2016; 61:594-606. [PMID: 27122395 PMCID: PMC5019183 DOI: 10.1111/1556-4029.13026] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Revised: 03/13/2015] [Accepted: 06/06/2015] [Indexed: 11/30/2022]
Abstract
Phenotypic and genotypic characteristics of the cat can be obtained from single nucleotide polymorphisms (SNPs) analyses of fur. This study developed miniplexes using SNPs with high discriminating power for random‐bred domestic cats, focusing on individual and phenotypic identification. Seventy‐eight SNPs were investigated using a multiplex PCR followed by a fluorescently labeled single base extension (SBE) technique (SNaPshot®). The SNP miniplexes were evaluated for reliability, reproducibility, sensitivity, species specificity, detection limitations, and assignment accuracy. Six SNPplexes were developed containing 39 intergenic SNPs and 26 phenotypic SNPs, including a sex identification marker, ZFXY. The combined random match probability (cRMP) was 6.58 × 10−19 across all Western cat populations and the likelihood ratio was 1.52 × 1018. These SNPplexes can distinguish individual cats and their phenotypic traits, which could provide insight into crime reconstructions. A SNP database of 237 cats from 13 worldwide populations is now available for forensic applications.
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Affiliation(s)
- Ashley Brooks
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California - Davis, One Shields Avenue, Davis, CA, 95616
| | - Erica K Creighton
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri - Columbia, 1600 East Rollins Street, Columbia, MO, 65211
| | - Barbara Gandolfi
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California - Davis, One Shields Avenue, Davis, CA, 95616.,Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri - Columbia, 1600 East Rollins Street, Columbia, MO, 65211
| | - Razib Khan
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California - Davis, One Shields Avenue, Davis, CA, 95616
| | - Robert A Grahn
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California - Davis, One Shields Avenue, Davis, CA, 95616
| | - Leslie A Lyons
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California - Davis, One Shields Avenue, Davis, CA, 95616.,Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri - Columbia, 1600 East Rollins Street, Columbia, MO, 65211
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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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45
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Pacifiplex : an ancestry-informative SNP panel centred on Australia and the Pacific region. Forensic Sci Int Genet 2016; 20:71-80. [DOI: 10.1016/j.fsigen.2015.10.003] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Revised: 09/22/2015] [Accepted: 10/06/2015] [Indexed: 12/18/2022]
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Santos C, Phillips C, Gomez-Tato A, Alvarez-Dios J, Carracedo Á, Lareu MV. Inference of Ancestry in Forensic Analysis II: Analysis of Genetic Data. Methods Mol Biol 2016; 1420:255-285. [PMID: 27259745 DOI: 10.1007/978-1-4939-3597-0_19] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Three approaches applicable to the analysis of forensic ancestry-informative marker data-STRUCTURE, principal component analysis, and the Snipper Bayesian classification system-are reviewed. Detailed step-by-step guidance is provided for adjusting parameter settings in STRUCTURE with particular regard to their effect when differentiating populations. Several enhancements to the Snipper online forensic classification portal are described, highlighting the added functionality they bring to particular aspects of ancestry-informative SNP analysis in a forensic context.
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Affiliation(s)
- Carla Santos
- Forensic Genetics Unit, Luis Concheiro Institute of Forensic Sciences, Genomic Medicine Group, University of Santiago de Compostela, Galicia, 15782, Spain.
| | - Chris Phillips
- Forensic Genetics Unit, Luis Concheiro Institute of Forensic Sciences, Genomic Medicine Group, University of Santiago de Compostela, Galicia, 15782, Spain
| | - A Gomez-Tato
- Faculty of Mathematics, University of Santiago de Compostela, Galicia, Spain
| | - J Alvarez-Dios
- Faculty of Mathematics, University of Santiago de Compostela, Galicia, 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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Jiang Y, Wang L, Li Z, Zhu J, Peng D, Su Q, Mao J, Wang H, Liang W, Zhang L. A 21-plex DIP panel’s application in multinational Chinese population. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2015. [DOI: 10.1016/j.fsigss.2015.09.212] [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]
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48
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Baeta M, Núñez C, Cardoso S, Palencia-Madrid L, Herrasti L, Etxeberria F, de Pancorbo MM. Digging up the recent Spanish memory: genetic identification of human remains from mass graves of the Spanish Civil War and posterior dictatorship. Forensic Sci Int Genet 2015; 19:272-279. [DOI: 10.1016/j.fsigen.2015.09.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Revised: 07/20/2015] [Accepted: 09/02/2015] [Indexed: 11/15/2022]
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49
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Børsting C, Morling N. Next generation sequencing and its applications in forensic genetics. Forensic Sci Int Genet 2015; 18:78-89. [DOI: 10.1016/j.fsigen.2015.02.002] [Citation(s) in RCA: 268] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Revised: 01/12/2015] [Accepted: 02/11/2015] [Indexed: 12/13/2022]
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50
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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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