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Alinaghi S, Mohseni M, Fattahi Z, Beheshtian M, Ghodratpour F, Zare Ashrafi F, Arzhangi S, Jalalvand K, Najafipour R, Khorram Khorshid HR, Kahrizi K, Najmabadi H. Genetic Analysis of 27 Y-STR Haplotypes in 11 Iranian Ethnic Groups. ARCHIVES OF IRANIAN MEDICINE 2024; 27:79-88. [PMID: 38619031 PMCID: PMC11017261 DOI: 10.34172/aim.2024.13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 01/23/2024] [Indexed: 04/16/2024]
Abstract
BACKGROUND The study of Y-chromosomal variations provides valuable insights into male susceptibility in certain diseases like cardiovascular disease (CVD). In this study, we analyzed paternal lineage in different Iranian ethnic groups, not only to identify developing medical etiology, but also to pave the way for gender-specific targeted strategies and personalized medicine in medical genetic research studies. METHODS The diversity of eleven Iranian ethnic groups was studied using 27 Y-chromosomal short tandem repeat (Y-STR) haplotypes from Y-filer® Plus kit. Analysis of molecular variance (AMOVA) based on pair-wise RST along with multidimensional scaling (MDS) calculation and Network phylogenic analysis was employed to quantify the differences between 503 unrelated individuals from each ethnicity. RESULTS Results from AMOVA calculation confirmed that Gilaks and Azeris showed the largest genetic distance (RST=0.35434); however, Sistanis and Lurs had the smallest considerable genetic distance (RST=0.00483) compared to other ethnicities. Although Azeris had a considerable distance from other ethnicities, they were still close to Turkmens. MDS analysis of ethnic groups gave the indication of lack of similarity between different ethnicities. Besides, network phylogenic analysis demonstrated insignificant clustering between samples. CONCLUSION The AMOVA analysis results explain that the close distance of Azeris and Turkmens may be the effect of male-dominant expansions across Central Asia that contributed to historical and demographics of populations in the region. Insignificant differences in network analysis could be the consequence of high mutation events that happened in the Y-STR regions over the years. Considering the ethnic group affiliations in medical research, our results provided an understanding and characterization of Iranian male population for future medical and population genetics studies.
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Affiliation(s)
- Somayeh Alinaghi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Marzieh Mohseni
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Zohreh Fattahi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Maryam Beheshtian
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Fatemeh Ghodratpour
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Farzane Zare Ashrafi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Sanaz Arzhangi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Khadijeh Jalalvand
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Reza Najafipour
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | | | - Kimia Kahrizi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Hossein Najmabadi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
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Červenák Z, Červenák F, Choma A, Baldovič M, Masnicová S. Population genetic analysis of 12 X-STR markers in Slovakia. Ann Hum Biol 2023; 50:431-435. [PMID: 37812207 DOI: 10.1080/03014460.2023.2264769] [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: 04/04/2023] [Accepted: 09/19/2023] [Indexed: 10/10/2023]
Abstract
Background: During the last 20 years, X-chromosomal STR markers have become widely used in forensic genetics and paternity testing. Nevertheless, to exploit their full potential in any given population, a reliable reference dataset needs to be established. Since no relevant studies concerning these markers have been performed on the Slovak population so far, we decided to analyse several commonly used markers in this population.Aim: To create an informative set of Slovak population data concerning X-STR markers.Subjects and methods: We genotyped 378 individuals and analysed 12 loci (DXS10148, DX10135, DXS8378, DXS7132, DXS10079, DXS10074, DXS10103, HPRTB, DXS10101, DXS10146, DXS10134 and DXS742) localised in four distinct linkage groups.Results: Our analysis showed that the most informative marker is DXS10135 (PIC = 0,927) and the most informative linkage group (LG) is LG1 with 149 different haplotypes. This analysis also confirmed linkage disequilibrium for two pairs of markers (DX10101-DX10103 and DX10101-HPRTB) within LG3 in female samples. No statistically significant departure from HWE was observed for any locus. Moreover, the interpopulation comparison of 8 European populations based on haplotype frequencies showed no statistically significant FST values in any LG, except for LG2 in comparison with the German population.Conclusion: We created a haplotype database for forensic analyses and kinship testing in Slovakia, as well as the CE dataset which can be used to further increase the decision power in similar analyses in the future.
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Affiliation(s)
- Zdenko Červenák
- Comenius University, Clinical Research Unit, 5. Department of Internal Medicine, Comenius University Science Park, Bratislava, Slovakia
| | - Filip Červenák
- Department of Genetics, Comenius University, Bratislava, Slovakia
| | - Andrej Choma
- Department of Criminalistic Biology and Genetic Analysis, Institute of Forensic Science, Bratislava, Slovakia
| | - Marián Baldovič
- Department of Molecular Biology, Comenius University, Bratislava, Slovak Republic
- GHC GENETICS SK, S.R.O, Bratislava, Slovak Republic
| | - Soňa Masnicová
- Department of Criminalistics and Forensic Sciences, Academy of Police Force in Bratislava, Bratislava, Slovak Republic
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Development and validation of a new multiplex for upgrading Y-STRs population databases from 12 to 23 markers and its forensic casework application. Sci Rep 2022; 12:21734. [PMID: 36526709 PMCID: PMC9758231 DOI: 10.1038/s41598-022-25785-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 12/05/2022] [Indexed: 12/23/2022] Open
Abstract
Y chromosomal short tandem repeats (Y-STRs) are used in forensic investigations as a useful complementary tool to autosomal markers. The ongoing development of new kits with an increasing number of markers makes it necessary to update populations typed in the Y-STR Haplotype Reference Database to reach at least 23 Y-STRs. A novel Y-STR multiplex panel was developed to offer a cost-efficient alternative to update Y-STR haplotypes from 12 to 23 loci. This panel includes the eleven markers, DYS448, DYS456, DYS458, DYS635, Y-GATA H4, DYS576, DYS481, DYS549, DYS533, DYS570 and DYS643, as well as DYS385a/b for traceability purpose. Developmental validation of this panel was conducted following the recommendations of the Scientific Working Group on DNA Analysis Methods (SWGDAM), showing high sensitivity, tolerance to common inhibitors as well as high species specificity. It was efficient for degraded DNA samples and for detection of male mixtures. When applying it for extending the current data of the Ibiza population, both the discrimination capacity and the haplotype diversity increased from 0.5952 to 0.9048 and from 0.9808 to 0.9977, respectively. Together, the study demonstrates the suitability of this panel in forensic casework.
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Curtis R, Ward D, Taylor D, Henry J. Investigation of X-STR haplotype diversity in the Australian Aboriginal population. AUST J FORENSIC SCI 2022. [DOI: 10.1080/00450618.2022.2048690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Rhianna Curtis
- Division of Biology, Forensic Science SA, Adelaide, South Australia
| | - Denise Ward
- Division of Biology, Forensic Science SA, Adelaide, South Australia
| | - Duncan Taylor
- Division of Biology, Forensic Science SA, Adelaide, South Australia
- College of Science and Engineering, Flinders University of South Australia, Adelaide, South Australia
| | - Julianne Henry
- Division of Biology, Forensic Science SA, Adelaide, South Australia
- College of Science and Engineering, Flinders University of South Australia, Adelaide, South Australia
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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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Haidar M, Alsaleh H, Haddrill PR. Evaluation of 30 insertion/deletion polymorphisms as forensic markers in the Kuwaiti population. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2019. [DOI: 10.1016/j.fsigss.2019.10.157] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Li Y, Li X, Chen W, Fan Y, Xie M, Wu J. Allele and haplotype frequencies of 19 X-STRs in the Kyrgyz and Han populations from Kizilsu Prefecture. Forensic Sci Int Genet 2019; 40:e259-e261. [DOI: 10.1016/j.fsigen.2019.02.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Revised: 02/06/2019] [Accepted: 02/06/2019] [Indexed: 01/22/2023]
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Salvador JM, Apaga DLT, Delfin FC, Calacal GC, Dennis SE, De Ungria MCA. Filipino DNA variation at 12 X-chromosome short tandem repeat markers. Forensic Sci Int Genet 2018; 36:e8-e12. [DOI: 10.1016/j.fsigen.2018.06.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 06/06/2018] [Accepted: 06/07/2018] [Indexed: 01/11/2023]
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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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Bozman N, Gurkan C, Sevay H, Demirdov DK, Ozbas-Gerceker F. Genetic characterisation of 19 autosomal STR loci in a population sample from the Southeastern Anatolia Region of Turkey. Ann Hum Biol 2018. [DOI: 10.1080/03014460.2018.1444202] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- Nazli Bozman
- Department of Biology, Section of Molecular Biology, Faculty of Arts and Science, University of Gaziantep, Gaziantep, Turkey
| | - Cemal Gurkan
- Turkish Cypriot DNA Laboratory, Committee on Missing Persons in Cyprus Turkish Cypriot Member Office, Nicosia (North Cyprus), Turkey
- Dr. Fazıl Küçük Faculty of Medicine, Eastern Mediterranean University, Famagusta (North Cyprus), Turkey
| | - Huseyin Sevay
- Department of Information Systems Engineering, Near East University, Nicosia (North Cyprus), Turkey
| | - Damla Kanliada Demirdov
- Turkish Cypriot DNA Laboratory, Committee on Missing Persons in Cyprus Turkish Cypriot Member Office, Nicosia (North Cyprus), Turkey
| | - Filiz Ozbas-Gerceker
- Department of Biology, Section of Molecular Biology, Faculty of Arts and Science, University of Gaziantep, Gaziantep, Turkey
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Investigation of 12 X-STR loci in Mongolian and Eastern Han populations of China with comparison to other populations. Sci Rep 2018. [PMID: 29523825 PMCID: PMC5844901 DOI: 10.1038/s41598-018-22665-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Due to the unique inheritance pattern, X-chromosomal short tandem repeats (X-STRs) have several advantages in complex kinship cases, such as deficiency cases or grandparent-grandchild and half-sisters testing. In our study, 541 unrelated individuals gathered from Mongolian and Eastern Chinese Han populations were successfully genotyped using the Investigator Argus X-12 kit. We calculated allele/haplotype frequencies and other forensic parameters of the two populations and further explored their genetic distance with already published Chinese populations and six global populations. Our results showed that the 12 X-STR markers were highly informative in the two populations when compared with nine other Chinese populations: significant differences were found at several loci. Geographically neighboring populations or different ethnic groups within the same area appeared to have closer evolutionary relationships. We also analyzed population genetic structure by performing clustering with the STRUCTURE program and Principal Coordinate Analysis (PCoA), and we found that the Chinese and other populations enrolled in this study could be distinguished. Furthermore, Mongolian males were distinguishable from the other studied males by a moderate genetic distance. Our study also expanded the X-STR database, which could facilitate the appropriate application of the 12 X-STR markers in the forensic field in China.
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12
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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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Robino C, Lacerenza D, Aneli S, Di Gaetano C, Matullo G, Robledo R, Calò C. Allele and haplotype diversity of 12 X-STRs in Sardinia. Forensic Sci Int Genet 2017; 33:e1-e3. [PMID: 29221994 DOI: 10.1016/j.fsigen.2017.12.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 11/11/2017] [Accepted: 12/02/2017] [Indexed: 11/27/2022]
Abstract
The analysis of clusters of tightly linked X-chromosome short tandem repeat (STR) markers can assist the interpretation of complex kinship cases. However, when linkage disequilibrium (LD) is present in the population of origin of tested individuals, haplotype rather than allele frequencies should be used in likelihood calculations. The diversity of twelve X-STRs arranged in four linkage groups (I: DXS10148-DXS10135-DXS8378; II: DXS7132-DXS10079-DXS10074; III: DXS10103-HPRTB-DXS10101; IV: DXS10146-DXS10134-DXS7423) was tested in a Sardinian population sample (n=516) including three open populations from the Northern, Central and Southern part of the island, and three isolates (Benetutti, Desulo, Carloforte). Evidence of LD was detected in Sardinia within each linkage group. Significant differences in haplotype and allele frequency distribution of X-STR markers was seen between isolates and open populations, which on the contrary appeared highly homogeneous. The percentage of Sardinian haplotypes previously unobserved in a similar dataset compiled for the Italian population was: 76.3% (linkage group I), 61.3% (linkage group II), 54.1% (linkage group III), 58.9% (linkage group IV). Significant pairwise genetic differences were seen between mainland Italy, the three Sardinian isolates, and the open population of Southern Sardinia. The study confirms the presence of high levels and complex patterns of LD along the X chromosome in Sardinia, and provides population-specific haplotype data for biostatistical evaluation in kinship testing.
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Affiliation(s)
- C Robino
- Dipartimento di Scienze della Sanità Pubblica e Pediatriche, Università di Torino, Italy.
| | - D Lacerenza
- Dipartimento di Scienze della Sanità Pubblica e Pediatriche, Università di Torino, Italy
| | - S Aneli
- Dipartimento di Scienze Mediche, Università di Torino, Italy; Italian Institute of Genomic Medicine, Torino, Italy
| | - C Di Gaetano
- Dipartimento di Scienze Mediche, Università di Torino, Italy; Italian Institute of Genomic Medicine, Torino, Italy
| | - G Matullo
- Dipartimento di Scienze Mediche, Università di Torino, Italy; Italian Institute of Genomic Medicine, Torino, Italy
| | - R Robledo
- Dipartimento di Scienze Biomediche, Università di Cagliari, Italy
| | - C Calò
- Dipartimento di Scienze della Vita e dell'Ambiente, Università di Cagliari, Italy
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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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Núñez C, Baeta M, Ibarbia N, Ortueta U, Jiménez-Moreno S, Blazquez-Caeiro JL, Builes JJ, Herrera RJ, Martínez-Jarreta B, de Pancorbo MM. 17 to 23: A novel complementary mini Y-STR panel to extend the Y-STR databases from 17 to 23 markers for forensic purposes. Electrophoresis 2017; 38:1016-1021. [PMID: 27987217 DOI: 10.1002/elps.201600313] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 11/19/2016] [Accepted: 12/10/2016] [Indexed: 11/08/2022]
Abstract
A Y-STR multiplex system has been developed with the purpose of complementing the widely used 17 Y-STR haplotyping (AmpFlSTR Y Filer® PCR Amplification kit) routinely employed in forensic and population genetic studies. This new multiplex system includes six additional STR loci (DYS576, DYS481, DYS549, DYS533, DYS570, and DYS643) to reach the 23 Y-STR of the PowerPlex® Y23 System. In addition, this kit includes the DYS456 and DYS385 loci for traceability purposes. Male samples from 625 individuals from ten worldwide populations were genotyped, including three sample sets from populations previously published with the 17 Y-STR system to expand their current data. Validation studies demonstrated good performance of the panel set in terms of concordance, sensitivity, and stability in the presence of inhibitors and artificially degraded DNA. The results obtained for haplotype diversity and discrimination capacity with this multiplex system were considerably high, providing further evidences of the suitability of this novel Y-STR system for forensic purposes. Thus, the use of this multiplex for samples previously genotyped with 17 Y-STRs will be an efficient and low-cost alternative to complete the set of 23 Y-STRs and improve allele databases for population and forensic purposes.
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Affiliation(s)
- Carolina Núñez
- BIOMICs Research Group, Lascaray Research Center, University of the Basque Country UPV/EHU. Avda. Miguel de Unamuno, Vitoria-Gasteiz, Spain
| | - Miriam Baeta
- BIOMICs Research Group, Lascaray Research Center, University of the Basque Country UPV/EHU. Avda. Miguel de Unamuno, Vitoria-Gasteiz, Spain
| | - Nerea Ibarbia
- BIOMICs Research Group, Lascaray Research Center, University of the Basque Country UPV/EHU. Avda. Miguel de Unamuno, Vitoria-Gasteiz, Spain
| | - Urko Ortueta
- BIOMICs Research Group, Lascaray Research Center, University of the Basque Country UPV/EHU. Avda. Miguel de Unamuno, Vitoria-Gasteiz, Spain
| | - Susana Jiménez-Moreno
- Área Medicina Legal y Forense, Department of Patología y Cirugía, Universidad Miguel Hernández de Elche, Elche, Alicante, Spain
| | | | - Juan José Builes
- Laboratorios Genes Ltd., Medellín, Colombia.,Instituto de Biología, Universidad de Antioquia, Medellín, Colombia
| | - Rene J Herrera
- Department of Molecular Biology, Colorado College, Colorado Springs, CO, USA
| | | | - Marian M de Pancorbo
- BIOMICs Research Group, Lascaray Research Center, University of the Basque Country UPV/EHU. Avda. Miguel de Unamuno, Vitoria-Gasteiz, Spain
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16
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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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17
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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: 10] [Impact Index Per Article: 1.3] [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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18
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Tomas C, Poulsen L, Drobnič K, Ivanova V, Jankauskiene J, Bunokiene D, Børsting C, Morling N. Thirty autosomal insertion-deletion polymorphisms analyzed using the Investigator ® DIPplex Kit in populations from Iraq, Lithuania, Slovenia, and Turkey. Forensic Sci Int Genet 2016; 25:142-144. [PMID: 27599378 DOI: 10.1016/j.fsigen.2016.08.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 07/29/2016] [Accepted: 08/19/2016] [Indexed: 10/21/2022]
Abstract
Thirty autosomal insertion-deletion (InDel) polymorphisms were analyzed in four populations from Iraq, Lithuania, Slovenia, and Turkey using the commercial kit Investigator® DIPplex. Genotyping issues were encountered for five of the 30 InDels. They were most probably caused by polymorphisms located in the primer binding sites. Population and forensic parameters were calculated. No significant deviations from Hardy-Weinberg equilibrium or significant linkage disequilibrium were detected. The observed heterozygosities ranged from 33% to 61% depending on the marker and the population. The combined probability of exclusion for the 30 markers was 99.7% in all four populations and the matching probabilities were 1 in 3-4×1012 individuals. The multidimensional scaling plot drawn from FST distances showed a good concordance between the relative position of the 15 populations included in the plot and their geographic locations.
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Affiliation(s)
- C Tomas
- 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.
| | - L Poulsen
- 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
| | - K Drobnič
- National Forensic Laboratory, Police, Ministry of the Interior, Vodovodna 95, 1000 Ljubljana, Slovenia
| | - V Ivanova
- State Forensic Medicine Service under the Ministry of Justice of the Republic of Lithuania, Vilnius, Lithuania
| | - J Jankauskiene
- State Forensic Medicine Service under the Ministry of Justice of the Republic of Lithuania, Vilnius, Lithuania
| | - D Bunokiene
- State Forensic Medicine Service under the Ministry of Justice of the Republic of Lithuania, Vilnius, Lithuania
| | - 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
| | - 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
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19
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Canturk KM, Gurkan C, Sevay H, Emre R. Evaluation of the genetic parameters for 10 common and five new ESS core autosomal STR loci in seven major geographic regions and the largest metropolitan province of Turkey. Ann Hum Biol 2016; 44:149-163. [DOI: 10.1080/03014460.2016.1183709] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
| | - Cemal Gurkan
- Turkish Cypriot DNA Laboratory, Committee on Missing Persons in Cyprus Turkish Cypriot Member Office, Nicosia (North Cyprus), Turkey
| | - Huseyin Sevay
- Department of Information Systems Engineering, Near East University, Nicosia (North Cyprus), Turkey
| | - Ramazan Emre
- Council of Forensic Medicine, Ministry of Justice, Istanbul, Turkey
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20
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Poulsen L, Tomas C, Drobnič K, Ivanova V, Mogensen H, Kondili A, Miniati P, Bunokiene D, Jankauskiene J, Pereira V, Morling N. NGMSElect™ and Investigator ® Argus X-12 analysis in population samples from Albania, Iraq, Lithuania, Slovenia, and Turkey. Forensic Sci Int Genet 2016; 22:110-112. [DOI: 10.1016/j.fsigen.2016.02.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Revised: 01/29/2016] [Accepted: 02/09/2016] [Indexed: 11/25/2022]
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21
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Population and forensic data for three sets of forensic genetic markers in four ethnic groups from Iran: Persians, Lurs, Kurds and Azeris. Forensic Sci Int Genet 2015; 17:43-46. [DOI: 10.1016/j.fsigen.2015.03.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 03/13/2015] [Accepted: 03/15/2015] [Indexed: 12/22/2022]
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