51
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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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52
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Performance of ancestry-informative SNP and microhaplotype markers. Forensic Sci Int Genet 2019; 43:102141. [PMID: 31442930 DOI: 10.1016/j.fsigen.2019.102141] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 07/21/2019] [Accepted: 08/07/2019] [Indexed: 11/21/2022]
Abstract
The use of microhaplotypes (MHs) for ancestry inference has added to an increasing number of ancestry-informative markers (AIMs) for forensic application that includes autosomal single nucleotide polymorphisms (SNPs) and insertions/deletions (indels). This study compares bi-allelic and tri-allelic SNPs as well as MH markers for their ability to differentiate African, European, South Asian, East Asian, and American population groups from the 1000 Genomes Phase 3 database. A range of well-established metrics were applied to rank each marker according to the population differentiation potential they measured. These comprised: absolute allele frequency differences (δ); Rosenberg's informativeness for (ancestry) assignment (In); the fixation index (FST); and the effective number of alleles (Ae). A panel consisting of all three marker types resulted in the lowest mean divergence per population per individual (MDPI = 2.16%) when selected by In. However, when marker types were not mixed, MHs were the highest performing markers by most metrics (MDPI < 4%) for differentiation between the five continental populations.
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53
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Ancestry informative markers (AIMs) for Korean and other East Asian and South East Asian populations. Int J Legal Med 2019; 133:1711-1719. [DOI: 10.1007/s00414-019-02129-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Accepted: 07/26/2019] [Indexed: 01/28/2023]
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54
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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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55
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England R, Harbison S. A review of the method and validation of the MiSeq FGx™ Forensic Genomics Solution. ACTA ACUST UNITED AC 2019. [DOI: 10.1002/wfs2.1351] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Ryan England
- Forensic Science Program, School of Chemical Sciences University of Auckland Auckland New Zealand
| | - Sallyann Harbison
- Institute of Environmental Science and Research Ltd Auckland New Zealand
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56
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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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57
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Hollard C, Ausset L, Chantrel Y, Jullien S, Clot M, Faivre M, Suzanne É, Pène L, Laurent FX. Automation and developmental validation of the ForenSeq™ DNA Signature Preparation kit for high-throughput analysis in forensic laboratories. Forensic Sci Int Genet 2019; 40:37-45. [DOI: 10.1016/j.fsigen.2019.01.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 11/30/2018] [Accepted: 01/30/2019] [Indexed: 01/10/2023]
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58
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Zhao S, Shi CM, Ma L, Liu Q, Liu Y, Wu F, Chi L, Chen H. AIM-SNPtag: A computationally efficient approach for developing ancestry-informative SNP panels. Forensic Sci Int Genet 2019; 38:245-253. [DOI: 10.1016/j.fsigen.2018.10.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 10/03/2018] [Accepted: 10/23/2018] [Indexed: 01/13/2023]
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59
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Esposito U, Das R, Syed S, Pirooznia M, Elhaik E. Ancient Ancestry Informative Markers for Identifying Fine-Scale Ancient Population Structure in Eurasians. Genes (Basel) 2018; 9:E625. [PMID: 30545160 PMCID: PMC6316245 DOI: 10.3390/genes9120625] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 12/05/2018] [Accepted: 12/10/2018] [Indexed: 12/23/2022] Open
Abstract
The rapid accumulation of ancient human genomes from various areas and time periods potentially enables the expansion of studies of biodiversity, biogeography, forensics, population history, and epidemiology into past populations. However, most ancient DNA (aDNA) data were generated through microarrays designed for modern-day populations, which are known to misrepresent the population structure. Past studies addressed these problems by using ancestry informative markers (AIMs). It is, thereby, unclear whether AIMs derived from contemporary human genomes can capture ancient population structures, and whether AIM-finding methods are applicable to aDNA, provided that the high missingness rates in ancient-and oftentimes haploid-DNA can also distort the population structure. Here, we define ancient AIMs (aAIMs) and develop a framework to evaluate established and novel AIM-finding methods in identifying the most informative markers. We show that aAIMs identified by a novel principal component analysis (PCA)-based method outperform all of the competing methods in classifying ancient individuals into populations and identifying admixed individuals. In some cases, predictions made using the aAIMs were more accurate than those made with a complete marker set. We discuss the features of the ancient Eurasian population structure and strategies to identify aAIMs. This work informs the design of single nucleotide polymorphism (SNP) microarrays and the interpretation of aDNA results, which enables a population-wide testing of primordialist theories.
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Affiliation(s)
- Umberto Esposito
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK.
| | - Ranajit Das
- Manipal University, Manipal Centre for Natural Sciences (MCNS), Manipal, Karnataka, 576104, India.
| | - Syakir Syed
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK.
| | - Mehdi Pirooznia
- Bioinformatics and Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA .
| | - Eran Elhaik
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK.
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60
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The QIAGEN 140-locus single-nucleotide polymorphism (SNP) panel for forensic identification using massively parallel sequencing (MPS): an evaluation and a direct-to-PCR trial. Int J Legal Med 2018; 133:677-688. [DOI: 10.1007/s00414-018-1975-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 11/23/2018] [Indexed: 02/04/2023]
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61
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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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62
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Bradbury C, Köttgen A, Staubach F. Off-target phenotypes in forensic DNA phenotyping and biogeographic ancestry inference: A resource. Forensic Sci Int Genet 2018; 38:93-104. [PMID: 30391626 DOI: 10.1016/j.fsigen.2018.10.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 08/27/2018] [Accepted: 10/13/2018] [Indexed: 01/04/2023]
Abstract
With recent advances in DNA sequencing technologies it has become feasible and cost effective to genotype larger marker sets for forensic purposes. Two technologies that make use of the larger marker sets have come into focus in forensic research and applications; inference of biogeographic ancestry (BGA) and forensic DNA phenotyping (FDP). These methods hold the promise to reveal information about a yet unknown perpetrator from a DNA sample. In contrast, DNA-profiling, that is a standard practice in case work, relies on matching DNA-profiles between crime scene material and suspects on a database of DNA-profiles. Markers for DNA-profiling were developed under the premise to reveal as little additional information about the human source of the profile as possible, the rationale being that personal privacy rights have to be balanced against the public interest in solving a crime. The same argument holds for markers used in BGA and FDP; these markers might also reveal information on off-target phenotypes (OTPs), that go beyond BGA and the phenotypes targeted in FDP. In particular, health related OTPs might shift the balance between privacy protection and public interest. However, to our knowledge, there is currently no convenient resource available to incorporate knowledge on OTPs in BGA and FDP assay design and application. In order to provide such a resource, we performed a systematic search for OTPs associated with a comprehensive set of markers (1766 SNPs) used or suggested to be used for BGA inference and FDP. In this set, we identified a relatively small number of 27 SNPs (1.53%) that convey information on diverse health related OTPs such as cancer risk, induced asthma, or risk of alcoholism. Some of these SNPs are commonly used for FDP and BGA across different marker sets. We conclude that the effects of SNP markers used in FDP and BGA on OTPs are currently limited, with few exceptions that should be considered in a balanced decision on assay design and application.
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Affiliation(s)
- Cedric Bradbury
- University College Freiburg, Albert-Ludwigs-University Freiburg, Freiburg, Germany
| | - Anna Köttgen
- Institute of Genetic Epidemiology, Dept. of Biometry, Epidemiology and Medical Bioinformatics, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Fabian Staubach
- Institute of Biology I, Dept. of Evolutionary Biology and Ecology, Albert-Ludwigs-University Freiburg, Freiburg, Germany.
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63
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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: 94] [Impact Index Per Article: 15.7] [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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64
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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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65
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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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66
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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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67
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Chen P, Zhu W, Tong F, Pu Y, Yu Y, Huang S, Li Z, Zhang L, Liang W, Chen F. Identifying novel microhaplotypes for ancestry inference. Int J Legal Med 2018; 133:983-988. [DOI: 10.1007/s00414-018-1881-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 06/15/2018] [Indexed: 01/14/2023]
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68
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Hao WQ, Liu J, Jiang L, Han JP, Wang L, Li JL, Ma Q, Liu C, Wang HJ, Li CX. Exploring the ancestry differentiation and inference capacity of the 28-plex AISNPs. Int J Legal Med 2018; 133:975-982. [PMID: 29882060 DOI: 10.1007/s00414-018-1863-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Accepted: 05/14/2018] [Indexed: 01/05/2023]
Abstract
Inferring an unknown DNA's ancestry using a set of ancestry-informative single nucleotide polymorphisms (SNPs) in forensic science is useful to provide investigative leads. This is especially true when there is no DNA database match or specified suspect. Thus, a set of SNPs with highly robust and balanced differential power is strongly demanded in forensic science. In addition, it is also necessary to build a genotyping database for estimating the ancestry of an individual or an unknown DNA. For the differentiation of Africans, Europeans, East Asians, Native Americans, and Oceanians, the Global Nano set that includes just 31 SNPs was developed by de la Puente et al. Its ability for differentiation and balance was evaluated using the genotype data of the 1000 Genomes Phase III project and the Stanford University HGDP-CEPH. Just 402 samples were genotyped and analyzed as a reference set based on statistical methods. To validate the differentiating capacity using more samples, we developed a single-tube 28-plex SNP assay in which the SNPs were chosen from the 31 allelic loci of the Global AIMs Nano set. Three tri-allelic SNPs used to differentiate mixed-source DNA contribute little to population differentiation and were excluded here. Then, 998 individuals from 21 populations were typed, and these genotypes were combined with the genotype data obtained from 1000 Genomes Phase III and the Stanford University HGDP-CEPH (3090 total samples,43 populations) to estimate the power of this multiplex assay and build a database for the further inference of an individual or an unknown DNA sample in forensic practice.
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Affiliation(s)
- Wei-Qi Hao
- Institute of Forensic Medicine, Southern Medical University, Guangzhou, 510515, Guangdong, China
- Beijing Engineering Research Center of Crime Scene Evidence Examination, National Engineering Laboratory for Forensic Science, Institute of Forensic Science, Beijing, 100038, People's Republic of China
| | - Jing Liu
- Beijing Engineering Research Center of Crime Scene Evidence Examination, National Engineering Laboratory for Forensic Science, Institute of Forensic Science, Beijing, 100038, People's Republic of China
| | - Li Jiang
- Beijing Engineering Research Center of Crime Scene Evidence Examination, National Engineering Laboratory for Forensic Science, Institute of Forensic Science, Beijing, 100038, People's Republic of China
| | - Jun-Ping Han
- Beijing Engineering Research Center of Crime Scene Evidence Examination, National Engineering Laboratory for Forensic Science, Institute of Forensic Science, Beijing, 100038, People's Republic of China
- Technology Department of Chaoyang Sub-bureau, Beijing Public Security Bureau, Beijing, 100102, China
| | - Ling Wang
- Beijing Engineering Research Center of Crime Scene Evidence Examination, National Engineering Laboratory for Forensic Science, Institute of Forensic Science, Beijing, 100038, People's Republic of China
| | - Jiu-Ling Li
- Beijing Engineering Research Center of Crime Scene Evidence Examination, National Engineering Laboratory for Forensic Science, Institute of Forensic Science, Beijing, 100038, People's Republic of China
| | - Quan Ma
- Beijing Engineering Research Center of Crime Scene Evidence Examination, National Engineering Laboratory for Forensic Science, Institute of Forensic Science, Beijing, 100038, People's Republic of China
| | - Chao Liu
- Institute of Forensic Medicine, Southern Medical University, Guangzhou, 510515, Guangdong, China.
- Guangdong Province Key Laboratory of Forensic Genetics, Guangzhou Forensic Science Institute, Guangzhou, 510030, Guangdong, China.
| | - Hui-Jun Wang
- Institute of Forensic Medicine, Southern Medical University, Guangzhou, 510515, Guangdong, China.
| | - Cai-Xia Li
- Beijing Engineering Research Center of Crime Scene Evidence Examination, National Engineering Laboratory for Forensic Science, Institute of Forensic Science, Beijing, 100038, People's Republic of China.
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69
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Yuasa I, Akane A, Yamamoto T, Matsusue A, Endoh M, Nakagawa M, Umetsu K, Ishikawa T, Iino M. Japaneseplex: A forensic SNP assay for identification of Japanese people using Japanese-specific alleles. Leg Med (Tokyo) 2018; 33:17-22. [PMID: 29705644 DOI: 10.1016/j.legalmed.2018.04.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 02/15/2018] [Accepted: 04/23/2018] [Indexed: 11/17/2022]
Abstract
It is sometimes necessary to determine whether a forensic biological sample came from a Japanese person. In this study, we developed a 60-locus SNP assay designed for the differentiation of Japanese people from other East Asians using entirely and nearly Japanese-specific alleles. This multiplex assay consisted of 6 independent PCR reactions followed by single nucleotide extension. The average number and standard deviation of Japanese-specific alleles possessed by an individual were 0.81 ± 0.93 in 108 Koreans from Seoul, 8.87 ± 2.89 in 103 Japanese from Tottori, 17.20 ± 3.80 in 88 Japanese from Okinawa, and 0 in 220 Han Chinese from Wuxi and Changsha. The Koreans had 0-4 Japanese-specific alleles per individual, whereas the Japanese had 4-26 Japanese-specific alleles. Almost all Japanese were distinguished from the Koreans and other people by the factorial correspondence and principal component analyses. The Snipper program was also useful to estimate the degree of Japaneseness. The method described here was successfully applied to the differentiation of Japanese from non-Japanese people in forensic cases. This Japanese-specific SNP assay was named Japaneseplex.
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Affiliation(s)
- Isao Yuasa
- Division of Legal Medicine, Faculty of Medicine, Tottori University, Yonago 683-8503, Japan.
| | - Atsushi Akane
- Department of Legal Medicine, Kansai Medical University, Hirakata, Japan
| | - Toshimichi Yamamoto
- Department of Legal Medicine and Bioethics, Nagoya University School of Medicine, Nagoya, Japan
| | - Aya Matsusue
- Department of Forensic Medicine, Fukuoka University School of Medicine, Fukuoka, Japan
| | - Minoru Endoh
- Division of Legal Medicine, Faculty of Medicine, Tottori University, Yonago 683-8503, Japan
| | - Mayumi Nakagawa
- Department of Pathobiological Science and Technology, Faculty of Medicine, Tottori University, Yonago, Japan
| | - Kazuo Umetsu
- Department of Forensic Medicine, Yamagata University School of Medicine, Yamagata, Japan
| | - Takaki Ishikawa
- Department of Legal Medicine, Osaka City University Medical School, Osaka, Japan
| | - Morio Iino
- Division of Legal Medicine, Faculty of Medicine, Tottori University, Yonago 683-8503, Japan
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70
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Shraga R, Yarnall S, Elango S, Manoharan A, Rodriguez SA, Bristow SL, Kumar N, Niknazar M, Hoffman D, Ghadir S, Vassena R, Chen SH, Hershlag A, Grifo J, Puig O. Evaluating genetic ancestry and self-reported ethnicity in the context of carrier screening. BMC Genet 2017; 18:99. [PMID: 29179688 PMCID: PMC5704547 DOI: 10.1186/s12863-017-0570-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 11/16/2017] [Indexed: 11/10/2022] Open
Abstract
Background Current professional society guidelines recommend genetic carrier screening be offered on the basis of ethnicity, or when using expanded carrier screening panels, they recommend to compute residual risk based on ethnicity. We investigated the reliability of self-reported ethnicity in 9138 subjects referred to carrier screening. Self-reported ethnicity gathered from test requisition forms and during post-test genetic counseling, and genetic ancestry predicted by a statistical model, were compared for concordance. Results We identified several discrepancies between the two sources of self-reported ethnicity and genetic ancestry. Only 30.3% of individuals who indicated Mediterranean ancestry during consultation self-reported this on requisition forms. Additionally, the proportion of individuals who reported Southeast Asian but were estimated to have a different genetic ancestry was found to depend on the source of self-report. Finally, individuals who reported Latin American demonstrated a high degree of ancestral admixture. As a result, carrier rates and residual risks provided for patient decision-making are impacted if using self-reported ethnicity. Conclusion Our analysis highlights the unreliability of ethnicity classification based on patient self-reports. We recommend the routine use of pan-ethnic carrier screening panels in reproductive medicine. Furthermore, the use of an ancestry model would allow better estimation of carrier rates and residual risks. Electronic supplementary material The online version of this article (10.1186/s12863-017-0570-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Roman Shraga
- Phosphorus, Inc, 25 West 26th St, New York, NY, 10010, USA
| | | | - Sonya Elango
- Sarah Lawrence College, Bronxville, New York, USA
| | | | | | - Sara L Bristow
- Phosphorus, Inc, 25 West 26th St, New York, NY, 10010, USA.,Northwell Fertility, North Shore University Hospital, Manhasset, NY, USA
| | | | | | - David Hoffman
- IVF Florida Reproductive Associates, Margate, FL, USA
| | - Shahin Ghadir
- Department of Obstetrics and Gynecology, The David Geffen School of Medicine at UCLA, California, Los Angeles, USA
| | | | - Serena H Chen
- Institute for Reproductive Medicine and Science, Saint Barnabas Medical Center, Livingston, NJ, USA
| | - Avner Hershlag
- Division of Reproductive Endocrinology, Department of Obstetrics and Gynecology, Hofstra Northwell School of Medicine, Manhasset, NY, USA
| | - Jamie Grifo
- Division of Reproductive Endocrinology & Infertility, Department of Obstetrics and Gynecology, NYU Langone, New York, NY, USA
| | - Oscar Puig
- Phosphorus, Inc, 25 West 26th St, New York, NY, 10010, USA.
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71
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Ramani A, Wong Y, Tan SZ, Shue BH, Syn C. Ancestry prediction in Singapore population samples using the Illumina ForenSeq kit. Forensic Sci Int Genet 2017; 31:171-179. [DOI: 10.1016/j.fsigen.2017.08.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 07/18/2017] [Accepted: 08/11/2017] [Indexed: 11/24/2022]
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72
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What Ancestry Can Tell Us About the Genetic Origins of Inter-Ethnic Differences in Asthma Expression. Curr Allergy Asthma Rep 2017; 16:53. [PMID: 27393700 DOI: 10.1007/s11882-016-0635-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Differences in asthma prevalence have been described across different populations, suggesting that genetic ancestry can play an important role in this disease. In fact, several studies have demonstrated an association between African ancestry with increased asthma susceptibility and severity, higher immunoglobulin E levels, and lower lung function. In contrast, Native American ancestry has been shown to have a protective role for this disease. Genome-wide association studies have allowed the identification of population-specific genetic variants with varying allele frequency among populations. Additionally, the correlation of genetic ancestry at the chromosomal level with asthma and related traits by means of admixture mapping has revealed regions of the genome where ancestry is correlated with the disease. In this review, we discuss the evidence supporting the association of genetic ancestry with asthma susceptibility and asthma-related traits, and highlight the regions of the genome harboring ancestry-specific genetic risk factors.
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73
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Xavier C, Parson W. Evaluation of the Illumina ForenSeq™ DNA Signature Prep Kit – MPS forensic application for the MiSeq FGx™ benchtop sequencer. Forensic Sci Int Genet 2017; 28:188-194. [DOI: 10.1016/j.fsigen.2017.02.018] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Revised: 02/22/2017] [Accepted: 02/28/2017] [Indexed: 01/23/2023]
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74
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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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75
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Sun K, Ye Y, Luo T, Hou Y. Multi-InDel Analysis for Ancestry Inference of Sub-Populations in China. Sci Rep 2016; 6:39797. [PMID: 28004788 PMCID: PMC5177877 DOI: 10.1038/srep39797] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 11/29/2016] [Indexed: 01/03/2023] Open
Abstract
Ancestry inference is of great interest in diverse areas of scientific researches, including the forensic biology, medical genetics and anthropology. Various methods have been published for distinguishing populations. However, few reports refer to sub-populations (like ethnic groups) within Asian populations for the limitation of markers. Several InDel loci located very tightly in physical positions were treated as one marker by us, which is multi-InDel. The multi-InDel shows potential as Ancestry Inference Marker (AIM). In this study, we performed a genome-wide scan for multi-InDels as AIM. After examining the FST distributions in the 1000 Genomes Database, 12 candidates were selected and validated for eastern Asian populations. A multiplexed assay was developed as a panel to genotype 12 multi-InDel markers simultaneously. Ancestry component analysis with STRUCTURE and principal component analysis (PCA) were employed to estimate its capability for ancestry inference. Furthermore, ancestry assignments of trial individuals were conducted. It proved to be very effective when 210 samples from Han and Tibetan individuals in China were tested. The panel consisting of multi-InDel markers exhibited considerable potency in ancestry inference, and was suggested to be applied in forensic practices and genetic population studies.
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Affiliation(s)
- Kuan Sun
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, P.R. China
| | - Yi Ye
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, P.R. China
| | - Tao Luo
- Laboratory of Infection and Immunity, School of Basic Medical Sciences, West China Center of Medical Science, Sichuan University, Chengdu P.R. China
| | - Yiping Hou
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, P.R. China
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76
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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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77
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Hollard C, Keyser C, Delabarde T, Gonzalez A, Vilela Lamego C, Zvénigorosky V, Ludes B. Case report: on the use of the HID-Ion AmpliSeq™ Ancestry Panel in a real forensic case. Int J Legal Med 2016; 131:351-358. [DOI: 10.1007/s00414-016-1425-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 07/19/2016] [Indexed: 12/23/2022]
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78
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Bulbul O, Cherni L, Khodjet-el-khil H, Rajeevan H, Kidd KK. Evaluating a subset of ancestry informative SNPs for discriminating among Southwest Asian and circum-Mediterranean populations. Forensic Sci Int Genet 2016; 23:153-158. [DOI: 10.1016/j.fsigen.2016.04.010] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Revised: 04/22/2016] [Accepted: 04/26/2016] [Indexed: 12/27/2022]
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79
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Soundararajan U, Yun L, Shi M, Kidd KK. Minimal SNP overlap among multiple panels of ancestry informative markers argues for more international collaboration. Forensic Sci Int Genet 2016; 23:25-32. [DOI: 10.1016/j.fsigen.2016.01.013] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 12/24/2015] [Accepted: 01/20/2016] [Indexed: 12/16/2022]
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80
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Eduardoff M, Gross TE, Santos C, de la Puente M, Ballard D, Strobl C, Børsting C, Morling N, Fusco L, Hussing C, Egyed B, Souto L, Uacyisrael J, Syndercombe Court D, Carracedo Á, Lareu MV, Schneider PM, Parson W, Phillips C, Parson W, Phillips C. Inter-laboratory evaluation of the EUROFORGEN Global ancestry-informative SNP panel by massively parallel sequencing using the Ion PGM™. Forensic Sci Int Genet 2016; 23:178-189. [PMID: 27208666 DOI: 10.1016/j.fsigen.2016.04.008] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Revised: 04/14/2016] [Accepted: 04/15/2016] [Indexed: 10/21/2022]
Abstract
The EUROFORGEN Global ancestry-informative SNP (AIM-SNPs) panel is a forensic multiplex of 128 markers designed to differentiate an individual's ancestry from amongst the five continental population groups of Africa, Europe, East Asia, Native America, and Oceania. A custom multiplex of AmpliSeq™ PCR primers was designed for the Global AIM-SNPs to perform massively parallel sequencing using the Ion PGM™ system. This study assessed individual SNP genotyping precision using the Ion PGM™, the forensic sensitivity of the multiplex using dilution series, degraded DNA plus simple mixtures, and the ancestry differentiation power of the final panel design, which required substitution of three original ancestry-informative SNPs with alternatives. Fourteen populations that had not been previously analyzed were genotyped using the custom multiplex and these studies allowed assessment of genotyping performance by comparison of data across five laboratories. Results indicate a low level of genotyping error can still occur from sequence misalignment caused by homopolymeric tracts close to the target SNP, despite careful scrutiny of candidate SNPs at the design stage. Such sequence misalignment required the exclusion of component SNP rs2080161 from the Global AIM-SNPs panel. However, the overall genotyping precision and sensitivity of this custom multiplex indicates the Ion PGM™ assay for the Global AIM-SNPs is highly suitable for forensic ancestry analysis with massively parallel sequencing.
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Affiliation(s)
- M Eduardoff
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - T E Gross
- Institute of Legal Medicine, Faculty of Medicine, University of Cologne, Cologne, Germany
| | - C Santos
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - M de la Puente
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - D Ballard
- Faculty of Life Sciences and Medicine, King's College, London, UK
| | - C Strobl
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - C Børsting
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - N Morling
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - L Fusco
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - C Hussing
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - B Egyed
- Department of Genetics, Faculty of Science, Eötvös Loránd University Budapest, Hungary
| | - L Souto
- Department of Biology, University of Aveiro, Aveiro, Portugal
| | - J Uacyisrael
- Fiji Police Forensic Biology and DNA Laboratory, Nasova, Suva, Fiji
| | | | - Á Carracedo
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Santiago de Compostela, Spain; Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
| | - M V Lareu
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - P M Schneider
- Institute of Legal Medicine, Faculty of Medicine, University of Cologne, Cologne, Germany
| | - W Parson
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria; Forensic Science Program, The Pennsylvania State University, PA, USA
| | - C Phillips
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Santiago de Compostela, Spain.
| | | | - W Parson
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria; Forensic Science Program, The Pennsylvania State University, PA, USA
| | - C Phillips
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Santiago de Compostela, Spain.
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81
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冯 杏, 孙 启, 刘 宏, 魏 以, 杜 蔚, 李 彩, 陈 玲, 刘 超. [Efficiency of 27-plex single nucleotide polymorphism multiplex system for ancestry inference in different populations]. NAN FANG YI KE DA XUE XUE BAO = JOURNAL OF SOUTHERN MEDICAL UNIVERSITY 2016; 37:555-562. [PMID: 28446414 PMCID: PMC6744106 DOI: 10.3969/j.issn.1673-4254.2017.04.24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Indexed: 06/07/2023]
Abstract
OBJECTIVE To validate the efficiency of 27-plex single nucleotide polymorphism (SNP) multiplex system for ancestry inference. METHODS The 27-plex SNP system was validated for its sensitivity and species specificity. A total of 533 samples were collected from African, Southern Chinese Han, China's ethic minorities (Yi, Hui, Miao, Tibet, and Uygur), European, Central Asian, Western Asian, Southern Asian, Southeast Asian and South American populations for clustering analysis of the genotypes by citing 3 representative continental ancestral groups [East Asia (CHB), Europe (CEU), and Africa (YRI)] from HapMap database. RESULTS The system sensitivity is 0.125 ng. Twenty and six genotypes were detected in chimpanzee and monkeys, respectively. Except in rs10496971, no more products were found in other animals. The system was capable of differentiating intercontinental populations but not of distinguishing between East Asian and Southeast Asian population or between Southern Chinese Han population and Chinese Ethnic populations (Hui, Miao, Yi and Tibet). This system achieved a 100% accuracy for intercontinental population source inference for 46 blind test samples. CONCLUSION 27-plex SNPs multiplex system has a high sensitivity and species specificity and can correctly differentiate the ancestry origins of individuals from African, European and East Asian for criminal case investigation. But this system is not capable of distinguishing subpopulation groups and more specific ancestry-informative markers are needed to improve its recognition of Southeast Asian and Chinese ethnic populations.
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Affiliation(s)
- 杏玲 冯
- 南方医科大学法医学院,广东 广州 510515School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China
| | - 启凡 孙
- 公安部物证鉴定中心//现场物证溯源国家工程实验室//法医遗传学公安部重点实验室,北京 100038National Engineering Laboratory for Crime Scene Evidence Examination, Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Beijing 100038, China
| | - 宏 刘
- 广州市刑事科学技术研究所//广东省法医遗传学重点实验室,广东 广州 510030Guangzhou Institute of Criminal Science and Technology/Key Laboratory of Forensic Pathology of Ministry of Public Security, Guangzhou 510030, China
| | - 以梁 魏
- 天津医科大学,天津 300070Tianjin Medical University, Tianjin 300070, China
| | - 蔚安 杜
- 南方医科大学法医学院,广东 广州 510515School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China
| | - 彩霞 李
- 公安部物证鉴定中心//现场物证溯源国家工程实验室//法医遗传学公安部重点实验室,北京 100038National Engineering Laboratory for Crime Scene Evidence Examination, Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Beijing 100038, China
| | - 玲 陈
- 南方医科大学法医学院,广东 广州 510515School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China
| | - 超 刘
- 南方医科大学法医学院,广东 广州 510515School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China
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82
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Wei YL, Sun QF, Li Q, Yi JL, Zhao L, Ou Y, Jiang L, Zhang T, Liu HB, Chen JG, Zhu BF, Ye J, Hu L, Li CX. Genetic structure and differentiation analysis of a Eurasian Uyghur population by use of 27 continental ancestry-informative SNPs. Int J Legal Med 2016; 130:897-903. [DOI: 10.1007/s00414-016-1335-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 02/10/2016] [Indexed: 01/12/2023]
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83
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de la Puente M, Santos C, Fondevila M, Manzo L, Carracedo Á, Lareu MV, Phillips C. The Global AIMs Nano set: A 31-plex SNaPshot assay of ancestry-informative SNPs. Forensic Sci Int Genet 2016; 22:81-88. [PMID: 26881328 DOI: 10.1016/j.fsigen.2016.01.015] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Revised: 01/20/2016] [Accepted: 01/21/2016] [Indexed: 01/06/2023]
Abstract
A 31-plex SNaPshot assay, named 'Global AIMs Nano', has been developed by reassembling the most differentiated markers of the EUROFORGEN Global AIM-SNP set. The SNPs include three tri-allelic loci and were selected with the goal of maintaining a balanced differentiation of: Africans, Europeans, East Asians, Oceanians and Native Americans. The Global AIMs Nano SNP set provides higher divergence between each of the five continental population groups than previous small-scale AIM sets developed for forensic ancestry analysis with SNaPshot. Both of these characteristics minimise potential bias when estimating co-ancestry proportions in individuals with admixed ancestry; more likely to be observed when using markers disproportionately informative for only certain population group comparisons. The optimised multiplex is designed to be easily implemented using standard capillary electrophoresis regimes and has been used to successfully genotype challenging forensic samples from highly degraded material with low level DNA. The ancestry predictive performance of the Global AIMs Nano set has been evaluated by the analysis of samples previously characterised with larger AIM sets.
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Affiliation(s)
- M de la Puente
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Spain
| | - C Santos
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Spain
| | - M Fondevila
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Spain
| | - L Manzo
- 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
| | - M V Lareu
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Spain
| | - C Phillips
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Spain.
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84
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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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85
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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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86
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Zeng X, Chakraborty R, King JL, LaRue B, Moura-Neto RS, Budowle B. Selection of highly informative SNP markers for population affiliation of major US populations. Int J Legal Med 2015; 130:341-52. [DOI: 10.1007/s00414-015-1297-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 11/23/2015] [Indexed: 01/17/2023]
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87
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Yun L, Gao T, Sun K, Gu Y, Hou Y. Comparison of two online algorithm methods for forensic ancestry inference. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2015. [DOI: 10.1016/j.fsigss.2015.09.221] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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88
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Ribeiro J, Pereira V, Kondili A, Miniati P, Børsting C, Morling N. Typing of 111 ancestry informative markers in an Albanian population. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2015. [DOI: 10.1016/j.fsigss.2015.09.050] [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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89
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Phillips C, Amigo J, Carracedo Á, Lareu M. Tetra-allelic SNPs: Informative forensic markers compiled from public whole-genome sequence data. Forensic Sci Int Genet 2015. [DOI: 10.1016/j.fsigen.2015.06.011] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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90
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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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91
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A single-tube 27-plex SNP assay for estimating individual ancestry and admixture from three continents. Int J Legal Med 2015; 130:27-37. [DOI: 10.1007/s00414-015-1183-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Accepted: 03/18/2015] [Indexed: 01/08/2023]
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92
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Strike LT, Couvy-Duchesne B, Hansell NK, Cuellar-Partida G, Medland SE, Wright MJ. Genetics and Brain Morphology. Neuropsychol Rev 2015; 25:63-96. [DOI: 10.1007/s11065-015-9281-1] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 02/08/2015] [Indexed: 12/17/2022]
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93
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Rogalla U, Rychlicka E, Derenko MV, Malyarchuk BA, Grzybowski T. Simple and cost-effective 14-loci SNP assay designed for differentiation of European, East Asian and African samples. Forensic Sci Int Genet 2015; 14:42-9. [DOI: 10.1016/j.fsigen.2014.09.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2014] [Revised: 08/27/2014] [Accepted: 09/14/2014] [Indexed: 12/19/2022]
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94
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Romanini C, Romero M, Salado Puerto M, Catelli L, Phillips C, Pereira R, Gusmão L, Vullo C. Ancestry informative markers: inference of ancestry in aged bone samples using an autosomal AIM-Indel multiplex. Forensic Sci Int Genet 2014; 16:58-63. [PMID: 25531060 DOI: 10.1016/j.fsigen.2014.11.025] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Revised: 10/25/2014] [Accepted: 11/28/2014] [Indexed: 01/22/2023]
Abstract
Ancestry informative markers (AIMs) can be useful to infer ancestry proportions of the donors of forensic evidence. The probability of success typing degraded samples, such as human skeletal remains, is strongly influenced by the DNA fragment lengths that can be amplified and the presence of PCR inhibitors. Several AIM panels are available amongst the many forensic marker sets developed for genotyping degraded DNA. Using a 46 AIM Insertion Deletion (Indel) multiplex, we analyzed human skeletal remains of post mortem time ranging from 35 to 60 years from four different continents (Sub-Saharan Africa, South and Central America, East Asia and Europe) to ascertain the genetic ancestry components. Samples belonging to non-admixed individuals could be assigned to their corresponding continental group. For the remaining samples with admixed ancestry, it was possible to estimate the proportion of co-ancestry components from the four reference population groups. The 46 AIM Indel set was informative enough to efficiently estimate the proportion of ancestry even in samples yielding partial profiles, a frequent occurrence when analyzing inhibited and/or degraded DNA extracts.
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Affiliation(s)
- Carola Romanini
- Forensic DNA Laboratory, Argentinean Forensic Anthropology Team (EAAF) Independencia 644,3A, 5000 Cordoba, Argentina
| | - Magdalena Romero
- Forensic DNA Laboratory, Argentinean Forensic Anthropology Team (EAAF) Independencia 644,3A, 5000 Cordoba, Argentina
| | - Mercedes Salado Puerto
- Forensic DNA Laboratory, Argentinean Forensic Anthropology Team (EAAF) Independencia 644,3A, 5000 Cordoba, Argentina
| | - Laura Catelli
- Forensic DNA Laboratory, Argentinean Forensic Anthropology Team (EAAF) Independencia 644,3A, 5000 Cordoba, Argentina
| | - Christopher Phillips
- Forensic Genetics Unit, Institute of Legal Medicine, Faculty of Medicine, University of Santiago de Compostela, ES-15705 Santiago de Compostela, Galicia, Spain
| | - Rui Pereira
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
| | - Leonor Gusmão
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal; DNA Diagnostic Laboratory (LDD), State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
| | - Carlos Vullo
- Forensic DNA Laboratory, Argentinean Forensic Anthropology Team (EAAF) Independencia 644,3A, 5000 Cordoba, Argentina.
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95
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Kidd KK, Pakstis AJ, Speed WC, Lagacé R, Chang J, Wootton S, Haigh E, Kidd JR. Current sequencing technology makes microhaplotypes a powerful new type of genetic marker for forensics. Forensic Sci Int Genet 2014; 12:215-24. [PMID: 25038325 DOI: 10.1016/j.fsigen.2014.06.014] [Citation(s) in RCA: 135] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Revised: 06/01/2014] [Accepted: 06/23/2014] [Indexed: 11/24/2022]
Abstract
SNPs that are molecularly very close (<10kb) will generally have extremely low recombination rates, much less than 10(-4). Multiple haplotypes will often exist because of the history of the origins of the variants at the different sites, rare recombinants, and the vagaries of random genetic drift and/or selection. Such multiallelic haplotype loci are potentially important in forensic work for individual identification, for defining ancestry, and for identifying familial relationships. The new DNA sequencing capabilities currently available make possible continuous runs of a few hundred base pairs so that we can now determine the allelic combination of multiple SNPs on each chromosome of an individual, i.e., the phase, for multiple SNPs within a small segment of DNA. Therefore, we have begun to identify regions, encompassing two to four SNPs with an extent of <200bp that define multiallelic haplotype loci. We have identified candidate regions and have collected pilot data on many candidate microhaplotype loci. Here we present 31 microhaplotype loci that have at least three alleles, have high heterozygosity, are globally informative, and are statistically independent at the population level. This study of microhaplotype loci (microhaps) provides proof of principle that such markers exist and validates their usefulness for ancestry inference, lineage-clan-family inference, and individual identification. The true value of microhaplotypes will come with sequencing methods that can establish alleles unambiguously, including disentangling of mixtures, because a single sequencing run on a single strand of DNA will encompass all of the SNPs.
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Affiliation(s)
- Kenneth K Kidd
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520-8005, USA.
| | - Andrew J Pakstis
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520-8005, USA
| | - William C Speed
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520-8005, USA
| | - Robert Lagacé
- Human Identification Group, Thermo Fisher Scientific, 180 Oyster Point Blvd., South San Francisco, CA 94080, USA
| | - Joseph Chang
- Human Identification Group, Thermo Fisher Scientific, 180 Oyster Point Blvd., South San Francisco, CA 94080, USA
| | - Sharon Wootton
- Human Identification Group, Thermo Fisher Scientific, 180 Oyster Point Blvd., South San Francisco, CA 94080, USA
| | - Eva Haigh
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520-8005, USA
| | - Judith R Kidd
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520-8005, USA
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