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Bini C, Sarno S, Tangorra E, Iuvaro A, De Fanti S, Tseghereda YG, Pelotti S, Luiselli D. Haplotype data and forensic evaluation of 23 Y-STR and 12 X-STR loci in eight ethnic groups from Eritrea. Int J Legal Med 2020; 135:449-453. [PMID: 33089342 PMCID: PMC7870587 DOI: 10.1007/s00414-020-02446-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 10/14/2020] [Indexed: 11/26/2022]
Abstract
Eritrea is a multi-ethnic country of over 3 million of people consisting of different ethnic groups, having each its own language and cultural tradition. Due to the lack of population genetic data for markers of forensic interest, in this study, we analyzed the genetic polymorphisms of 23 Y-chromosome STR loci and of 12 X-chromosome STR loci in a sample of 255 unrelated individuals from 8 Eritrean ethnic groups, with the aim to generate a reference haplotype database for anthropological and forensic applications. X- and Y-chromosomes markers may indeed offer information especially in personal identification and kinship testing, when relying on the availability of large local population data to derive sufficiently accurate frequency estimates. The population genetic analyses in the Eritrean sample for both the two set of Y- and X-STR markers showed high power of discrimination both at country-based and population levels. Comparison population results highlight the importance of considering the ethnic composition within the analyzed country and the necessity of increasing available data especially when referring to heterogeneous populations such as the African ones.
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Affiliation(s)
- Carla Bini
- Department of Medical and Surgical Sciences, Unit of Legal Medicine, University of Bologna, via Irnerio, 49, 40126 Bologna, Italy
| | - Stefania Sarno
- Department of Biological, Geological and Environmental Sciences-Lab. of Molecular Anthropology & Centre for Genome Biology, University of Bologna, Via Selmi 3, 40126 Bologna, Italy
| | - Elisabetta Tangorra
- Department of Medical and Surgical Sciences, Unit of Legal Medicine, University of Bologna, via Irnerio, 49, 40126 Bologna, Italy
| | - Alessandra Iuvaro
- Department of Medical and Surgical Sciences, Unit of Legal Medicine, University of Bologna, via Irnerio, 49, 40126 Bologna, Italy
| | - Sara De Fanti
- Department of Biological, Geological and Environmental Sciences-Lab. of Molecular Anthropology & Centre for Genome Biology, University of Bologna, Via Selmi 3, 40126 Bologna, Italy
- Interdepartmental Centre “Alma Mater Research Institute on Global Challenges and Climate Change (Alma Climate)”, University of Bologna, Bologna, Italy
| | | | - Susi Pelotti
- Department of Medical and Surgical Sciences, Unit of Legal Medicine, University of Bologna, via Irnerio, 49, 40126 Bologna, Italy
| | - Donata Luiselli
- Department of Biological, Geological and Environmental Sciences-Lab. of Molecular Anthropology & Centre for Genome Biology, University of Bologna, Via Selmi 3, 40126 Bologna, Italy
- Department of Cultural Heritage, Ravenna Campus, University of Bologna, Via degli Ariani 1, 48121 Ravenna, Italy
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Mršić G, Ozretić P, Crnjac J, Merkaš S, Sukser V, Račić I, Rožić S, Barbarić L, Popović M, Korolija M. Expanded Croatian 12 X-STR loci database with an overview of anomalous profiles. Forensic Sci Int Genet 2018; 34:249-256. [PMID: 29573605 DOI: 10.1016/j.fsigen.2018.03.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 01/16/2018] [Accepted: 03/02/2018] [Indexed: 02/08/2023]
Abstract
In order to implement X-chromosome short tandem repeat (X-STR) typing into routine forensic practice, reference database of a given population should be established. Therefore we extended already published data with additional 397 blood samples from unrelated Croatian citizens, and analyzed the total of 995 samples (549 male and 446 female) typed by Investigator® Argus X-12 Kit. To test genetic homogeneity of consecutively processed five historic-cultural regions covering the entire national territory, we calculated pairwise Fst genetic distances between regions based on allele and full haplotype frequencies. Since the comparison did not yield any statistically significant difference, we integrated STR profile information from all regions and used the whole data set to calculate forensic parameters. The most informative marker is DXS10135 (polymorphism information content (PIC = 0.929) and the most informative linkage group (LG) is LG1 (PIC = 0.996). We confirmed linkage disequilibrium (LD) for seven marker pairs belonging to LG2, LG3 and LG4. By including LD information, we calculated cumulative power of discrimination that amounted to 0.999999999997 in females and 0.999999005 in males. We also compared Croatia with 13 European populations based on haplotype frequencies and detected no statistically significant Fst values after Bonferroni correction in any LG. Multi-dimensional scaling plot revealed tight grouping of four Croatian regions amongst populations of southern, central and northern Europe, with the exception of northern Croatia. In this study we gave the first extensive overview of aberrant profiles encountered during Investigator® Argus X-12 typing. We found ten profiles consistent with single locus duplication followed by tetranucleotide tract length polymorphism. Locus DXS10079 is by far the most frequently affected one, presumably mutated in eight samples. We also found four profiles consistent with X-chromosome aneuploidy (three profiles with XXX pattern and one profile with XXY pattern). In conclusion, we established integral forensic Croatian X-chromosome database, proved forensic pertinence of Investigator® Argus X-12 Kit for the entire Croatian population and identified locus DXS10079 as a potential duplication hotspot.
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Affiliation(s)
- Gordan Mršić
- Forensic Science Centre "Ivan Vučetić", Ilica 335, 10000 Zagreb, Croatia; Forensic Science Office, University of Zagreb, Ulica Ivana Lučića 5-6, 10000 Zagreb, Croatia
| | - Petar Ozretić
- Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
| | - Josip Crnjac
- University Department for Forensic Sciences, University of Split, Ruđera Boškovića 31, 21000 Split, Croatia
| | - Siniša Merkaš
- Forensic Science Centre "Ivan Vučetić", Ilica 335, 10000 Zagreb, Croatia; Forensic Science Office, University of Zagreb, Ulica Ivana Lučića 5-6, 10000 Zagreb, Croatia
| | - Viktorija Sukser
- Forensic Science Centre "Ivan Vučetić", Ilica 335, 10000 Zagreb, Croatia; Forensic Science Office, University of Zagreb, Ulica Ivana Lučića 5-6, 10000 Zagreb, Croatia
| | - Ivana Račić
- Forensic Science Centre "Ivan Vučetić", Ilica 335, 10000 Zagreb, Croatia; Forensic Science Office, University of Zagreb, Ulica Ivana Lučića 5-6, 10000 Zagreb, Croatia
| | - Sara Rožić
- Forensic Science Centre "Ivan Vučetić", Ilica 335, 10000 Zagreb, Croatia; Forensic Science Office, University of Zagreb, Ulica Ivana Lučića 5-6, 10000 Zagreb, Croatia
| | - Lucija Barbarić
- Forensic Science Centre "Ivan Vučetić", Ilica 335, 10000 Zagreb, Croatia; Forensic Science Office, University of Zagreb, Ulica Ivana Lučića 5-6, 10000 Zagreb, Croatia
| | - Maja Popović
- Faculty of Veterinary Medicine, University of Zagreb, Heinzelova ulica 55, 10000 Zagreb, Croatia
| | - Marina Korolija
- Forensic Science Centre "Ivan Vučetić", Ilica 335, 10000 Zagreb, Croatia; Forensic Science Office, University of Zagreb, Ulica Ivana Lučića 5-6, 10000 Zagreb, Croatia.
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Almarri MA, Lootah RA. Allelic and haplotype diversity of 12 X-STRs in the United Arab Emirates. Forensic Sci Int Genet 2018; 33:e4-e6. [DOI: 10.1016/j.fsigen.2017.12.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Revised: 12/19/2017] [Accepted: 12/28/2017] [Indexed: 11/17/2022]
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Mršić G, Ozretić P, Crnjac J, Merkaš S, Račić I, Rožić S, Sukser V, Popović M, Korolija M. Analysis of 12 X-STR loci in the population of south Croatia. Mol Biol Rep 2017; 44:183-189. [PMID: 28070706 DOI: 10.1007/s11033-017-4096-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 01/02/2017] [Indexed: 02/08/2023]
Abstract
The aim of the study was to assess forensic pertinence of 12 short tandem repeats (STRs) on X-chromosome in south Croatia population. Investigator® Argus X-12 kit was used to co-amplify 12 STR loci belonging to four linkage groups (LGs) on X-chromosome in 99 male and 98 female DNA samples of unrelated donors. PCR products were analyzed by capillary electrophoresis. Population genetic and forensic parameters were calculated by the Arlequin and POPTREE2 software, and an on-line tool available at ChrX-STR.org. Hardy-Weinberg equilibrium was confirmed for all X-STR markers in female samples. Biallelic patterns at DXS10079 locus were detected in four male samples. Polymorphism information content for the most (DXS10135) and the least (DXS8378) informative markers was 0.9212 and 0.6347, respectively. In both male and female samples, combined power of discrimination exceeded 0.999999999. As confirmed by linkage disequilibrium test, significant association of marker pair DXS10074-DXS10079 (P = 0.0004) within LG2 and marker pair DXS10101-DXS10103 (P = 0.0003) within LG3 was found only in male samples. Number of observed haplotypes in our sample pool amounted 3.01, 7.53, 5 and 3.25% of the number of possible haplotypes for LG1, LG2, LG3 and LG4, respectively. According to haplotype diversity value of 0.9981, LG1 was the most informative. In comparison of south Croatia with 26 world populations, pair-wise [Formula: see text] values increase in parallel with geographical distance. Overall statistical assessment confirmed suitability of Investigator® Argus X-12 kit for forensic casework in both identification and familial testing in the population of south Croatia.
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Affiliation(s)
- Gordan Mršić
- Forensic Science Centre "Ivan Vučetić", Zagreb, Croatia
- Forensic Science Office, University of Zagreb, Zagreb, Croatia
| | | | - Josip Crnjac
- University Department for Forensic Sciences, University of Split, Split, Croatia
| | - Siniša Merkaš
- Forensic Science Centre "Ivan Vučetić", Zagreb, Croatia
- Forensic Science Office, University of Zagreb, Zagreb, Croatia
| | - Ivana Račić
- Forensic Science Centre "Ivan Vučetić", Zagreb, Croatia
- Forensic Science Office, University of Zagreb, Zagreb, Croatia
| | - Sara Rožić
- Forensic Science Centre "Ivan Vučetić", Zagreb, Croatia
- Forensic Science Office, University of Zagreb, Zagreb, Croatia
| | - Viktorija Sukser
- Forensic Science Centre "Ivan Vučetić", Zagreb, Croatia
- Forensic Science Office, University of Zagreb, Zagreb, Croatia
| | - Maja Popović
- Faculty of Veterinary Medicine, University of Zagreb, Zagreb, Croatia
| | - Marina Korolija
- Forensic Science Centre "Ivan Vučetić", Zagreb, Croatia.
- Forensic Science Office, University of Zagreb, Zagreb, Croatia.
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Guo F. Population genetic data for 12 X-STR loci in the Northern Han Chinese and StatsX package as tools for population statistics on X-STR. Forensic Sci Int Genet 2017; 26:e1-e8. [DOI: 10.1016/j.fsigen.2016.10.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 10/03/2016] [Accepted: 10/23/2016] [Indexed: 12/29/2022]
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Resende A, Amorim A, da Silva CV, Ribeiro T, Porto MJ, Costa Santos J, Afonso Costa H. Study of genetic markers of CODIS and ESS systems in a population of individuals from Cabo Verde living in Lisboa. Int J Legal Med 2017; 131:119-121. [DOI: 10.1007/s00414-016-1431-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 07/26/2016] [Indexed: 10/21/2022]
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Inácio A, Costa HA, da Silva CV, Ribeiro T, Porto MJ, Santos JC, Igrejas G, Amorim A. Study of InDel genetic markers with forensic and ancestry informative interest in PALOP's immigrant populations in Lisboa. Int J Legal Med 2016; 131:657-660. [PMID: 27796588 DOI: 10.1007/s00414-016-1484-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 10/20/2016] [Indexed: 10/20/2022]
Abstract
The migratory phenomenon in Portugal has become one of the main factors for the genetic variability. In the last few years, a new class of autosomal insertion/deletion markers-InDel-has attracted interest in forensic genetics. Since there is no data for InDel markers of Portuguese-speaking African countries (PALOP) immigrants living in Lisboa, our aim is the characterization of those groups of individuals by typing them with at least 30 InDel markers and to compare different groups of individuals/populations. We studied 454 bloodstain samples belonging to immigrant individuals from Angola, Guinea-Bissau, and Mozambique. DNA extraction was performed with the Chelex® 100 method. After extraction, all samples were typed with the Investigator® DIPplex method. Through the obtained results, allelic frequencies show that all markers are at Hardy-Weinberg equilibrium, and we can confirm that those populations show significant genetic distances between themselves, between them, and the host Lisboa population. Because of this, they introduce genetic variability in Lisboa population.
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Affiliation(s)
- Ana Inácio
- Instituto Nacional de Medicina Legal e Ciências Forenses, Coimbra, Portugal
- Departamento de Genética e Biotecnologia, Universidade de Trás-os-Montes e Alto Douro, Vila Real, Portugal
| | - Heloísa Afonso Costa
- Instituto Nacional de Medicina Legal e Ciências Forenses, Coimbra, Portugal
- Centro de Ciências Forenses (CENCIFOR), Coimbra, Portugal
| | - Cláudia Vieira da Silva
- Instituto Nacional de Medicina Legal e Ciências Forenses, Coimbra, Portugal
- Centro de Ciências Forenses (CENCIFOR), Coimbra, Portugal
| | - Teresa Ribeiro
- Instituto Nacional de Medicina Legal e Ciências Forenses, Coimbra, Portugal
- Centro de Ciências Forenses (CENCIFOR), Coimbra, Portugal
| | - Maria João Porto
- Instituto Nacional de Medicina Legal e Ciências Forenses, Coimbra, Portugal
- Centro de Ciências Forenses (CENCIFOR), Coimbra, Portugal
| | - Jorge Costa Santos
- Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
- Instituto Superior de Ciências da Saúde Egas Moniz, Monte de Caparica, Portugal
- Centro de Ciências Forenses (CENCIFOR), Coimbra, Portugal
| | - Gilberto Igrejas
- Departamento de Genética e Biotecnologia, Universidade de Trás-os-Montes e Alto Douro, Vila Real, Portugal
| | - António Amorim
- Instituto Nacional de Medicina Legal e Ciências Forenses, Coimbra, Portugal.
- Instituto Superior de Ciências da Saúde Egas Moniz, Monte de Caparica, Portugal.
- Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal.
- Centro de Ciências Forenses (CENCIFOR), Coimbra, Portugal.
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Stepanov VA, Vagaitseva KV, Kharkov VN, Cherednichenko AA, Bocharova AV. Panel of X-linked single-nucleotide polymorphic markers for DNA identification (XSNPid) based on multiplex genotyping by multilocus PCR and MALDI-TOF mass spectrometry. Mol Biol 2016. [DOI: 10.1134/s0026893316030158] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Inácio A, Costa HA, Silva CVD, Ribeiro T, Porto MJ, Santos JC, Igrejas G, Amorim A. Study of y-SNPs genetic markers with forensic interest and ancestry informative power in PALOP’s immigrant populations in Lisboa. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2015. [DOI: 10.1016/j.fsigss.2015.09.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Genetic portrait of Lisboa immigrant population from Cabo Verde with mitochondrial DNA analysis. J Genet 2015; 94:509-12. [PMID: 26440093 DOI: 10.1007/s12041-015-0552-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Forensic typing of short tandem repeat markers on the X and Y chromosomes. Forensic Sci Int Genet 2015; 18:140-51. [DOI: 10.1016/j.fsigen.2015.03.013] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Revised: 03/22/2015] [Accepted: 03/24/2015] [Indexed: 11/17/2022]
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12
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Expanding X-chromosomal forensic haplotype frequencies database: Italian population data of four linkage groups. Forensic Sci Int Genet 2015; 15:127-30. [DOI: 10.1016/j.fsigen.2014.11.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Revised: 10/30/2014] [Accepted: 11/01/2014] [Indexed: 11/19/2022]
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