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Köksal Z, Meyer OL, Andersen JD, Gusmão L, Mogensen HS, Pereira V, Børsting C. Pitfalls and challenges with population assignments of individuals from admixed populations: Applying Genogeographer on Brazilian individuals. Forensic Sci Int Genet 2023; 67:102934. [PMID: 37713981 DOI: 10.1016/j.fsigen.2023.102934] [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: 01/09/2023] [Revised: 06/06/2023] [Accepted: 09/06/2023] [Indexed: 09/17/2023]
Abstract
The assignment of individuals to a population can be of importance for the identification of mass disaster victims or criminal offenders in the field of forensic genetics. This assignment is based on biostatistical methods that process data of ancestry informative markers (AIMs), which are selected based on large allele frequency differences between the populations of interest. However, population assignments of individuals with an admixed genetic background are challenging. Admixed individuals are genetic mosaics of chromosomal segments from the parental populations, which may lead to ambiguous or no population assignment. This is problematic since admixture events are a substantial part of human history. In this study, we present challenges of interpreting the evidential weight of population assignments. We used Genogeographer for likelihood ratio (LR) calculations and Brazilians as examples of admixed individuals. Brazilians are a very heterogenous population representing a three-way admixture between Native Americans, Europeans, and Africans. Ancestry informative markers were typed in a total of 589 individuals from Brazil using the Precision ID Ancestry Panel. The Brazilians were assigned to six metapopulations (East Asia, Europe, Middle East, North Africa, South-Central Asia, Sub-Saharan Africa) defined in the Genogeographer software and LRs were calculated if the AIM profile was not an outlier in all metapopulations and simulated two-way (1:1) admixtures of the six metapopulations. Population assignments failed for 55% of the samples. These samples had significantly higher genetic contributions from East Asia, South-Central Asia and Sub-Saharan Africa, and significantly lower genetic contributions from Europe. Most of the individuals with population assignments were assigned to the metapopulations of Middle East (58%) or North Africa (36%), followed by Europe (4%), South-Central Asia (1%), and Sub-Saharan Africa (1%). For 8% of the samples, population assignments were only possible when assignments to simulated two-way (1:1) admixtures of the six metapopulations were considered. Most of these individuals were assigned to two-way admixtures of North Africa, South-Central Asia, or Sub-Saharan Africa. Relatively low median likelihood ratios (LRs<1000) were observed when comparing population likelihoods for Europe, Middle East, North Africa, South-Central Asia, or simulated 1:1 admixtures of these metapopulations. Comparisons including East Asian or Sub-Saharan African populations resulted in larger median LRs (LR>1010). The results suggested that the Precision ID Ancestry Panel provided too little information and that additional markers specifically selected for sub-continental differentiation may be required for accurate population assignment of admixed individuals. Furthermore, a Genogeographer database with additional populations including admixed populations would be advantageous for interpretation of admixed AIM profiles. It would likely increase the number of population assignments and illustrate alternatives to the most likely population, which would be valuable information for the case officer when writing the case report.
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Affiliation(s)
- Zehra Köksal
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Olivia Luxford Meyer
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jeppe Dyrberg Andersen
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Leonor Gusmão
- DNA Diagnostic Laboratory (LDD), State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
| | - Helle Smidt Mogensen
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Vania Pereira
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Claus Børsting
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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Cui W, Nie S, Fang Y, Chen M, Zhao M, Lan Q, Shen C, Zhu B. Insights into AIM-InDel diversities in Yunnan Miao and Hani ethnic groups of China for forensic and population genetic purposes. Hereditas 2022; 159:22. [PMID: 35590349 PMCID: PMC9121611 DOI: 10.1186/s41065-022-00238-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 05/11/2022] [Indexed: 11/10/2022] Open
Abstract
Background Ancestry informative markers are regarded as useful tools for inferring the ancestral information of an individual, which have been widely used in the criminal investigations and population genetic studies. Previously, a multiplex amplification panel containing 39 AIM-InDel loci was constructed. This study aims to investigate the genetic polymorphisms of these 39 AIM-InDel loci in Yunnan Hani and Miao ethnic groups, and to uncover their genetic affinities with reference populations based on the AIM-InDel markers. Materials and methods In this research, 39 AIM-InDel profiles of 203 unrelated Miao individuals and 203 unrelated Hani individuals in Yunnan province of China were acquired. Additionally, we evaluated the genetic polymorphisms of 39 InDel loci in Yunnan Miao and Hani groups. Moreover, the genetic relationships among Yunnan Miao, Hani and reference populations were also clarified based on Nei’s genetic distances, pairwise fixation indexes, principal component analyses, phylogenetic analyses, and STRUCTURE analyses. Results Genetic diversity analyses demonstrated that these InDel loci showed varying degrees of genetic polymorphisms, and could be utilized in forensic identifications in Yunnan Miao and Hani groups. The results of principal component analyses, phylogenetic analyses and Structure analyses revealed that Yunnan Miao and Hani groups had closer genetic relationships with East Asian populations, especially with the populations from Southern China. This research enriched the genetic data of Chinese ethnic minority, and provided ancestral information of Yunnan Miao and Hani groups from the perspective of population genetics. Supplementary Information The online version contains supplementary material available at 10.1186/s41065-022-00238-9.
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Affiliation(s)
- Wei Cui
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, 510515, China.,Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, 510282, China
| | - Shengjie Nie
- School of Forensic Medicine, Kunming Medical University, Kunming, 650500, China
| | - Yating Fang
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Man Chen
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Ming Zhao
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Qiong Lan
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Chunmei Shen
- Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.
| | - Bofeng Zhu
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, 510515, China. .,Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, 510282, China. .,Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, 710004, China.
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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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4
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Truelsen D, Freire-Aradas A, Nazari M, Aliferi A, Ballard D, Phillips C, Morling N, Pereira V, Børsting C. Evaluation of a custom QIAseq targeted DNA panel with 164 ancestry informative markers sequenced with the Illumina MiSeq. Sci Rep 2021; 11:21040. [PMID: 34702940 PMCID: PMC8548529 DOI: 10.1038/s41598-021-99933-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 09/29/2021] [Indexed: 11/08/2022] Open
Abstract
Introduction of new methods requires meticulous evaluation before they can be applied to forensic genetic case work. Here, a custom QIAseq Targeted DNA panel with 164 ancestry informative markers was assessed using the MiSeq sequencing platform. Concordance, sensitivity, and the capability for analysis of mixtures were tested. The assay gave reproducible and nearly concordant results with an input of 10 and 2 ng DNA. Lower DNA input led to an increase in both locus and allele drop-outs, and a higher variation in heterozygote balance. Locus or allele drop-outs in the samples with less than 2 ng DNA input were not necessarily associated with the overall performance of a locus. Thus, the QIAseq assay will be difficult to implement in a forensic genetic setting where the sample material is often scarce and of poor quality. With equal or near equal mixture ratios, the mixture DNA profiles were easily identified by an increased number of imbalanced heterozygotes. For more skewed mixture ratios, the mixture DNA profiles were identified by an increased noise level. Lastly, individuals from Great Britain and the Middle East were investigated. The Middle Eastern individuals showed a greater affinity with South European populations compared to North European populations.
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Affiliation(s)
- D Truelsen
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2100, Copenhagen, Denmark.
| | - A Freire-Aradas
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - M Nazari
- Faculty of Life Sciences and Medicine, King's College, London, UK
| | - A Aliferi
- Faculty of Life Sciences and Medicine, King's College, London, UK
| | - D Ballard
- Faculty of Life Sciences and Medicine, King's College, London, UK
| | - C Phillips
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - N Morling
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2100, Copenhagen, Denmark
- Department of Mathematical Sciences, Aalborg University, 9220, Aalborg, Denmark
| | - V Pereira
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2100, Copenhagen, Denmark
| | - C Børsting
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2100, Copenhagen, Denmark
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Truelsen D, Tvedebrink T, Mogensen HS, Farzad MS, Shan MA, Morling N, Pereira V, Børsting C. Assessment of the effectiveness of the EUROFORGEN NAME and Precision ID Ancestry panel markers for ancestry investigations. Sci Rep 2021; 11:18595. [PMID: 34545122 PMCID: PMC8452675 DOI: 10.1038/s41598-021-97654-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 08/11/2021] [Indexed: 11/08/2022] Open
Abstract
The EUROFORGEN NAME panel is a regional ancestry panel designed to differentiate individuals from the Middle East, North Africa, and Europe. The first version of the panel was developed for the MassARRAY system and included 111 SNPs. Here, a custom AmpliSeq EUROFORGEN NAME panel with 102 of the original 111 loci was used to sequence 1098 individuals from 14 populations from Europe, the Middle East, North Africa, North-East Africa, and South-Central Asia. These samples were also sequenced with a global ancestry panel, the Precision ID Ancestry Panel. The GenoGeographer software was used to assign the AIM profiles to reference populations and calculate the weight of the evidence as likelihood ratios. The combination of the EUROFORGEN NAME and Precision ID Ancestry panels led to fewer ambiguous assignments, especially for individuals from the Middle East and South-Central Asia. The likelihood ratios showed that North African individuals could be separated from European and Middle Eastern individuals using the Precision ID Ancestry Panel. The separation improved with the addition of the EUROFORGEN NAME panel. The analyses also showed that the separation of Middle Eastern populations from European and South-Central Asian populations was challenging even when both panels were applied.
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Affiliation(s)
- D Truelsen
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2100, Copenhagen, Denmark.
| | - T Tvedebrink
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2100, Copenhagen, Denmark
- Department of Mathematical Sciences, Aalborg University, 9220, Aalborg, Denmark
| | - H S Mogensen
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2100, Copenhagen, Denmark
| | - M S Farzad
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2100, Copenhagen, Denmark
| | - M A Shan
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2100, Copenhagen, Denmark
| | - N Morling
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2100, Copenhagen, Denmark
- Department of Mathematical Sciences, Aalborg University, 9220, Aalborg, Denmark
| | - V Pereira
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2100, Copenhagen, Denmark
| | - C Børsting
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2100, Copenhagen, Denmark
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Weisz NA, Roberts KA, Hardy WR. Reliability of phenotype estimation and extended classification of ancestry using decedent samples. Int J Legal Med 2021; 135:2221-2233. [PMID: 34436656 DOI: 10.1007/s00414-021-02631-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 06/04/2021] [Indexed: 11/30/2022]
Abstract
The Illumina® MiSeq FGx™, in conjunction with the ForenSeq™ DNA Signature Prep kit, produces genotypes of the CODIS-required short tandem repeats and provides phenotype and biogeographical ancestry estimations via phenotype-informative and ancestry-informative markers, respectively. Although both markers have been validated for use in forensic biology, there is little data to determine the practical utility of these estimations to assist in identifying missing persons using decedent casework samples. The accuracy and utility of phenotypic and ancestral estimations were investigated for 300 samples received by the Los Angeles County Department of Medical Examiner-Coroner. piSNP genotypes were translated into hair and eye colors using the Forenseq™ Universal Analysis Software (UAS) on the MiSeq FGx™ and the HIrisPlex System, and statistical accuracy was evaluated in context with the reported decedent characteristics. Similarly, estimates of each decedent's biogeographical ancestry were compared to assess the efficacy of these markers to predict ancestry correctly. The average UAS and the HIrisPlex system prediction accuracy for brown and blue eyes were 95.3% and 96.2%, respectively. Intermediate eye color could not be predicted with high accuracy using either system. Other than the black hair phenotype reporting an accuracy that exceeded 90% using either system, hair color was also too variable to be predicted with high accuracy. The FROG-kb database distinguishes decedents adequately beyond the Asian, African, European, and Admixed American global ancestries provided by the MiSeq FGx™ UAS PCA plots. FROG-kb correctly identified Middle Eastern, Pacific Islander, Latin American, or Jewish ancestries with accuracies of 70.0%, 81.8%, 73.8%, and 86.7%, respectively.
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Affiliation(s)
- Naomi A Weisz
- School of Criminal Justice and Criminalistics, California State University, Los Angeles, 1800 Paseo Rancho Castilla, Los Angeles, CA, 90032, USA
| | - Katherine A Roberts
- School of Criminal Justice and Criminalistics, California State University, Los Angeles, 1800 Paseo Rancho Castilla, Los Angeles, CA, 90032, USA. .,California Forensic Science Institute, California State University, Los Angeles, 5151 State University Drive, Los Angeles, CA, 90032, USA.
| | - W Reef Hardy
- Human Genomics Unit, Los Angeles County Department of Medical Examiner-Coroner, 1104 N Mission Road, Los Angeles, CA, 90033, USA
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7
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Genetic relationships of Southwest Asian and Mediterranean populations. Forensic Sci Int Genet 2021; 53:102528. [PMID: 34020230 DOI: 10.1016/j.fsigen.2021.102528] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 04/28/2021] [Accepted: 05/01/2021] [Indexed: 11/23/2022]
Abstract
The Southwest Asian, circum-Mediterranean, and Southern European populations (collectively, SWAMSE) together with Northern European populations form one of five "continental" groups of global populations in many analyses of population relationships. This region is of great anthropologic and forensic interest but relationships of large numbers of populations within the region have not been able to be cleanly resolved with autosomal genetic markers. To examine the genetic boundaries to the SWAMSE region and whether internal structure can be detected we have assembled data for a total of 151 separate autosomal genetic markers on populations in this region and other parts of the world for a global set of 95 populations. The markers include 83 ancestry informative SNPs as singletons and 68 microhaplotype loci defined by 204 SNPs. The 151 loci are ancestry informative on a global scale, identifying at least five biogeographic clusters. One of those clusters is a clear grouping of 37 populations containing the SWAMSE plus northern European populations to the exclusion of populations in South Central Asia and populations from farther East. A refined analysis of the 37 populations shows the northern European populations clustering separately from the SWAMSE populations. Within Southwest Asia the Samaritans and Shabaks are distinct outliers. The Yemenite Jews, Saudi, Kuwaiti, Palestinian Arabs, and Southern Tunisians cluster together loosely while the remaining populations from Northern Iraq, Mediterranean Europe, the Caucasus region, and Iran cluster in a more complex graded fashion. The majority of the SWAMSE populations from the mainland of Southwest Asia form a cluster with little internal structure reflecting a very complex history of endogamy and migrations. The set of 151 DNA polymorphisms not only distinguishes major geographical regions globally but can distinguish ancestry to a small degree within geographical regions such as SWAMSE. We discuss forensic characteristics of the polymorphisms and also identify those that rank highest by Rosenberg's In measure for the SWAMSE region populations and for the global set of populations analyzed. DATA AVAILABILITY: Genotypes on all 151 markers for all 3790 individuals typed in the Kidd Lab on the 72 Kidd lab populations have been deposited in the Zenodo archive and can be freely accessed at https://doi.org/10.5281/zenodo.4658892. Some of the data has been made public previously as supplemental files appended to publications. Data for the additional individuals included in the analyses was taken from already public datasets as indicated in the text.
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Evaluation of the Ion AmpliSeq™ PhenoTrivium Panel: MPS-Based Assay for Ancestry and Phenotype Predictions Challenged by Casework Samples. Genes (Basel) 2020; 11:genes11121398. [PMID: 33255693 PMCID: PMC7760956 DOI: 10.3390/genes11121398] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 11/19/2020] [Accepted: 11/22/2020] [Indexed: 12/21/2022] Open
Abstract
As the field of forensic DNA analysis has started to transition from genetics to genomics, new methods to aid in crime scene investigations have arisen. The development of informative single nucleotide polymorphism (SNP) markers has led the forensic community to question if DNA can be a reliable "eye-witness" and whether the data it provides can shed light on unknown perpetrators. We have developed an assay called the Ion AmpliSeq™ PhenoTrivium Panel, which combines three groups of markers: 41 phenotype- and 163 ancestry-informative autosomal SNPs together with 120 lineage-specific Y-SNPs. Here, we report the results of testing the assay's sensitivity and the predictions obtained for known reference samples. Moreover, we present the outcome of a blind study performed on real casework samples in order to understand the value and reliability of the information that would be provided to police investigators. Furthermore, we evaluated the accuracy of admixture prediction in Converge™ Software. The results show the panel to be a robust and sensitive assay which can be used to analyze casework samples. We conclude that the combination of the obtained predictions of phenotype, biogeographical ancestry, and male lineage can serve as a potential lead in challenging police investigations such as cold cases or cases with no suspect.
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9
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Pereira V, Santangelo R, Børsting C, Tvedebrink T, Almeida APF, Carvalho EF, Morling N, Gusmão L. Evaluation of the Precision of Ancestry Inferences in South American Admixed Populations. Front Genet 2020; 11:966. [PMID: 32973885 PMCID: PMC7472784 DOI: 10.3389/fgene.2020.00966] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 07/31/2020] [Indexed: 11/13/2022] Open
Abstract
Ancestry informative markers (AIMs) are used in forensic genetics to infer biogeographical ancestry (BGA) of individuals and may also have a prominent role in future police and identification investigations. In the last few years, many studies have been published reporting new AIM sets. These sets include markers (usually around 100 or less) selected with different purposes and different population resolutions. Regardless of the ability of these sets to separate populations from different continents or regions, the uncertainty associated with the estimates provided by these panels and their capacity to accurately report the different ancestral contributions in individuals of admixed populations has rarely been investigated. This issue is addressed in this study by evaluating different AIM sets. Ancestry inference was carried out in admixed South American populations, both at population and individual levels. The results of ancestry inferences using AIM sets with different numbers of markers among admixed reference populations were compared. To evaluate the performance of the different ancestry panels at the individual level, expected and observed estimates among families and their offspring were compared, considering that (1) the apportionment of ancestry in the offspring should be closer to the average ancestry of the parents, and (2) full siblings should present similar ancestry values. The results obtained illustrate the importance of having a good balance/compromise between not only the number of markers and their ability to differentiate ancestral populations, but also a balanced differentiation among reference groups, to obtain more precise values of genetic ancestry. This work also highlights the importance of estimating errors associated with the use of a limited number of markers. We demonstrate that although these errors have a moderate effect at the population level, they may have an important impact at the individual level. Considering that many AIM-sets are being described for inferences at the individual level and not at the population level, e.g., in association studies or the determination of a suspect's BGA, the results of this work point to the need of a more careful evaluation of the uncertainty associated with the ancestry estimates in admixed populations, when small AIM-sets are used.
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Affiliation(s)
- Vania Pereira
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Roberta Santangelo
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Claus Børsting
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Torben Tvedebrink
- Department of Mathematical Sciences, Aalborg University, Aalborg, Denmark
| | - Ana Paula F Almeida
- DNA Diagnostic Laboratory, State University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Elizeu F Carvalho
- DNA Diagnostic Laboratory, State University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Niels Morling
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Leonor Gusmão
- DNA Diagnostic Laboratory, State University of Rio de Janeiro, Rio de Janeiro, Brazil.,Instituto de Investigação e Inovação em Saúde, i3S, Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
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10
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Liu Y, Jin X, Mei S, Xu H, Zhao C, Lan Q, Xie T, Fang Y, Li S, Zhu B. Insights into the genetic characteristics and population structures of Chinese two Tibetan groups using 35 insertion/deletion polymorphic loci. Mol Genet Genomics 2020; 295:957-968. [PMID: 32333170 DOI: 10.1007/s00438-020-01670-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 03/30/2020] [Indexed: 12/14/2022]
Abstract
Studying the genetic structure of each ethnic group is helpful to clarify the genetic background and trace back to the ethnic origin. Tibetan people have lived in the Qinghai-Tibet Plateau (mean elevation over 4500 m) for generations, and have well adapted to the high-altitude environment. Due to the relatively closed geographical environment, Tibetans have preserved their representative physical characteristics and genetic information, thereby become an important research group in human genetics. In this study, genetic characteristics and population structures of two Tibetan groups (Qinghai Tibetans and Tibet Tibetans) were revealed by 35 insertion/deletion polymorphism (DIP) loci, aiming to provide valuable genetic information for population genetic differentiation analyses and forensic identifications. The combined discrimination power, cumulative exclusion probability and combined match probability of the 35 DIP loci in Qinghai Tibetan and Tibet Tibetan groups were 0.9999999999999945, 0.9988, 5.56623 × 10-15; and 0.9999999999999904, 0.9990, 9.69071 × 10-15, respectively, indicating that the panel possessed a strong capability for Tibetan personal identifications. Population differentiations and genetic relationship analyses among the two studied Tibetan groups and other 27 comparison populations were carried out using the Nei's DA genetic distances, population pairwise genetic distances F-statistics (FST), analysis of molecular variance (AMOVA), phylogenetic tree reconstruction, principal component analysis and STRUCTURE methods. Results demonstrated that the most intimate genetic relationships existed in these two Tibetan groups; and genetic similarities between two Tibetan groups and the populations from East Asia were much stronger than that between the Tibetan groups and other geographical populations. Furthermore, forensic ancestral informativeness assessments suggested that several loci could be regarded as ancestry informative markers inferring individual biogeographic origins as well as contributing to forensic anthropology and population genetic researches.
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Affiliation(s)
- Yanfang Liu
- Multi‑Omics Innovative Research Center of Forensic Identification; Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Xiaoye Jin
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, 710004, China.,Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, 710004, China.,College of Forensic Medicine, Xi'an Jiaotong University Health Science Center, Xi'an, 710061, China
| | - Shuyan Mei
- Multi‑Omics Innovative Research Center of Forensic Identification; Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Hui Xu
- Multi‑Omics Innovative Research Center of Forensic Identification; Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Congying Zhao
- Multi‑Omics Innovative Research Center of Forensic Identification; Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Qiong Lan
- Multi‑Omics Innovative Research Center of Forensic Identification; Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Tong Xie
- Multi‑Omics Innovative Research Center of Forensic Identification; Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Yating Fang
- Multi‑Omics Innovative Research Center of Forensic Identification; Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Shuanglin Li
- Multi‑Omics Innovative Research Center of Forensic Identification; Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Bofeng Zhu
- Multi‑Omics Innovative Research Center of Forensic Identification; Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou, 510515, China. .,Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, 710004, China. .,Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, 710004, China.
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Characterization of ancestry informative markers in the Tigray population of Ethiopia: A contribution to the identification process of dead migrants in the Mediterranean Sea. Forensic Sci Int Genet 2020; 45:102207. [DOI: 10.1016/j.fsigen.2019.102207] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 11/16/2019] [Accepted: 11/19/2019] [Indexed: 01/16/2023]
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12
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Phillips C, McNevin D, Kidd K, Lagacé R, Wootton S, de la Puente M, Freire-Aradas A, Mosquera-Miguel A, Eduardoff M, Gross T, Dagostino L, Power D, Olson S, Hashiyada M, Oz C, Parson W, Schneider P, Lareu M, Daniel R. MAPlex - A massively parallel sequencing ancestry analysis multiplex for Asia-Pacific populations. Forensic Sci Int Genet 2019; 42:213-226. [DOI: 10.1016/j.fsigen.2019.06.022] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Revised: 06/04/2019] [Accepted: 06/26/2019] [Indexed: 11/25/2022]
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13
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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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14
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Pereira V, Freire-Aradas A, Ballard D, Børsting C, Diez V, Pruszkowska-Przybylska P, Ribeiro J, Achakzai NM, Aliferi A, Bulbul O, Carceles MDP, Triki-Fendri S, Rebai A, Court DS, Morling N, Lareu MV, Carracedo Á, Phillips C. Development and validation of the EUROFORGEN NAME (North African and Middle Eastern) ancestry panel. Forensic Sci Int Genet 2019; 42:260-267. [PMID: 31404905 DOI: 10.1016/j.fsigen.2019.06.010] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 06/07/2019] [Accepted: 06/13/2019] [Indexed: 01/06/2023]
Abstract
Inference of biogeographic origin is an important factor in clinical, population and forensic genetics. The information provided by AIMs (Ancestry Informative Markers) can allow the differentiation of major continental population groups, and several AIM panels have been developed for this purpose. However, from these major population groups, Eurasia covers a wide area between two continents that is difficult to differentiate genetically. These populations display a gradual genetic cline from West Europe to South Asia in terms of allele frequency distribution. Although differences have been reported between Europe and South Asia, Middle East populations continue to be a target of further investigations due to the lack of genetic variability, therefore hampering their genetic differentiation from neighboring populations. In the present study, a custom-built ancestry panel was developed to analyze North African and Middle Eastern populations, designated the 'NAME' panel. The NAME panel contains 111 SNPs that have patterns of allele frequency differentiation that can distinguish individuals originating in North Africa and the Middle East when combined with a previous set of 126 Global AIM-SNPs.
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Affiliation(s)
- V Pereira
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Frederik V's Vej 11, DK-2100 Copenhagen, Denmark
| | - A Freire-Aradas
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Spain
| | - D Ballard
- Faculty of Life Sciences and Medicine, King's College, London, UK
| | - C Børsting
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Frederik V's Vej 11, DK-2100 Copenhagen, Denmark
| | - V Diez
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Frederik V's Vej 11, DK-2100 Copenhagen, Denmark
| | - P Pruszkowska-Przybylska
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Frederik V's Vej 11, DK-2100 Copenhagen, Denmark; Department of Anthropology, Faculty of Biology and Environmental Protection, University of Łódź, Poland
| | - J Ribeiro
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Frederik V's Vej 11, DK-2100 Copenhagen, Denmark
| | - N M Achakzai
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Spain
| | - A Aliferi
- Faculty of Life Sciences and Medicine, King's College, London, UK
| | - O Bulbul
- Institute of Forensic Science, Istanbul University, Istanbul, Turkey
| | | | - S Triki-Fendri
- Centre of Biotechnology of Sfax, Bioinformatics Research Group, Sfax, Tunisia
| | - A Rebai
- Centre of Biotechnology of Sfax, Bioinformatics Research Group, Sfax, Tunisia
| | | | - N Morling
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Frederik V's Vej 11, DK-2100 Copenhagen, Denmark
| | - M V Lareu
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Spain
| | - Á Carracedo
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Spain; Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
| | | | - C Phillips
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Spain.
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15
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Shi C, Liu Q, Zhao S, Chen H. Ancestry informative SNP panels for discriminating the major East Asian populations: Han Chinese, Japanese and Korean. Ann Hum Genet 2019; 83:348-354. [DOI: 10.1111/ahg.12320] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 03/21/2019] [Accepted: 04/02/2019] [Indexed: 01/01/2023]
Affiliation(s)
- Cheng‐Min Shi
- CAS Key Laboratory of Genomic and Precision Medicine Beijing Institute of Genomics, Chinese Academy of Sciences Beijing China
| | - Qi Liu
- CAS Key Laboratory of Genomic and Precision Medicine Beijing Institute of Genomics, Chinese Academy of Sciences Beijing China
- University of Chinese Academy of Sciences Beijing China
| | - Shilei Zhao
- CAS Key Laboratory of Genomic and Precision Medicine Beijing Institute of Genomics, Chinese Academy of Sciences Beijing China
- University of Chinese Academy of Sciences Beijing China
| | - Hua Chen
- CAS Key Laboratory of Genomic and Precision Medicine Beijing Institute of Genomics, Chinese Academy of Sciences Beijing China
- CAS Center for Excellence in Animal Evolution and Genetics Chinese Academy of Sciences Kunming China
- University of Chinese Academy of Sciences Beijing China
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16
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Oldoni F, Kidd KK, Podini D. Microhaplotypes in forensic genetics. Forensic Sci Int Genet 2018; 38:54-69. [PMID: 30347322 DOI: 10.1016/j.fsigen.2018.09.009] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 09/21/2018] [Accepted: 09/25/2018] [Indexed: 01/28/2023]
Abstract
Microhaplotype loci (microhaps, MHs) are a novel type of molecular marker of less than 300 nucleotides, defined by two or more closely linked SNPs associated in multiple allelic combinations. The value of these markers is enhanced by massively parallel sequencing (MPS), which allows the sequencing of both parental haplotypes at each of the many multiplexed loci. This review describes the features of these multi-SNP markers and documents their value in forensic genetics, focusing on individualization, biogeographic ancestry inference, and mixture deconvolution. Foreseeable applications also include missing person identification, relationship testing, and medical diagnostic applications. The technique is not restricted to humans.
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Affiliation(s)
- Fabio Oldoni
- Department of Forensic Sciences, The George Washington University, 2100 Foxhall Road NW, Washington, DC, 20007, United States
| | - Kenneth K Kidd
- Yale University School of Medicine, Department of Genetics, 333 Cedar Street, New Haven, CT, 06520, United States
| | - Daniele Podini
- Department of Forensic Sciences, The George Washington University, 2100 Foxhall Road NW, Washington, DC, 20007, United States.
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17
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Bulbul O, Filoglu G. Development of a SNP panel for predicting biogeographical ancestry and phenotype using massively parallel sequencing. Electrophoresis 2018; 39:2743-2751. [DOI: 10.1002/elps.201800243] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 07/18/2018] [Accepted: 07/23/2018] [Indexed: 11/08/2022]
Affiliation(s)
- Ozlem Bulbul
- Institute of Forensic Science; Istanbul University; Istanbul Turkey
| | - Gonul Filoglu
- Institute of Forensic Science; Istanbul University; Istanbul Turkey
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18
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Improving ancestry distinctions among Southwest Asian populations. Forensic Sci Int Genet 2018; 35:14-20. [DOI: 10.1016/j.fsigen.2018.03.010] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 01/10/2018] [Accepted: 03/22/2018] [Indexed: 12/20/2022]
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19
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Gao Z, Chen X, Zhao Y, Zhao X, Zhang S, Yang Y, Wang Y, Zhang J. Forensic genetic informativeness of an SNP panel consisting of 19 multi-allelic SNPs. Forensic Sci Int Genet 2018; 34:49-56. [DOI: 10.1016/j.fsigen.2018.01.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 01/07/2018] [Accepted: 01/26/2018] [Indexed: 11/28/2022]
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20
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Bulbul O, Pakstis AJ, Soundararajan U, Gurkan C, Brissenden JE, Roscoe JM, Evsanaa B, Togtokh A, Paschou P, Grigorenko EL, Gurwitz D, Wootton S, Lagace R, Chang J, Speed WC, Kidd KK. Ancestry inference of 96 population samples using microhaplotypes. Int J Legal Med 2017; 132:703-711. [PMID: 29248957 PMCID: PMC5920014 DOI: 10.1007/s00414-017-1748-6] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 11/20/2017] [Indexed: 11/28/2022]
Abstract
Microhaplotypes have become a new type of forensic marker with a great ability to identify and deconvolute mixtures because massively parallel sequencing (MPS) allows the alleles (haplotypes) of the multi-SNP loci to be determined directly for an individual. As originally defined, a microhaplotype locus is a short segment of DNA with two or more SNPs defining three or more haplotypes. The length is short enough, less than about 300 bp, that the read length of current MPS technology can produce a phase-known sequence of each chromosome of an individual. As part of the discovery phase of our studies, data on 130 microhaplotype loci with estimates of haplotype frequency data on 83 populations have been published. To provide a better picture of global allele frequency variation, we have now tested 13 more populations for 65 of the microhaplotype loci from among those with higher levels of inter-population gene frequency variation, including 8 loci not previously published. These loci provide clear distinctions among 6 biogeographic regions and provide some information distinguishing up to 10 clusters of populations.
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Affiliation(s)
- Ozlem Bulbul
- Institute of Forensic Science, Istanbul University, 34098, Istanbul, Turkey
| | - Andrew J Pakstis
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT, 06520-8005, USA
| | - Usha Soundararajan
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT, 06520-8005, USA
| | - Cemal Gurkan
- Turkish Cypriot DNA Laboratory, Committee on Missing Persons in Cyprus Turkish Cypriot Member Office, 99010 (North Cyprus), Nicosia, Turkey.,Dr. Fazıl Küçük Faculty of Medicine, Eastern Mediterranean University, 99628 (North Cyprus), Famagusta, Turkey
| | - Jane E Brissenden
- Department of Medicine, University of Toronto, Toronto, ON, M5S, Canada
| | - Janet M Roscoe
- Department of Medicine, University of Toronto, Toronto, ON, M5S, Canada.,Department of Medicine, The Scarborough Hospital, Toronto, ON, M1P 2V5, Canada
| | - Baigalmaa Evsanaa
- Department of Nephrology, Mongolian National University of Medical Sciences, Khoroo 1, Ulaanbataar, Mongolia
| | - Ariunaa Togtokh
- Department of Nephrology, Mongolian National University of Medical Sciences, Khoroo 1, Ulaanbataar, Mongolia
| | - Peristera Paschou
- Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | - Elena L Grigorenko
- Developmental Cognitive Neuroscience, University of Houston, Houston, TX, 77204, USA.,Laboratory of Translational Sciences of Human Development, St. Petersburg University, St. Petersburg, 199034, Russian Federation
| | - David Gurwitz
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, 69978, Tel Aviv, Israel
| | - Sharon Wootton
- Human Identification Group, ThermoFisher Scientific, 180 Oyster Point Blvd, South San Francisco, CA, 94080, USA
| | - Robert Lagace
- Human Identification Group, ThermoFisher Scientific, 180 Oyster Point Blvd, South San Francisco, CA, 94080, USA
| | - Joseph Chang
- Human Identification Group, ThermoFisher Scientific, 180 Oyster Point Blvd, South San Francisco, CA, 94080, USA
| | - William C Speed
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT, 06520-8005, USA
| | - Kenneth K Kidd
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT, 06520-8005, USA.
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21
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García O, Ajuriagerra J, Alday A, Alonso S, Pérez J, Soto A, Uriarte I, Yurrebaso I. Frequencies of the precision ID ancestry panel markers in Basques using the Ion Torrent PGM TM platform. Forensic Sci Int Genet 2017; 31:e1-e4. [DOI: 10.1016/j.fsigen.2017.09.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Revised: 09/03/2017] [Accepted: 09/08/2017] [Indexed: 01/13/2023]
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22
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Pereira V, Mogensen HS, Børsting C, Morling N. Evaluation of the Precision ID Ancestry Panel for crime case work: A SNP typing assay developed for typing of 165 ancestral informative markers. Forensic Sci Int Genet 2017; 28:138-145. [DOI: 10.1016/j.fsigen.2017.02.013] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 02/20/2017] [Accepted: 02/23/2017] [Indexed: 11/24/2022]
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23
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A panel of 130 autosomal single-nucleotide polymorphisms for ancestry assignment in five Asian populations and in Caucasians. Forensic Sci Med Pathol 2017; 13:177-187. [DOI: 10.1007/s12024-017-9863-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/27/2017] [Indexed: 10/19/2022]
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