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Tomas C, Rodrigues P, Jønck CG, Barekzay Z, Simayijiang H, Pereira V, Børsting C. Performance of a 74-Microhaplotype Assay in Kinship Analyses. Genes (Basel) 2024; 15:224. [PMID: 38397213 PMCID: PMC10888013 DOI: 10.3390/genes15020224] [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: 01/09/2024] [Revised: 02/07/2024] [Accepted: 02/08/2024] [Indexed: 02/25/2024] Open
Abstract
Microhaplotypes (MHs) consisting of multiple SNPs and indels on short stretches of DNA are new and interesting loci for forensic genetic investigations. In this study, we analysed 74 previously defined MHs in two of the populations that our laboratory provides with forensic genetic services, Danes and Greenlanders. In addition to the 229 SNPs that originally made up the 74 MHs, 66 SNPs and 3 indels were identified in the two populations, and 45 of these variants were included in new definitions of the MHs, whereas 24 SNPs were considered rare and of little value for case work. The average effective number of alleles (Ae) was 3.2, 3.0, and 2.6 in Danes, West Greenlanders, and East Greenlanders, respectively. High levels of linkage disequilibrium were observed in East Greenlanders, which reflects the characteristics of this population that has a small size, and signs of admixture and substructure. Pairwise kinship simulations of full siblings, half-siblings, first cousins, and unrelated individuals were performed using allele frequencies from MHs, STRs and SNPs from Danish and Greenlandic populations. The MH panel outperformed the currently used STR and SNP marker sets and was able to differentiate siblings from unrelated individuals with a 0% false positive rate and a 1.1% false negative rate using an LR threshold of 10,000 in the Danish population. However, the panel was not able to differentiate half-siblings or first cousins from unrelated individuals. The results generated in this study will be used to implement MHs as investigative markers for relationship testing in our laboratory.
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Affiliation(s)
| | | | | | | | | | | | - Claus 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; (C.T.); (P.R.); (C.G.J.); (Z.B.); (V.P.)
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Al-Haj-Taib R, Mejri A, Børsting C, Pereira V, Elkamel S, Herrera RJ, Benammar-Elgaaied A, Fadhlaoui-Zid K. Genetic analysis of sixteen autosomal STR loci in three Tunisian populations from Makthar, Nabeul and Sousse. Ann Hum Biol 2022; 48:590-597. [DOI: 10.1080/03014460.2022.2032338] [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)
- Rim Al-Haj-Taib
- Laboratory of Genetics, Immunology and Human Pathologies, Faculty of Science of Tunis, University Tunis El Manar, Tunis, 2092, Tunisia
| | - Abir Mejri
- Laboratory of Genetics, Immunology and Human Pathologies, Faculty of Science of Tunis, University Tunis El Manar, Tunis, 2092, Tunisia
| | - Claus Børsting
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen.
| | - Vania Pereira
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen.
| | - Sarra Elkamel
- Laboratory of Genetics, Immunology and Human Pathologies, Faculty of Science of Tunis, University Tunis El Manar, Tunis, 2092, Tunisia
| | - Rene J. Herrera
- Department of Molecular Biology, Colorado College, Colorado Springs, CO 80903, USA
| | - Amel Benammar-Elgaaied
- Laboratory of Genetics, Immunology and Human Pathologies, Faculty of Science of Tunis, University Tunis El Manar, Tunis, 2092, Tunisia
| | - Karima Fadhlaoui-Zid
- Laboratory of Genetics, Immunology and Human Pathologies, Faculty of Science of Tunis, University Tunis El Manar, Tunis, 2092, Tunisia
- Department of Biology, College of Science, Taibah University, Al Madinah Al Monawarah, Saudi Arabia
- Higher Institute of Biotechnology of Beja, University of Jendouba, Beja, Tunisia
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Muinde JM, Chandra Bhanu DR, Neumann R, Oduor RO, Kanja W, Kimani JK, Mutugi MW, Smith L, Jobling MA, Wetton JH. Geographical and linguistic structure in the people of Kenya demonstrated using 21 autosomal STRs. Forensic Sci Int Genet 2021; 53:102535. [PMID: 34051692 DOI: 10.1016/j.fsigen.2021.102535] [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: 03/07/2021] [Revised: 05/11/2021] [Accepted: 05/16/2021] [Indexed: 11/15/2022]
Abstract
Kenya is a diverse and populous nation that employs DNA evidence in its criminal justice system, and therefore requires reliable information on autosomal STR allele frequency variation across the country and in its many ethnic groups. In order to provide reference data and to assess population structure, we analysed the 21 autosomal STRs in the GlobalFiler multiplex in a sample of 510 indigenous Kenyans representing the country's eight former provinces, 43 of its 47 counties, three main linguistic families and all 29 ethnic groups that each comprise >0.5% of the 2019 census population. The indigenous population originated from successive migrations of Cushitic, Nilotic and Bantu speaking groups who settled in regions that suited their distinctive sustenance lifestyles. Consequently, they now largely reside in a patchwork of communities with strong associations with particular counties and provinces and limited degrees of inter-group marriage, as shown by DNA donors' ancestry details. We found significant genetic differentiation between the three Nilotic language sub-families, with Western Nilotes (the Luo ethnic group) showing greater similarity to the Bantu than the Southern and Eastern Nilotes which themselves showed closer affinity to the Cushitic speakers. This concurs with previous genetic, linguistic and social studies. Comparisons with other African populations also showed that linguistic affiliation is a stronger factor than geography. This study revealed several rare off-ladder alleles whose structure was determined by Sanger sequencing. Among the unusual features that could affect profile interpretation were a deletion of Amelogenin Y but no other forensic marker (autosomal or Y-chromosomal), a triallelic pattern at TPOX and an extremely short SE33 allele falling within the expected size range of D7S820. Compared with the currently implemented Identifiler multiplex, Random Match Probabilities decreased from 6.4 × 10-19 to 3.9 × 10-27. The appreciation of local population structure provided by the geographically and ethnically representative sample in this study highlights the structured genetic landscape of Kenya.
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Affiliation(s)
- Jane Mbithe Muinde
- Department of Biochemistry, Microbiology & Biotechnology, Kenyatta University, Nairobi, Kenya
| | | | - Rita Neumann
- Department of Genetics & Genome Biology, University of Leicester, Leicester, UK
| | - Richard Okoth Oduor
- Department of Biochemistry, Microbiology & Biotechnology, Kenyatta University, Nairobi, Kenya
| | | | | | | | - Lisa Smith
- Department of Criminology, University of Leicester, Leicester, UK
| | - Mark A Jobling
- Department of Genetics & Genome Biology, University of Leicester, Leicester, UK.
| | - Jon H Wetton
- Department of Genetics & Genome Biology, University of Leicester, Leicester, UK.
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Bertoglio B, Grignani P, Di Simone P, Polizzi N, De Angelis D, Cattaneo C, Iadicicco A, Fattorini P, Presciuttini S, Previderè C. Disaster victim identification by kinship analysis: the Lampedusa October 3rd, 2013 shipwreck. Forensic Sci Int Genet 2020; 44:102156. [DOI: 10.1016/j.fsigen.2019.102156] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 08/14/2019] [Accepted: 08/27/2019] [Indexed: 12/30/2022]
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Zieger M, Utz S. A "forensic biobank" to establish comprehensive genetic frequency data for Switzerland. Forensic Sci Int Genet 2019; 40:46-51. [PMID: 30739831 DOI: 10.1016/j.fsigen.2019.02.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 01/10/2019] [Accepted: 02/03/2019] [Indexed: 10/27/2022]
Abstract
Comparatively little knowledge is available about the genetic structure of the Swiss population. Missing allele frequency data for some markers frequently used in forensics and paternity / kinship testing is just one practical aspect of this lack of genetic data. Therefore, in an attempt to fill this gap, we established a biobank of 1198 Swiss blood samples, systematically collected throughout the whole country. For the first time, this collection contains a population sample from the southernmost Italian speaking canton of Ticino. In this article, we share the experiences gained with the sampling procedure. Furthermore we present autosomal allele frequencies for 23 loci and a concordance check between the two multiplex PCR kits GlobalFiler® and PowerPlex® Fusion 6C. Statistical evaluation of the data revealed only small genetic differences among regional subpopulations and among language subgroups. The autosomal allele frequencies can therefore be used for forensics and paternity / kinship testing as a valid nationwide dataset. Additionally, the informative value of the three Y-STR markers included in the PowerPlex® Fusion 6C kit was assessed. We could demonstrate that the 3-loci-haplotype can be very informative, with an average haplotype frequency in the relevant Western European metapopulation of 0.026.
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Affiliation(s)
- Martin Zieger
- Institute of Forensic Medicine, Forensic Molecular Biology Dpt., University of Bern, Sulgenauweg 40, 3007, Bern, Switzerland.
| | - Silvia Utz
- Institute of Forensic Medicine, Forensic Molecular Biology Dpt., University of Bern, Sulgenauweg 40, 3007, Bern, Switzerland.
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Signs of continental ancestry in urban populations of Peru through autosomal STR loci and mitochondrial DNA typing. PLoS One 2018; 13:e0200796. [PMID: 30020992 PMCID: PMC6051651 DOI: 10.1371/journal.pone.0200796] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 07/03/2018] [Indexed: 11/30/2022] Open
Abstract
The human genetic diversity around the world was studied through several high variable genetic markers. In South America the demic consequences of admixture events between Native people, European colonists and African slaves have been displayed by uniparental markers variability. The mitochondrial DNA (mtDNA) has been the most widely used genetic marker for studying American mixed populations, although nuclear markers, such as microsatellite loci (STRs) commonly used in forensic science, showed to be genetically and geographically structured. In this work, we analyzed DNA from buccal swab samples of 296 individuals across Peru: 156 Native Amazons (Ashaninka, Cashibo and Shipibo from Ucayali, Huambiza from Loreto and Moche from Lambayeque) and 140 urban Peruvians from Lima and other 33 urban areas. The aim was to evaluate, through STRs and mtDNA variability, recent migrations in urban Peruvian populations and to gain more information about their continental ancestry. STR data highlighted that most individuals (67%) of the urban Peruvian sample have a strong similarity to the Amazon Native population, whereas 22% have similarity to African populations and only ~1% to European populations. Also the maternally-transmitted mtDNA confirmed the strong Native contribution (~90% of Native American haplogroups) and the lower frequencies of African (~6%) and European (~3%) haplogroups. This study provides a detailed description of the urban Peruvian genetic structure and proposes forensic STRs as a useful tool for studying recent migrations, especially when coupled with mtDNA.
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Massively parallel sequencing of 68 insertion/deletion markers identifies novel microhaplotypes for utility in human identity testing. Forensic Sci Int Genet 2016; 25:198-209. [PMID: 27685342 DOI: 10.1016/j.fsigen.2016.09.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2016] [Revised: 08/01/2016] [Accepted: 09/19/2016] [Indexed: 11/23/2022]
Abstract
Short tandem repeat (STR) loci are the traditional markers used for kinship, missing persons, and direct comparison human identity testing. These markers hold considerable value due to their highly polymorphic nature, amplicon size, and ability to be multiplexed. However, many STRs are still too large for use in analysis of highly degraded DNA. Small bi-allelic polymorphisms, such as insertions/deletions (INDELs), may be better suited for analyzing compromised samples, and their allele size differences are amenable to analysis by capillary electrophoresis. The INDEL marker allelic states range in size from 2 to 6 base pairs, enabling small amplicon size. In addition, heterozygote balance may be increased by minimizing preferential amplification of the smaller allele, as is more common with STR markers. Multiplexing a large number of INDELs allows for generating panels with high discrimination power. The Nextera™ Rapid Capture Custom Enrichment Kit (Illumina, Inc., San Diego, CA) and massively parallel sequencing (MPS) on the Illumina MiSeq were used to sequence 68 well-characterized INDELs in four major US population groups. In addition, the STR Allele Identification Tool: Razor (STRait Razor) was used in a novel way to analyze INDEL sequences and detect adjacent single nucleotide polymorphisms (SNPs) and other polymorphisms. This application enabled the discovery of unique allelic variants, which increased the discrimination power and decreased the single-locus random match probabilities (RMPs) of 22 of these well-characterized INDELs which can be considered as microhaplotypes. These findings suggest that additional microhaplotypes containing human identification (HID) INDELs may exist elsewhere in the genome.
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Parolin ML, Real LE, Martinazzo LB, Basso NG. Population genetic analyses of the Powerplex ® Fusion kit in a cosmopolitan sample of Chubut Province (Patagonia Argentina). Forensic Sci Int Genet 2015; 19:221-222. [DOI: 10.1016/j.fsigen.2015.07.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 07/29/2015] [Accepted: 07/30/2015] [Indexed: 10/23/2022]
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Børsting C, Morling N. Next generation sequencing and its applications in forensic genetics. Forensic Sci Int Genet 2015; 18:78-89. [DOI: 10.1016/j.fsigen.2015.02.002] [Citation(s) in RCA: 268] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Revised: 01/12/2015] [Accepted: 02/11/2015] [Indexed: 12/13/2022]
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Olofsson JK, Mogensen HS, Buchard A, Børsting C, Morling N. Forensic and population genetic analyses of Danes, Greenlanders and Somalis typed with the Yfiler ® Plus PCR amplification kit. Forensic Sci Int Genet 2015; 16:232-236. [DOI: 10.1016/j.fsigen.2015.02.006] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 02/09/2015] [Accepted: 02/15/2015] [Indexed: 11/29/2022]
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Tomas C, Skitsa I, Steinmeier E, Poulsen L, Ampati A, Børsting C, Morling N. Results for five sets of forensic genetic markers studied in a Greek population sample. Forensic Sci Int Genet 2015; 16:132-137. [DOI: 10.1016/j.fsigen.2015.01.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Revised: 12/16/2014] [Accepted: 01/02/2015] [Indexed: 11/30/2022]
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Fordyce SL, Mogensen HS, Børsting C, Lagacé RE, Chang CW, Rajagopalan N, Morling N. Second-generation sequencing of forensic STRs using the Ion Torrent™ HID STR 10-plex and the Ion PGM™. Forensic Sci Int Genet 2015; 14:132-40. [DOI: 10.1016/j.fsigen.2014.09.020] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Revised: 08/20/2014] [Accepted: 09/23/2014] [Indexed: 01/07/2023]
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