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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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2
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Mejri A, Baeta M, Al-Haj-Taib R, Herrera RJ, Benammar-Elgaaied A, de Pancorbo MM, Fadhlaoui-Zid K. Genetic polymorphisms of 17 X-STR loci in two Tunisian populations from Sousse and Makthar. Ann Hum Biol 2022; 49:342-347. [PMID: 36255378 DOI: 10.1080/03014460.2022.2136755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
BACKGROUND Tunisia has a complex demographic history of migrations from within Africa, Europe, and the Middle East. However, only one population study based on X-STR markers has been reported so far. AIM To investigate the genetic polymorphisms of 17 X-STRs in two Tunisian populations from the cities of Sousse and Makthar, and to reveal the genetic relationships with other reference populations. SUBJECTS AND METHODS A total of 194 unrelated healthy individuals were analysed for 17 X-STR markers. RESULTS Our results indicate that DXS6809 is the most polymorphic locus, whereas DXS6807 is the least informative marker in the populations of Sousse and Makthar. In addition, forensic statistical parameters, such as the power of discrimination in males and females, as well as the mean of exclusion in duos and trios, reveal that the panel of 17 X-STRs is highly informative and useful in different forensic applications. Overall, pairwise genetic distances (Fst) and non-metric MDS plots demonstrate clustering of different populations according to their geographic locations and their historical relationships. CONCLUSION Overall, the study of X-STR markers of the Tunisian populations can help to promote the establishment of a forensic DNA reference database in Tunisia and provide reference for future anthropological research.
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Affiliation(s)
- Abir Mejri
- Laboratory of Genetics, Immunology, and Human Pathologies, Faculty of Science of Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Miriam Baeta
- BIOMICs Research Group, Lascaray Research Center, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain
| | - Rim Al-Haj-Taib
- Laboratory of Genetics, Immunology, and Human Pathologies, Faculty of Science of Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Rene J Herrera
- Department of Molecular Biology, Colorado College, Colorado Springs, CO, USA
| | - Amel Benammar-Elgaaied
- Laboratory of Genetics, Immunology, and Human Pathologies, Faculty of Science of Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Marian M de Pancorbo
- BIOMICs Research Group, Lascaray Research Center, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain
| | - Karima Fadhlaoui-Zid
- Laboratory of Genetics, Immunology, and Human Pathologies, Faculty of Science of Tunis, University Tunis El Manar, Tunis, 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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3
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Forensic Applications of Markers Present on the X Chromosome. Genes (Basel) 2022; 13:genes13091597. [PMID: 36140765 PMCID: PMC9498577 DOI: 10.3390/genes13091597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 08/23/2022] [Accepted: 09/02/2022] [Indexed: 11/17/2022] Open
Abstract
Microsatellite genetic markers are the gold standard for human genetic identification. Forensic analyses around the world are carried out through protocols using the analysis of STR markers in autosomal chromosomes and in the Y chromosome to solve crimes. However, these analyses do not allow for the resolution of all cases, such as rape situations with suspicion of incest, paternity without a maternal sample for comparison, and biological traces with DNA mixture where the profile sought is female, among other situations. In these complex cases, the study of X-chromosome STR markers significantly increases the probability of identification by complementing the data obtained for autosomal and Y-chromosome markers, due to the unique structure of the X chromosome and its exclusive method of inheritance. However, there are currently no validated Brazilian protocols for this purpose, nor are there any population data necessary for statistical analyses that must be included in the issuance of expert reports. Thus, the aim of this article is to provide a literary review of the applications of X-chromosomal markers in population genetics.
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Li XN, Adnan A, Hadi S, Al-Qahtani WS, Alwaili MA, Alshaya DS, Jalal AS, Amer SAM, Jin F. Genetic characterization of the highlander Tibetan population from Qinghai-Tibet Plateau revealed by X chromosomal STRs. PLoS One 2022; 17:e0271769. [PMID: 35926061 PMCID: PMC9352086 DOI: 10.1371/journal.pone.0271769] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 05/17/2022] [Indexed: 01/20/2023] Open
Abstract
Tibetans are considered an East Asian ethnic group and primarily live in the high Tibetan plateau, the western Sichuan and Yunnan mountains of central and southern China, and areas throughout the Himalayas and around the Tibetan plateau. These people exhibit rare molecular machinery that allows them to adapt to hypoxic environments in the Qinghai-Tibet Plateau and make them a potential candidate for providing insights related to medical genetic, molecular medicine and human population studies. In the current study, we have genotyped 549 individuals with Investigator Argus X-12 Kit. For 12 X-STRs, a total of 174 unique alleles were found, among them DXS10134 and DXS10135 were the most polymorphic loci. All of the loci were in Hardy-Weinberg Equilibrium (HWE). The numbers of observed haplotypes in Highlander Tibetans males were 161,112, 96 and 108, respectively, whereas haplotype diversities (HD) were 0.9959, 0.9880, 0.9809 and 0.9873, respectively. The combined discrimination power for males (PDm) was 0.999 999 99701 and for females (PDf) was 0.999 999 999 999 9958. This study represents an extensive report on X chromosomal STR markers variation in the Highlander Tibetans population for forensic applications and population genetic studies.
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Affiliation(s)
- Xiao-na Li
- School of Fundamental Sciences, China Medical University, Shenyang, Liaoning, P.R. China
| | - Atif Adnan
- Department of Forensic Sciences, College of Criminal Justice, Naif Universsity of Security Sciences, Riyadh, Kingdom of Saudi Arabia
- * E-mail: (FJ); (AA)
| | - Sibte Hadi
- Department of Forensic Sciences, College of Criminal Justice, Naif Universsity of Security Sciences, Riyadh, Kingdom of Saudi Arabia
| | - Wedad Saeed Al-Qahtani
- Department of Forensic Sciences, College of Criminal Justice, Naif Universsity of Security Sciences, Riyadh, Kingdom of Saudi Arabia
| | - Maha Abdullah Alwaili
- Department of Biology, Collage of Sciences, Princess Nourah Bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Dalal S. Alshaya
- Department of Biology, Collage of Sciences, Princess Nourah Bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Areej S. Jalal
- Department of Biology, Collage of Sciences, Princess Nourah Bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Sayed A. M. Amer
- Department of Forensic Sciences, College of Criminal Justice, Naif Universsity of Security Sciences, Riyadh, Kingdom of Saudi Arabia
| | - Feng Jin
- Department of Breast Surgery, The First Hospital of China Medical University, Shenyang, Liaoning, P.R. China
- * E-mail: (FJ); (AA)
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5
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Liu L, Yuan J, Miao L, Huang R, Zhang X, Nie S, Hu L. Genetic polymorphisms of 16 X-STR loci analyzed in the Han population of Yunnan Province, Southwest China. Leg Med (Tokyo) 2021; 54:101974. [PMID: 34736140 DOI: 10.1016/j.legalmed.2021.101974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 09/27/2021] [Accepted: 10/01/2021] [Indexed: 10/20/2022]
Abstract
To investigate the genetic diversity and forensic identification efficiency of X-chromosomal short tandem repeats (X-STRs) in the Yunnan Han population, 16 X-STRs in 415 Yunnan Han individuals (247 males and 168 females) were studied. A total of 137 alleles were detected, and all loci in the Yunnan Han population were highly polymorphic. The combined discrimination of males (PDm) and females (PDf) was 0.9999997769115 and 0.999999999999999999996, respectively. Interpopulation comparisons between the Yunnan Han population and 21 other populations showed that the evolutionary relationships between different groups with the same ethnic group or nearby geographic origins were closer. This study provides the first data on X-STR genetic polymorphisms in the Yunnan Han population and enriches the X-STR database for the Chinese Han population.
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Affiliation(s)
- Linlin Liu
- School of Forensic Medicine, Kunming Medical University, Kunming, Yunnan Province, People's Republic of China; Judicial Expertise Center of Kunming Medical University, Kunming, Yunnan Province, People's Republic of China
| | - Jiahui Yuan
- School of Forensic Medicine, Kunming Medical University, Kunming, Yunnan Province, People's Republic of China
| | - Lei Miao
- School of Forensic Medicine, Kunming Medical University, Kunming, Yunnan Province, People's Republic of China
| | - Renwu Huang
- Judicial Expertise Center of Kunming Medical University, Kunming, Yunnan Province, People's Republic of China
| | - Xiufeng Zhang
- School of Forensic Medicine, Kunming Medical University, Kunming, Yunnan Province, People's Republic of China; Judicial Expertise Center of Kunming Medical University, Kunming, Yunnan Province, People's Republic of China.
| | - Shengjie Nie
- School of Forensic Medicine, Kunming Medical University, Kunming, Yunnan Province, People's Republic of China; Judicial Expertise Center of Kunming Medical University, Kunming, Yunnan Province, People's Republic of China.
| | - Liping Hu
- School of Forensic Medicine, Kunming Medical University, Kunming, Yunnan Province, People's Republic of China; Judicial Expertise Center of Kunming Medical University, Kunming, Yunnan Province, People's Republic of China.
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6
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Zhang X, Yuan X, Huang Y, Yao J, Zhang J, Dai J, Liu L, Nie S, Hu L. Forensic genetic polymorphisms of 16 X-STR loci in the Yunnan Miao population and their relationship to other Chinese groups. Leg Med (Tokyo) 2021; 53:101961. [PMID: 34479066 DOI: 10.1016/j.legalmed.2021.101961] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 08/13/2021] [Accepted: 08/21/2021] [Indexed: 11/18/2022]
Abstract
Allele frequencies for 16 X-chromosomal STR (X-STR) loci were obtained from a sample set of 440 unrelated Yunnan Miao individuals in China. A total of 117 alleles were observed in this group, with allele frequencies ranging from 0.0016 to 0.7565. The most informative marker for the studied population was DXS10134, with a polymorphism information content (PIC) of 0.8499, and the least polymorphic locus was DXS6810 (PIC = 0.3071). The power of discrimination (PD) varied from 0.4046 (DXS6800) to 0.8642 (DXS10134) in males and from 0.6188 (DXS6800) to 0.9673 (DXS10134) in females. The combined PDM and PDF were 0.999999989975990 and 0.999999999999949, respectively. The combined MECD and MECT were 0.999983301904059 and 0.999999915883733, respectively. Furthermore, population genetic structure investigation between the Yunnan Miao and 20 other populations using principal component analysis (PCA), multidimensional scaling plot (MDS), and neighboring-joining (NJ) phylogenetic tree analyses illustrated significant genetic difference between the Yunnan Miao and the other populations. This study is the first to provide X chromosome genetic polymorphism data of the Miao population in Yunnan Province and can be used as a supplementary reference to enrich the national database.
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Affiliation(s)
- Xiufeng Zhang
- School of Forensic Medicine, Kunming Medical University, Kunming, Yunnan Province, People's Republic of China; Judicial Expertise Center of Kunming Medical University, Kunming, Yunnan Province, People's Republic of China
| | - Xiaokun Yuan
- Honghe Public Security Bureau, Honghe, Yunnan Province, People's Republic of China
| | - Yangzhi Huang
- School of Forensic Medicine, Kunming Medical University, Kunming, Yunnan Province, People's Republic of China
| | - Jinyong Yao
- Honghe Public Security Bureau, Honghe, Yunnan Province, People's Republic of China
| | - Jian Zhang
- School of Forensic Medicine, Kunming Medical University, Kunming, Yunnan Province, People's Republic of China
| | - Jiameng Dai
- School of Forensic Medicine, Kunming Medical University, Kunming, Yunnan Province, People's Republic of China
| | - Linlin Liu
- School of Forensic Medicine, Kunming Medical University, Kunming, Yunnan Province, People's Republic of China; Judicial Expertise Center of Kunming Medical University, Kunming, Yunnan Province, People's Republic of China.
| | - Shengjie Nie
- School of Forensic Medicine, Kunming Medical University, Kunming, Yunnan Province, People's Republic of China; Judicial Expertise Center of Kunming Medical University, Kunming, Yunnan Province, People's Republic of China.
| | - Liping Hu
- School of Forensic Medicine, Kunming Medical University, Kunming, Yunnan Province, People's Republic of China; Judicial Expertise Center of Kunming Medical University, Kunming, Yunnan Province, People's Republic of China.
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7
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Liu L, Yao J, Huang Y, Gao L, Dai J, Yuan X, Zhang X, Nie S, Hu L. Genetic polymorphisms of 16 X-STR loci in the Hani population from Southwest China. Forensic Sci Res 2021; 7:196-201. [PMID: 35784423 PMCID: PMC9246014 DOI: 10.1080/20961790.2021.1877389] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Affiliation(s)
- Linlin Liu
- School of Forensic Medicine, Kunming Medical University, Kunming, China
- Judicial Expertise Center, Kunming Medical University, Kunming, China
| | - Jinyong Yao
- Honghe Public Security Bureau, Honghe, China
| | | | - Lei Gao
- Honghe Public Security Bureau, Honghe, China
| | - Jiameng Dai
- School of Forensic Medicine, Kunming Medical University, Kunming, China
| | | | - Xiufeng Zhang
- School of Forensic Medicine, Kunming Medical University, Kunming, China
- Judicial Expertise Center, Kunming Medical University, Kunming, China
| | - Shengjie Nie
- School of Forensic Medicine, Kunming Medical University, Kunming, China
- Judicial Expertise Center, Kunming Medical University, Kunming, China
| | - Liping Hu
- School of Forensic Medicine, Kunming Medical University, Kunming, China
- Judicial Expertise Center, Kunming Medical University, Kunming, China
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8
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Genetic polymorphism investigation of 16 X-STR loci in the Bai ethnic minority in Yunnan Province, Southwest China. Int J Legal Med 2020; 136:543-545. [PMID: 33180199 DOI: 10.1007/s00414-020-02454-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 10/30/2020] [Indexed: 10/23/2022]
Abstract
To investigate the genetic variation and forensic efficiency of 16 X-chromosomal short tandem repeat (X-STR) loci (DX6795, DXS9902, DXS8378, HPRTB, GATA165B12, DXS7132, DXS7424, DXS6807, DXS6803, GATA172D05, DXS6800, DXS10134, GATA31E08, DXS10159, DXS6789, and DXS6810) in the Bai minority, we calculated allele frequencies, forensic parameters, and haplotype frequencies in 424 (202 males and 222 females) unrelated, healthy Bai individuals from Dali Bai Autonomous Prefecture in Yunnan Province, China. We observed a total of 132 alleles; 5-19 alleles were detected in each locus, and the corresponding allele frequencies ranged from 0.0016 to 0.7589. All of the loci detected were highly polymorphic in the Bai population in Yunnan Province, except DXS6800. The values for the combined power of discrimination in females (PDf) and males (PDm) were 0.999999999999996 and 0.999999997487061, respectively. According to a phylogenetic tree, neighboring populations and different nationalities in the same area appeared to have relatively close evolutionary relationships. This study provides and complements X-chromosome genetic polymorphism data for the Bai people in Yunnan Province, Southwest China, and enriches the available reference materials for this Chinese minority population.
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9
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Perera N, Galhena G, Ranawaka G. Development of a 16 X-STR multiplex PCR system for kinship analysis and its applicability for the Sinhalese population in Sri Lanka. Int J Legal Med 2020; 135:161-166. [PMID: 33140262 DOI: 10.1007/s00414-020-02450-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 10/26/2020] [Indexed: 10/23/2022]
Abstract
The study describes the development of a new multiplex PCR system that simultaneously amplifies 16 X chromosome short tandem repeats (X-STRs) loci in a single PCR reaction and its applicability on a sample of 200 from the Sinhalese population in Sri Lanka. 13 X-STR loci located in four clusters are selected for the assay (DXS10148-DXS10135-DXS8378, DXS7132-DXS10079-DXS10074-DXS10075, DXS6801-DXS6809-DXS6789 and DXS7424-DXS101-DXS7133). In addition, three single loci were also selected (DXS9902, HPRTB and DXS7423). Genomic DNA extracted using the Chelex-100 method was amplified with modified published primers and subjected to capillary gel electrophoresis. Complete DNA profiles were obtained with 0.20 ng 9947A DNA and the band sizes ranged between 100 and 320 bp with 10 loci having sizes below 237 bp. A total of 160 alleles were observed among the sample with 5-23 alleles for each locus. The forensic efficiency evaluation showed high values for the combined power of discrimination in males (1 in 1 × 1010) and females (1 in 1 × 1017). Combined mean exclusion chance (MEC) indices calculated for deficiency, normal trio and duo cases were equally high (> 0.99999). Application of the new multiplex system to two actual kinship cases of full sibling and deficient paternity suggested that these 16 short tandem repeat loci are highly appropriate for forensic and kinship testing among the Sinhalese population.
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Affiliation(s)
- Nandika Perera
- Genetech Molecular Diagnostics, Colombo, 08, Sri Lanka. .,Faculty of Health Sciences, The Open University of Sri Lanka, Nawala, Sri Lanka.
| | - Gayani Galhena
- Department of Zoology and Environment Sciences, University of Colombo, Colombo, 03, Sri Lanka
| | - Gaya Ranawaka
- Faculty of Health Sciences, The Open University of Sri Lanka, Nawala, Sri Lanka
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Gomes I, Pinto N, Antão-Sousa S, Gomes V, Gusmão L, Amorim A. Twenty Years Later: A Comprehensive Review of the X Chromosome Use in Forensic Genetics. Front Genet 2020; 11:926. [PMID: 33093840 PMCID: PMC7527635 DOI: 10.3389/fgene.2020.00926] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 07/24/2020] [Indexed: 12/12/2022] Open
Abstract
The unique structure of the X chromosome shaped by evolution has led to the present gender-specific genetic differences, which are not shared by its counterpart, the Y chromosome, and neither by the autosomes. In males, recombination between the X and Y chromosomes is limited to the pseudoautosomal regions, PAR1 and PAR2; therefore, in males, the X chromosome is (almost) entirely transmitted to female offspring. On the other hand, the X chromosome is present in females with two copies that recombine along the whole chromosome during female meiosis and that is transmitted to both female and male descendants. These transmission characteristics, besides the obvious clinical impact (sex chromosome aneuploidies are extremely frequent), make the X chromosome an irreplaceable genetic tool for population genetic-based studies as well as for kinship and forensic investigations. In the early 2000s, the number of publications using X-chromosomal polymorphisms in forensic and population genetic applications increased steadily. However, nearly 20 years later, we observe a conspicuous decrease in the rate of these publications. In light of this observation, the main aim of this article is to provide a comprehensive review of the advances and applications of X-chromosomal markers in population and forensic genetics over the last two decades. The foremost relevant topics are addressed as: (i) developments concerning the number and types of markers available, with special emphasis on short tandem repeat (STR) polymorphisms (STR nomenclatures and practical concerns); (ii) overview of worldwide population (frequency) data; (iii) the use of X-chromosomal markers in (complex) kinship testing and the forensic statistical evaluation of evidence; (iv) segregation and mutation studies; and (v) current weaknesses and future prospects.
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Affiliation(s)
- Iva Gomes
- Institute for Research and Innovation in Health Sciences (i3S), University of Porto, Porto, Portugal.,Institute of Molecular Pathology and Immunology, University of Porto (IPATIMUP), Porto, Portugal
| | - Nádia Pinto
- Institute for Research and Innovation in Health Sciences (i3S), University of Porto, Porto, Portugal.,Institute of Molecular Pathology and Immunology, University of Porto (IPATIMUP), Porto, Portugal.,Center of Mathematics, Faculty of Sciences, University of Porto, Porto, Portugal
| | - Sofia Antão-Sousa
- Institute for Research and Innovation in Health Sciences (i3S), University of Porto, Porto, Portugal.,Institute of Molecular Pathology and Immunology, University of Porto (IPATIMUP), Porto, Portugal.,Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal.,DNA Diagnostic Laboratory (LDD), State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
| | - Verónica Gomes
- Institute for Research and Innovation in Health Sciences (i3S), University of Porto, Porto, Portugal.,Institute of Molecular Pathology and Immunology, University of Porto (IPATIMUP), Porto, Portugal
| | - Leonor Gusmão
- DNA Diagnostic Laboratory (LDD), State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
| | - António Amorim
- Institute for Research and Innovation in Health Sciences (i3S), University of Porto, Porto, Portugal.,Institute of Molecular Pathology and Immunology, University of Porto (IPATIMUP), Porto, Portugal.,Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
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Lin L, Li J, Hu Y, Wang H, Marah FA, Moseray M, Kureshi A, Wang C, Zeye MMJ, Zha L. Genetic characterization of 19 X-STRs in Sierra Leone population from Freetown. Int J Legal Med 2020; 134:1659-1661. [PMID: 31897669 DOI: 10.1007/s00414-019-02243-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Accepted: 12/19/2019] [Indexed: 11/26/2022]
Abstract
A total of 550 individuals (265 males and 285 females) from Sierra Leone, a west-African coastal country, were genotyped using the Microreader™ 19X ID System kit. No significant deviations from the Hardy-Weinberg equilibrium were observed. A total of 250 alleles were identified with corresponding allele frequencies spanning from 0.0012 to 0.6762. PIC of the loci ranged from 0.4615 to 0.9481. The CPE, CPDF, and CPDM were 0.9999997856, 0.999999999999999999995774, and 0.999999999998997, respectively. The highly combined MECKruger, MECKishida, MECDesmarais, and MECDesmarais Duo were achieved as 0.99999992508, 0.999999999990802, 0.999999999990836, and 0.99999998412, respectively. Genetic comparisons revealed that genetic homogeneity existed in similar ethno origin or geographic origin populations. This is a pioneering genetic investigation using the Microreader™ 19X ID System kit in the population of Sierra Leone.
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Affiliation(s)
- Lin Lin
- Xiangya Hospital, Central South University, No87. Xiangya Road, Changsha, Hunan, People's Republic of China
- Reproductive Medicine Center, Fujian Provincial Maternity and Children's Hospital, No18. Daoshan Road, Fuzhou, Fujian, People's Republic of China
| | - Jienan Li
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, No172. Tongzipo Road, Changsha, 410013, Hunan Province, People's Republic of China
| | - Yize Hu
- Wuxi Municipal Public Security Bureau, Wuxi, Jiangsu, People's Republic of China
| | - Han Wang
- Department of Clinical Diagnostic Centre, the Fifth Medical Centre, Chinese PLA (People's Liberation Army) General Hospital, Beijing, People's Republic of China
| | - Foday Ambrose Marah
- The GREY Bush Community Health Center, Grey Bush, Ascension-town, Sierra Leone
| | - Moses Moseray
- Joint Medical Unit, Freetown, Sierra Leone
- Clinical Laboratory, 34 Military hospital, Freetown, Sierra Leone
| | - Aliye Kureshi
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, No172. Tongzipo Road, Changsha, 410013, Hunan Province, People's Republic of China
| | - Chudong Wang
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, No172. Tongzipo Road, Changsha, 410013, Hunan Province, People's Republic of China
| | - Moutanou Modeste Judes Zeye
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, No172. Tongzipo Road, Changsha, 410013, Hunan Province, People's Republic of China
- Laboratory of Molecular Biology and Genetics (LMBG), University Joseph KI - ZERBO, CERBA/LABIOGENE, 01 BP 364, Ouagadougou 01, Burkina Faso
| | - Lagabaiyila Zha
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, No172. Tongzipo Road, Changsha, 410013, Hunan Province, People's Republic of China.
- China-Africa Research Center of Infectious Deseases, Central South University, Changsha, People's Republic of China.
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Singh G, Sandhu HS, Srinivas Y, Matharoo K, Bhanwer AJS. Genetic portrait of North-West Indian population based on X chromosome Alu insertion markers. Int J Legal Med 2019; 134:1655-1657. [PMID: 31853675 DOI: 10.1007/s00414-019-02238-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 12/11/2019] [Indexed: 11/25/2022]
Abstract
In the present study, allele frequencies and forensic parameters of four ethnic groups (Brahmin, Khatri, Jat Sikh, and Scheduled Caste) of Punjab, India, at 10 Alu insertions of X chromosome were calculated. Six Alu markers were observed to be highly polymorphic with no significant deviations from Hardy-Weinberg equilibrium and no linkage disequilibrium present in any marker. Multidimensional plot showed higher genetic affinity of studied populations with Asian populations. Overall, the tested markers were reliable and were found suitable in human forensics and population genetic studies.
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Affiliation(s)
- Gagandeep Singh
- Department of Anthropology, Panjab University, Chandigarh, India.
- Department of Human Genetics, Guru Nanak Dev University, Amritsar, Punjab, India.
| | - Harkirat Singh Sandhu
- Icahn School of Medicine at Mount Sinai, Tisch Cancer Institute, 1470 Madison Avenue, New York, NY, USA
| | | | - Kawaljit Matharoo
- Department of Human Genetics, Guru Nanak Dev University, Amritsar, Punjab, India
| | - A J S Bhanwer
- Department of Human Genetics, Guru Nanak Dev University, Amritsar, Punjab, India
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Chia WC, Khoo TS, Abdul Wahid SFS, Razak NFA, Alauddin H, Raja Sabudin RZA, Othman A, Hassan R, Hussin NH. Multiplex STR panel for assessment of chimerism following hematopoietic stem cell transplantation (HSCT). Ann Hematol 2019; 98:1279-1291. [PMID: 30783731 DOI: 10.1007/s00277-019-03626-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Accepted: 01/28/2019] [Indexed: 11/26/2022]
Abstract
Short tandem repeat (STR) analysis is used in chimerism monitoring after allogeneic hematopoietic stem cell transplantation (HSCT) for patients with various hematologic malignancies. Commercial forensic STR kits often contain loci with huge differences in power of discrimination (PD) across populations, causing some loci to be less informative for chimerism analysis in certain populations. This study aimed to construct a new STR multiplex panel with highly informative loci for efficient chimerism analysis. Thirteen STR markers which exhibit high PD (> 0.9) in at least 80% of 50 populations globally were selected to form a new panel and used in STR analysis of 253 Malaysian subjects. Cumulative power of discrimination (CPD) and combined power of exclusion (CPE) were determined from 253 Malaysian individuals. Loci informativity was assessed and compared to the commercial AmpFLSTR Identifiler PCR Amplification kit in 14 donor-recipient pairs. The new panel had detected 202 unique alleles including five novel alleles from the 253 individuals with high CPD and CPE (> 0.99999999999999999 and > 0.999999997 respectively). All loci from the new panel in the donor-recipient pair analysis showed higher than 50% informativity, while five loci from the commercial kit demonstrated lower than 50% informativity. Four loci from the new panel ranked the highest informativity. A sequenced allelic ladder which consists of 202 unique alleles from the 253 subjects was also developed to ensure accurate allele designation. The new 13-loci STR panel, thus, could serve as an additional powerful, accurate, and highly informative panel for chimerism analysis for HSCT patients.
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Affiliation(s)
- Wui Chuen Chia
- Hematology Unit, Department of Pathology, Faculty of Medicine, Universiti Kebangsaan Malaysia Medical Centre, Jalan Yaacob Latif, Bandar Tun Razak, Cheras, 56000, Kuala Lumpur, Malaysia
| | - Tze Sean Khoo
- UKM Medical Molecular Biology Institute, National University of Malaysia, Jalan Yaacob Latif, Bandar Tun Razak, 56000 Cheras, Kuala Lumpur, Malaysia
| | - S Fadilah S Abdul Wahid
- Cell Therapy Center, Universiti Kebangsaan Malaysia Medical Centre, Jalan Yaacob Latif, Bandar Tun Razak, Cheras, 56000, Kuala Lumpur, Malaysia
| | - Noor Farisah Abdul Razak
- Hematology Unit, Department of Pathology, Faculty of Medicine, Universiti Kebangsaan Malaysia Medical Centre, Jalan Yaacob Latif, Bandar Tun Razak, Cheras, 56000, Kuala Lumpur, Malaysia
| | - Hafiza Alauddin
- Hematology Unit, Department of Pathology, Faculty of Medicine, Universiti Kebangsaan Malaysia Medical Centre, Jalan Yaacob Latif, Bandar Tun Razak, Cheras, 56000, Kuala Lumpur, Malaysia
| | - Raja Zahratul Azma Raja Sabudin
- Hematology Unit, Department of Pathology, Faculty of Medicine, Universiti Kebangsaan Malaysia Medical Centre, Jalan Yaacob Latif, Bandar Tun Razak, Cheras, 56000, Kuala Lumpur, Malaysia
| | - Ainoon Othman
- Department of Medical Science II, Faculty of Medicine and Health Science, Islamic Science University of Malaysia, Kuala Lumpur, Malaysia
| | - Roshida Hassan
- National Blood Centre, Jalan Tun Razak, Titiwangsa, 50400, Kuala Lumpur, Malaysia
| | - Noor Hamidah Hussin
- Hematology Unit, Department of Pathology, Faculty of Medicine, Universiti Kebangsaan Malaysia Medical Centre, Jalan Yaacob Latif, Bandar Tun Razak, Cheras, 56000, Kuala Lumpur, Malaysia.
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14
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Sun S, Yang Z, Wen D, Lan L, Xie P, Xiao J, Li G, Zhu W, Zha L. Genetic polymorphism investigation of 16 X-STR loci in a Han population in Central South China. Forensic Sci Int Genet 2018; 39:e21-e23. [PMID: 30538076 DOI: 10.1016/j.fsigen.2018.11.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 10/07/2018] [Accepted: 11/25/2018] [Indexed: 11/19/2022]
Affiliation(s)
- Shule Sun
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, Changsha, 410013, Hunan, PR China
| | - Zedeng Yang
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, Changsha, 410013, Hunan, PR China
| | - Dan Wen
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, Changsha, 410013, Hunan, PR China
| | - Lingmei Lan
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, Changsha, 410013, Hunan, PR China
| | - Pingli Xie
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, Changsha, 410013, Hunan, PR China
| | - Junxin Xiao
- Center of Forensic Services of Xiangya of Hunan Province, Changsha, 410013, Hunan, PR China
| | - Guanlin Li
- Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Key Clinical Laboratory of Henan Province, Zhengzhou, 450052, PR China
| | - Wenbing Zhu
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medicine, Central South University, Changsha, 410013, Hunan, PR China.
| | - Lagabaiyila Zha
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, Changsha, 410013, Hunan, PR China.
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Xing J, Adnan A, Rakha A, Kasim K, Noor A, Xuan J, Zhang X, Yao J, McNevin D, Wang B. Genetic analysis of 12 X-STRs for forensic purposes in Liaoning Manchu population from China. Gene 2018; 683:153-158. [PMID: 30326331 DOI: 10.1016/j.gene.2018.10.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 10/04/2018] [Accepted: 10/09/2018] [Indexed: 11/29/2022]
Abstract
X-chromosomal short tandem repeats (X-STRs) have been widely used in forensic practice involving complicated cases of kinship and also play an increasingly important role in population genetics. X-STRs have been studied in regional populations of China but there is a lack of data for the Manchu population. In this study, we have investigated the forensic genetic properties of 12 X-STRs in the Investigator Argus X-12 Kit (QIAGEN, Hilden, Germany) in 772 Manchu (male = 514, female = 258) individuals from the Xiuyan and Huanren Manchu autonomous counties of Liaoning province. We observed a total of 166 alleles at 12 X-STR loci with allele frequencies ranging from 0.001295to 0.615285. The most polymorphic locus was DXS10135 with 24 alleles while DXS7423 was the least polymorphic locus with 5 alleles. We found significant linkage disequilibrium (LD) between the following pairs of markers for males: DXS10103/DXS10101, DXS10135/DXS10146, DXS10101/DXS10148, DXS10135/DXS10148, DXS7423/DXS10148 and DXS10079/DXS10148. For females, LD was only observed for DXS10103/DXS10101. The combined power of discrimination was 0.9999999979699 for males and 0.999999999999998 for females. The numbers of observed haplotypes in Manchu males were 310, 172, 182 and 172 in four linkage groups; LG1, LG2, LG3 and LG4, respectively, however, these linkage groups did not form stable haplotypes as indicated by linkage equilibrium (LE) of STRs within the groups and significant LD between the groups. This study represents an extensive report on X-STR marker variation in the Manchu population for forensic applications and population genetic studies.
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Affiliation(s)
- Jiaxin Xing
- Department of Forensic Genetics, School of Forensic Medicine, China Medical University Shenyang, Liaoning 110122, China
| | - Atif Adnan
- Department of Forensic Genetics, School of Forensic Medicine, China Medical University Shenyang, Liaoning 110122, China.
| | - Allah Rakha
- Department of Forensic Science, University of Health Sciences, Lahore 54000, Pakistan
| | - Kadirya Kasim
- Department of Forensic Genetics, School of Forensic Medicine, China Medical University Shenyang, Liaoning 110122, China
| | - Anam Noor
- Department of Forensic Science, University of Health Sciences, Lahore 54000, Pakistan
| | - Jinfeng Xuan
- Department of Forensic Genetics, School of Forensic Medicine, China Medical University Shenyang, Liaoning 110122, China
| | - Xicen Zhang
- Department of Forensic Genetics, School of Forensic Medicine, China Medical University Shenyang, Liaoning 110122, China
| | - Jun Yao
- Department of Forensic Genetics, School of Forensic Medicine, China Medical University Shenyang, Liaoning 110122, China
| | - Dennis McNevin
- Centre for Forensic Science, School of Mathematical and Physical Sciences, University of Technology Sydney, Australia
| | - Baojie Wang
- Department of Forensic Genetics, School of Forensic Medicine, China Medical University Shenyang, Liaoning 110122, China.
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Di Santo Meztler GP, Del Palacio S, Esteban ME, Armoa I, Argüelles CF, Catanesi CI. Genetic Differentiation of North-East Argentina Populations Based on 30 Binary X Chromosome Markers. Front Genet 2018; 9:208. [PMID: 29951085 PMCID: PMC6008373 DOI: 10.3389/fgene.2018.00208] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 05/24/2018] [Indexed: 01/21/2023] Open
Abstract
Alu insertions, INDELs, and SNPs in the X chromosome can be useful not only for revealing relationships among populations but also for identification purposes. We present data of 10 Alu insertions, 5 INDELs, and 15 SNPs of X-chromosome from three Argentinian north-east cities in order to gain insight into the genetic diversity of the X chromosome within this region of the country. Data from 198 unrelated individuals belonging to Posadas, Corrientes, and Eldorado cities were genotyped for Ya5DP62, Yb8DP49, Ya5DP3, Ya5NBC37, Ya5DP77, Ya5NBC491, Ya5DP4, Ya5DP13, Yb8NBC634, and Yb8NBC102 Alu insertions, for MID193, MID1705, MID3754, MID3756 and MID1540 Indels and for rs6639398, rs5986751, rs5964206, rs9781645, rs2209420, rs1299087, rs318173, rs933315, rs1991961, rs4825889, rs1781116, rs1937193, rs1781104, rs149910, and rs652 SNPs. No deviations from Hardy-Weinberg equilibrium were observed for Posadas and Corrientes. However, Eldorado showed significant values, and it was found to have an internal substructuring with two groups of different origin, one showing higher similarity with European countries, and the other with more similarities to Posadas and Corrientes. Fst pairwise genetic distances emerged for some markers among the studied populations and also between our data and those from other countries and continents. Of particular interest, Alu insertions demonstrated the most differences, and could be of use in ancestry studies for these populations, while INDELs and SNPs variation were informative for differentiation within the country.
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Affiliation(s)
- Gabriela P Di Santo Meztler
- Laboratorio de Diversidad Genética, IMBICE, CICPBA-Consejo Nacional de Investigaciones Científicas y Técnicas, La Plata, Argentina
| | - Santiago Del Palacio
- Instituto Argentino de Radioastronomía, CCT-La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, CICPBA, Villa Elisa, Argentina
| | - María E Esteban
- Secció de Zoologia i Antropologia Biológica, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain.,Institut de Recerca de la Biodiversitat, Universitat de Barcelona, Barcelona, Spain
| | - Isaías Armoa
- Dirección de Desarrollo e Integración Regional Municipalidad de Eldorado, Misiones, Argentina
| | - Carina F Argüelles
- LACyGH-GIGA, Instituto de Biología Subtropical, nodo Posadas-Dpto. de Genética-FCEQyN UNaM-Consejo Nacional de Investigaciones Científicas y Técnicas, Posadas, Argentina
| | - Cecilia I Catanesi
- Laboratorio de Diversidad Genética, IMBICE, CICPBA-Consejo Nacional de Investigaciones Científicas y Técnicas, La Plata, Argentina.,Cátedra de Genética, Facultad de Cs. Naturales y Museo, UNLP, La Plata, Argentina
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17
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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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18
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Messoussi M, Prieto-Fernández E, Baeta M, Núñez C, Gaaied ABAE, de Pancorbo MM, Fadhlaoui-Zid K. Genetic variation of 17 X-chromosome STR loci in Tunisian population of Nabeul. Int J Legal Med 2018; 133:85-88. [PMID: 29569161 DOI: 10.1007/s00414-018-1827-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 03/13/2018] [Indexed: 10/17/2022]
Abstract
In the present study, the genetic variations of 17 X-STR markers (DXS8378, DXS9898, DXS7133, GATA31E08, GATA172D05, DXS6801, DXS7423, DXS6809, DXS6799, DXS7132, DXS9902, DXS6800, DXS6789, DXS10075, DXS10079, DXS6807, and DXS6803) were analyzed in 139 unrelated individuals in Nabeul, aiming to perform an X-STR database for anthropological and forensic purposes. Our results indicate that DXS6809 was the most polymorphic locus, whereas DXS6807 was the least informative marker. In addition, the obtained values for the statistical parameters of forensic interest, i.e., the power of discrimination in males (PDM) and females (PDF), as well as the mean exclusion chance in duos (MECD) and trios (MECT) have demonstrated that this panel of 17 X-STRs is highly informative and useful for forensic application and anthropological research. Additionally, pairwise genetic distances based on FST were calculated between Nabeul population and other populations extracted from the literature. Genetic distances were represented in a non-metric MDS plot and clustering of populations according to their geographic locations and their historical relationship was detected.
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Affiliation(s)
- Monia Messoussi
- Laboratory of Genetics, Immunology, and Human Pathologies, Faculty of Science of Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Endika Prieto-Fernández
- BIOMICs Research Group, Lascaray Research Center, University of the Basque Country UPV/EHU, Avda, Miguel de Unamuno, 3, 01006, Vitoria-Gasteiz, Spain
| | - Miriam Baeta
- BIOMICs Research Group, Lascaray Research Center, University of the Basque Country UPV/EHU, Avda, Miguel de Unamuno, 3, 01006, Vitoria-Gasteiz, Spain
| | - Carolina Núñez
- BIOMICs Research Group, Lascaray Research Center, University of the Basque Country UPV/EHU, Avda, Miguel de Unamuno, 3, 01006, Vitoria-Gasteiz, Spain
| | - Amel Ben Ammar-El Gaaied
- Laboratory of Genetics, Immunology, and Human Pathologies, Faculty of Science of Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Marian M de Pancorbo
- BIOMICs Research Group, Lascaray Research Center, University of the Basque Country UPV/EHU, Avda, Miguel de Unamuno, 3, 01006, Vitoria-Gasteiz, Spain
| | - Karima Fadhlaoui-Zid
- Laboratory of Genetics, Immunology, and Human Pathologies, Faculty of Science of Tunis, University Tunis El Manar, Tunis, Tunisia.
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StatsX v2.0: the interactive graphical software for population statistics on X-STR. Int J Legal Med 2018; 133:39-44. [DOI: 10.1007/s00414-018-1824-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 03/07/2018] [Indexed: 10/17/2022]
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20
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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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Whole Genome Amplification of Day 3 or Day 5 Human Embryos Biopsies Provides a Suitable DNA Template for PCR-Based Techniques for Genotyping, a Complement of Preimplantation Genetic Testing. BIOMED RESEARCH INTERNATIONAL 2017; 2017:1209158. [PMID: 28717645 PMCID: PMC5498896 DOI: 10.1155/2017/1209158] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2017] [Revised: 03/31/2017] [Accepted: 04/24/2017] [Indexed: 12/20/2022]
Abstract
Our objective was to determine if whole genome amplification (WGA) provides suitable DNA for qPCR-based genotyping for human embryos. Single blastomeres (Day 3) or trophoblastic cells (Day 5) were isolated from 342 embryos for WGA. Comparative Genomic Hybridization determined embryo sex as well as Trisomy 18 or Trisomy 21. To determine the embryo's sex, qPCR melting curve analysis for SRY and DYS14 was used. Logistic regression indicated a 4.4%, 57.1%, or 98.8% probability of a male embryo when neither gene, SRY only, or both genes were detected, respectively (accuracy = 94.1%, kappa = 0.882, and p < 0.001). Fluorescent Capillary Electrophoresis for the amelogenin genes (AMEL) was also used to determine sex. AMELY peak's height was higher and this peak's presence was highly predictive of male embryos (AUC = 0.93, accuracy = 81.7%, kappa = 0.974, and p < 0.001). Trisomy 18 and Trisomy 21 were determined using the threshold cycle difference for RPL17 and TTC3, respectively, which were significantly lower in the corresponding embryos. The Ct difference for TTC3 specifically determined Trisomy 21 (AUC = 0.89) and RPL17 for Trisomy 18 (AUC = 0.94). Here, WGA provides adequate DNA for PCR-based techniques for preimplantation genotyping.
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Genetic characterization of an X-STR decaplex system in the State of Mato Grosso, Brazil: distribution, forensic efficiency and population structure. Int J Legal Med 2017; 131:1523-1530. [PMID: 28405752 DOI: 10.1007/s00414-017-1578-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 03/17/2017] [Indexed: 10/19/2022]
Abstract
Studies with X-STR loci show population genetic substructure, which makes necessary the characterization of such markers in the different geographical and/or ethnic populations. Therefore, this study assessed the distribution and forensic efficiency of an X-STR decaplex system in the population of the State of Mato Grosso, as well as analysed the population structure of this State based on the aforementioned system. All X-STR markers were in Hardy-Weinberg equilibrium and linkage equilibrium, and the DXS6809 was the most informative marker. The power of discrimination value in females and males was 0.99999999995 and 0.9999994, respectively. Analysis of molecular variance indicated 1.10% (p < 0.00001) of heterogeneity among Europeans, Africans, Brazilians and other Latin Americans, and in relation to such groups, the population of the State of Mato Grosso showed lower genetic variation when compared with the Brazilian group (-0.10%, p = 0.67327). The genetic distance analysis showed lower values of F ST (0.0004 ≤ F ST ≤ 0.00331), with non-significant p value (p > 0.00024), between the populations of Mato Grosso and Mato Grosso do Sul, Paraná and the Southeast region of Brazil (except for one sample of Rio de Janeiro). F ST values with significant p values (p ≤ 0.00024) were obtained between the population of Mato Grosso and Iberian, African and some Latin American populations. The X-STR decaplex system proved to be extremely useful in the population of the State of Mato Grosso, and the data obtained does not show the need for a specific forensic database for this State in relation to the Brazilian populations compared in this study, except for population of Rio de Janeiro.
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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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Fan GY, Ye Y, Hou YP. Detecting a hierarchical genetic population structure via Multi-InDel markers on the X chromosome. Sci Rep 2016; 6:32178. [PMID: 27535707 PMCID: PMC4989243 DOI: 10.1038/srep32178] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 08/03/2016] [Indexed: 01/15/2023] Open
Abstract
Detecting population structure and estimating individual biogeographical ancestry are very important in population genetics studies, biomedical research and forensics. Single-nucleotide polymorphism (SNP) has long been considered to be a primary ancestry-informative marker (AIM), but it is constrained by complex and time-consuming genotyping protocols. Following up on our previous study, we propose that a multi-insertion-deletion polymorphism (Multi-InDel) with multiple haplotypes can be useful in ancestry inference and hierarchical genetic population structures. A validation study for the X chromosome Multi-InDel marker (X-Multi-InDel) as a novel AIM was conducted. Genetic polymorphisms and genetic distances among three Chinese populations and 14 worldwide populations obtained from the 1000 Genomes database were analyzed. A Bayesian clustering method (STRUCTURE) was used to discern the continental origins of Europe, East Asia, and Africa. A minimal panel of ten X-Multi-InDels was verified to be sufficient to distinguish human ancestries from three major continental regions with nearly the same efficiency of the earlier panel with 21 insertion-deletion AIMs. Along with the development of more X-Multi-InDels, an approach using this novel marker has the potential for broad applicability as a cost-effective tool toward more accurate determinations of individual biogeographical ancestry and population stratification.
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Affiliation(s)
- Guang Yao Fan
- Department of Forensic Genetics, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu 610041, Sichuan, China
- The Center for Forensic Science Research, Department of Public Security Technology, Railway Police College, Zhengzhou 450053, China
| | - Yi Ye
- The Center for Forensic Science Research, Department of Public Security Technology, Railway Police College, Zhengzhou 450053, China
- Department of Forensic Analytical Toxicology, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu 610041, Sichuan, China
| | - Yi Ping Hou
- Department of Forensic Genetics, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu 610041, Sichuan, China
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Crnjac J, Ozretić P, Merkaš S, Ratko M, Lozančić M, Rožić S, Špoljarić D, Korolija M, Popović M, Mršić G. Analysis of 12 X-chromosomal markers in the population of central Croatia. Leg Med (Tokyo) 2016; 21:77-84. [PMID: 27497338 DOI: 10.1016/j.legalmed.2016.07.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Revised: 05/12/2016] [Accepted: 07/01/2016] [Indexed: 02/05/2023]
Abstract
Investigator® Argus X-12 Kit is a commercially available set that allows simultaneous PCR amplification of 12 X-STR markers belonging to four linkage groups (LG). To assess the forensic efficiency of these markers for the population of central Croatia and consequent applicability in routine forensic casework, DNA from 200 blood samples of unrelated donors (100 female and 100 male) was amplified by Investigator® Argus X-12 Kit and analyzed by capillary electrophoresis. Statistical computations based on allele and haplotype frequencies for LG1 - LG4 were performed using Arlequin 3.5 software and on-line tool available at ChrX-STR.org. In female samples, all X-STR markers were in Hardy-Weinberg equilibrium (HWE). The most informative marker for central Croatia population was DXS10135 with polymorphism information content (PIC) 0.9296. The least polymorphic locus was DXS8378 (PIC=0.6363). Power of discrimination (PD) varied from 0.6968 to 0.9336 in male and from 0.8476 to 0.9916 in female samples. Combined PD exceeded 0.999999999 in both men and women. In male samples, linkage disequilibrium (LD) test revealed significant association (P=0.0000) of one marker pair in LG4 and two marker pairs in LG3. Portion of observed haplotypes in the number of possible haplotypes varied from 2.86% to 7.47% across all LGs. LG1 was the most informative with haplotype diversity (H) 0.9972. High PD of all analyzed markers exhibited for central Croatia population confirms suitability of Investigator® Argus X-12 for forensic pertinence. Moreover, results of this study will be included in establishing a national reference X-STR database based on 12 X-STR loci, which is necessary for the correct interpretation of the forensic casework results.
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Affiliation(s)
- 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
| | - Martina Ratko
- Forensic Science Centre "Ivan Vučetić", Zagreb, Croatia
| | | | - Sara Rožić
- Forensic Science Centre "Ivan Vučetić", Zagreb, Croatia; Forensic Science Office, University of Zagreb, Zagreb, Croatia
| | - Daniel Špoljarić
- 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
| | - Maja Popović
- Faculty of Veterinary Medicine, University of Zagreb, Zagreb, Croatia
| | - Gordan Mršić
- Forensic Science Centre "Ivan Vučetić", Zagreb, Croatia; Forensic Science Office, University of Zagreb, Zagreb, Croatia.
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Caputo M, Amador MA, Santos S, Corach D. Potential forensic use of a 33 X-InDel panel in the Argentinean population. Int J Legal Med 2016; 131:107-112. [DOI: 10.1007/s00414-016-1399-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 06/03/2016] [Indexed: 01/16/2023]
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Baluchi and Pakhtun population data of 9 X-chromosomal short tandem repeat loci. J Forensic Leg Med 2015; 37:45-9. [PMID: 26580724 DOI: 10.1016/j.jflm.2015.10.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Revised: 09/08/2015] [Accepted: 10/24/2015] [Indexed: 11/23/2022]
Abstract
Baluchistan is the largest province of Pakistan in terms of area, constituting approximately 44% of the country's total land mass, and the smallest in terms of population, being home to less than 5% of the country's population. Khyber Pakhtunkhwa (KPK) formerly called North-West Frontier Province is located in the north-west of Pakistan having an estimated 13.4% of total population of Pakistan in which Pakhtuns are the major ethnic group. A total of 250 samples from Baluchi population and 250 samples from Pakhtun population were typed for 9 X-chromosomal STR markers: DXS101, DXS6789, DXS7132, DXS7423, DXS7424, DXS8378, GATA31E08, GATA172D05 and HPRTB along with sex typing locus, Amelogenin. A total of 59 alleles were found in Baluchi population while 61 alleles were found in Pakhtun population. This is the first study of the two populations based on these markers and the population data can be used as reference database for Baluchi and Pakhtun populations.
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Fan G, Ye Y, Luo H, Hou Y. Use of multi-InDels as novel markers to analyze 13 X-chromosome haplotype loci for forensic purposes. Electrophoresis 2015; 36:2931-8. [PMID: 26265037 DOI: 10.1002/elps.201500159] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Revised: 06/11/2015] [Accepted: 08/04/2015] [Indexed: 12/27/2022]
Affiliation(s)
- Guangyao Fan
- Department of Forensic Genetics, West China School of Basic Science and Forensic Medicine; Sichuan University; Chengdu Sichuan P. R. China
| | - Yi Ye
- Department of Forensic Analytical Toxicology, West China School of Basic Science and Forensic Medicine; Sichuan University; Chengdu Sichuan P. R. China
| | - Haibo Luo
- Department of Forensic Genetics, West China School of Basic Science and Forensic Medicine; Sichuan University; Chengdu Sichuan P. R. China
| | - Yiping Hou
- Department of Forensic Genetics, West China School of Basic Science and Forensic Medicine; Sichuan University; Chengdu Sichuan P. R. China
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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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Variation of X-chromosomal microsatellites in Belarus within the context of their genetic diversity in Europe. Forensic Sci Int Genet 2015; 16:105-111. [DOI: 10.1016/j.fsigen.2014.12.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2014] [Revised: 12/30/2014] [Accepted: 12/31/2014] [Indexed: 11/20/2022]
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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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33
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Zidkova A, Capek P, Horinek A, Coufalova P. Investigator® Argus X-12 study on the population of Czech Republic: Comparison of linked and unlinked X-STRs for kinship analysis. Electrophoresis 2014; 35:1989-92. [DOI: 10.1002/elps.201400046] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Revised: 04/08/2014] [Accepted: 04/08/2014] [Indexed: 11/12/2022]
Affiliation(s)
- Anastassiya Zidkova
- Institute of Biology and Medical Genetics; First Faculty of Medicine; Charles University in Prague and General University
- Institute of Forensic Medicine and Toxicology; First Faculty of Medicine; Charles University in Prague; Prague Czech Republic
| | - Pavel Capek
- Institute of Criminalistics Prague; Prague Czech Republic
| | - Ales Horinek
- Institute of Biology and Medical Genetics; First Faculty of Medicine; Charles University in Prague and General University
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Israr M, Shahid AA, Rahman Z, Zar MS, Shahzad MS, Husnain T, Pfeifer C, Wiegand P. Development and characterization of a new 12-plex ChrX miniSTR system. Int J Legal Med 2014; 128:595-8. [PMID: 24789265 DOI: 10.1007/s00414-014-1009-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Accepted: 03/06/2014] [Indexed: 11/29/2022]
Abstract
Short tandem repeat (STR) markers are extensively used for human identification as well as paternity and forensic casework. X-chromosome STR (X-STR) markers are a powerful complementary system especially in deficiency paternity testing. This study presents the development and characterization of a new X-chromosomal short tandem repeat (STR) multiplex using short amplicon (<200 bp). A total of 366 samples from Punjabi population and 346 samples from Sindhi population were typed for 11 X-chromosomal STR markers: DXS101, DXS6789, DXS6793, DXS7132, DXS7423, DXS7424, DXS8378, DXS9902, GATA31E08, GATA172D05, and HPRTB along with sex-typing locus, amelogenin. Each marker showed a high degree of polymorphism, and the multiplex was sensitive down to 250 pg of human DNA. A total of 78 alleles were found with 5-11 alleles for each marker. The population data can be used as reference database for Sindhi and Punjabi populations.
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Affiliation(s)
- Muhammad Israr
- National Centre of Excellence in Molecular Biology, University of the Punjab, 87-West Canal Bank Road, Lahore, -53700, Pakistan,
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X-chromosome STR markers data in a Cabo Verde immigrant population of Lisboa. Mol Biol Rep 2014; 41:2559-69. [PMID: 24474659 DOI: 10.1007/s11033-014-3114-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Accepted: 01/10/2014] [Indexed: 10/25/2022]
Abstract
Population genetic data of 12 X chromosomal short tandem repeats markers (DXS10074, DXS10079, DXS10101, DXS10103, DXS10134, DXS10135, DXS10146, DXS10148, DXS7132, DXS7423, DXS8378 and HPRTB) were analysed in 54 females and 95 males of an immigrant population from Cabo Verde living in Lisboa. The obtained results for forensic statistical parameters such as observed heterozigosity, polymorphism information content, power of discrimination and mean exclusion chance, based on single allele frequencies, reveal that this multiplex system is highly informative and can represent an important tool for genetic identification purposes in the immigrant population of Cabo Verde. Since the studied short tandem repeats genetic markers are distributed on four linkage groups, that can provide independent genotype information, we studied those groups as haploytes. The forensic efficiency parameters for the linked groups were all higher than 0.97, with linkage group I being the most polymorphic and linkage group III the less informative.
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Population genetic data for 15 X chromosomal short tandem repeat markers in three U.S. populations. Forensic Sci Int Genet 2013; 8:64-7. [PMID: 24315590 DOI: 10.1016/j.fsigen.2013.07.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Revised: 07/07/2013] [Accepted: 07/11/2013] [Indexed: 11/21/2022]
Abstract
314 African American, 434 U.S. Caucasian, and 398 U.S. Hispanic individuals were typed at X STR markers DXS6795, DXS9902, DXS8378, DXS7132, DXS6803, DXS6789, DXS7424, DXS101, GATA172D05, DXS7130, GATA165B12, HPRTB, GATA31E08, DXS10147, DXS7423. High forensic efficiency parameter values confirm the potential usefulness of these markers in certain specific kinship situations involving female offspring as well as identity testing. Alleles previously unobserved in U.S. populations were noted in this study at 8 different markers. Additionally, null alleles and a triallelic pattern were observed and described. Pairwise comparisons indicated consistency with similar published populations at overlapping markers. These data represent a substantial increase in the quantity of U.S. X chromosomal short tandem repeat data available to the community.
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Gršković B, Zidkova A, Stenzl V, Popović M, Primorac D, Mršić G. Analysis of 8 X-chromosomal markers in the population of central Croatia. Croat Med J 2013; 54:238-47. [PMID: 23771754 PMCID: PMC3692332 DOI: 10.3325/cmj.2013.54.238] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Aim To analyze 8 X-linked short tandem repeat (STR) markers in the population of central Croatia and to evaluate their forensic efficiency. Methods We carried out a statistical analysis of the data from previously performed genetic analyses, collected during routine forensic work by the Forensic Science Centre ‘‘Ivan Vučetić.’’ Mentype® Argus X-8 PCR amplification kit was used for typing the data of 99 unrelated healthy women and 78 men from central Croatia. Haplotype frequencies were calculated only in male samples. Arlequin 3.5 software was used to assess Hardy-Weinberg equilibrium (HWE), linkage disequilibrium (LD), observed and expected heterozygosity. Power of discrimination (PD) for men and women, polymorphism information content (PIC), power of exclusion, and mean exclusion chance for deficiency cases, normal trios, and duos were determined using online database ChrX-STR.org. Results In female samples, deviations from HWE (P = 0.006) for each locus were not found. LD test performed both on female and male samples revealed no significant association between markers (P = 0.002). DXS10135 was the most polymorphic locus (PIC = 0.931). PD varied from 0.692 to 0.935 in male and from 0.845 to 0.992 in female samples. Combined PD reached 99.999999% in men and 99.9999999999% in women. Conclusion Performed analyses revealed that the studied marker set contained polymorphic markers with high power of discrimination. We can conclude that Mentype® Argus X-8 PCR kit is suitable for application in the population of central Croatia. Results of this study, together with collected allele and haplotype frequencies, are the first step in establishing a national reference X-STR database based on 8 X-STR loci.
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Affiliation(s)
- Branka Gršković
- Forensic Science Centre "Ivan Vucetic", General Police Directorate, Ministry of Interior, Ilica 335, 10000 Zagreb, Croatia.
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Tetzlaff S, Wegener R, Lindner I. Population genetic investigation of eight X-chromosomal short tandem repeat loci from a northeast German sample. Forensic Sci Int Genet 2012; 6:e155-6. [DOI: 10.1016/j.fsigen.2012.03.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2011] [Revised: 02/29/2012] [Accepted: 03/25/2012] [Indexed: 11/30/2022]
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Mukerjee S, Mukherjee M, Ghosh T, Kalpana D, Sharma AK. Population genetic data for 11 X-STR loci in eleven populations of India. Leg Med (Tokyo) 2012; 14:163-5. [DOI: 10.1016/j.legalmed.2012.01.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2011] [Revised: 01/10/2012] [Accepted: 01/10/2012] [Indexed: 11/24/2022]
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40
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Capillary electrophoresis of an X-chromosome STR decaplex for kinship deficiency cases. Methods Mol Biol 2012; 830:57-71. [PMID: 22139653 DOI: 10.1007/978-1-61779-461-2_5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
During the two last decades, STR markers located on the autosomes have been gaining relevance and have nearly replaced the use of other type of markers in most cases of genetic identification, paternity testing, as well as in other situations of kinship analysis. Nevertheless, in some complex cases, independently of the number of polymorphisms being typed, autosomal markers convey very little information. Depending on the parentage constellation available for analysis, as well as the gender of the subjects, this problem can sometimes be solved by using markers that have different modes of transmission. Therefore, most forensic laboratories are nowadays prepared to analyse lineage markers (Y chromosome and mtDNA) and many have recently set up methods for the analysis of X-STRs. In the present chapter, a method is described for the typing of ten X chromosome-specific markers in a single PCR amplification reaction, followed by capillary electrophoresis separation and fluorescent detection in an ABI Genetic Analyser apparatus. This typing strategy was developed and optimized for the simultaneous amplification of ten X-linked specific STRs well distributed along the chromosome: DXS8378, DXS9902, DXS7132, DXS9898, DXS6809, DXS6789, DXS7133, GATA172D05, GATA31E08 and DXS7423.
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Differential pattern of genetic variability at the DXYS156 locus on homologous regions of X and Y chromosomes in Indian population and its forensic implications. Int J Legal Med 2011; 127:1-6. [DOI: 10.1007/s00414-011-0646-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2011] [Accepted: 10/31/2011] [Indexed: 01/27/2023]
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Diegoli TM, Kovacevic L, Pojskic N, Coble MD, Marjanovic D. Population study of fourteen X chromosomal short tandem repeat loci in a population from Bosnia and Herzegovina. Forensic Sci Int Genet 2011; 5:350-1. [DOI: 10.1016/j.fsigen.2010.01.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2009] [Revised: 01/11/2010] [Accepted: 01/12/2010] [Indexed: 11/25/2022]
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43
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Allele and haplotype diversity of X-chromosomal STRs in Ivory Coast. Int J Legal Med 2011; 125:749-52. [DOI: 10.1007/s00414-011-0591-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2011] [Accepted: 06/16/2011] [Indexed: 10/18/2022]
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Liu QL, Lu DJ, Wu WW, Hao HL, Chen YF, Zhao H. Genetic analysis of the 10 ChrX STRs loci in Chinese Han nationality from Guangdong province. Mol Biol Rep 2010; 38:4879-83. [PMID: 21153922 DOI: 10.1007/s11033-010-0629-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2010] [Accepted: 12/03/2010] [Indexed: 11/27/2022]
Abstract
This study is to explore the polymorphic nature of X-Chromosome short tandem repeats (ChrX STRs) loci, and to determine its application in kinship tests for forensic cases. A new fluorescent multiplex PCR that simultaneously amplifies the 10 ChX STRs loci in the same PCR reaction had been set up. DXS7132, DXS981, DXS6801, DXS6809, DXS6789, DXS7424, DXS101, DXS7133, GATA165B12 and GATA31E08 were analyzed in a sample of 511 (399 males and 112 females) unrelated individuals from Guangdong Han nationality in China. One hundred and one alleles were observed in all the loci. Here, we investigated the allele frequencies and mutation rates of the ten loci, and then made the comparison of allele frequencies distribution among different populations. The results show the ten loci in the multiplex systems may provide high polymorphism information for kinship testing and relationship investigations, and it is necessary to gain allele frequency and mutation rate of different population for forensic application.
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Affiliation(s)
- Qiu-Ling Liu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, 74, Zhongshan 2nd Road, Guangzhou 510080, People's Republic of China
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Diegoli TM, Coble MD. Development and characterization of two mini-X chromosomal short tandem repeat multiplexes. Forensic Sci Int Genet 2010; 5:415-21. [PMID: 20943451 DOI: 10.1016/j.fsigen.2010.08.019] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2010] [Revised: 08/27/2010] [Accepted: 08/30/2010] [Indexed: 10/19/2022]
Abstract
This study presents the development and characterization of two X chromosomal short tandem repeat (STR) multiplexes utilizing reduced-size amplicons (less than 200 base pairs) for identity and kinship testing with degraded DNA. Approximately 1360 samples across 4 U.S. population groups were typed for 15 X chromosomal STR markers: DXS6789, DXS7130, DXS9902, GATA31E08, DXS7424, GATA165B12, DXS101, DXS6795, GATA172D05, DXS10147, DXS8378, DXS7132, DXS6803, HPRTB, and DXS7423. A high degree of polymorphism was observed for each marker and both multiplexes were sensitive down to 200pg of pristine DNA. The two proposed multiplexes are suitable for forensic use, and show potential for improved analysis of compromised bone samples.
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Affiliation(s)
- Toni M Diegoli
- Armed Forces DNA Identification Laboratory, Research Section, 1413 Research Blvd., Suite 101, Rockville, MD 20850, USA.
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Gebrauch X-chromosomaler Marker in der forensischen Genetik. Rechtsmedizin (Berl) 2010. [DOI: 10.1007/s00194-010-0662-8] [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]
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47
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Genetic variation of 10 X chromosomal STR loci in Indian population. Int J Legal Med 2010; 124:327-30. [DOI: 10.1007/s00414-010-0456-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2010] [Accepted: 03/31/2010] [Indexed: 10/19/2022]
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Bekada A, Benhamamouch S, Boudjema A, Fodil M, Menegon S, Torre C, Robino C. Analysis of 21 X-chromosomal STRs in an Algerian population sample. Int J Legal Med 2009; 124:287-94. [DOI: 10.1007/s00414-009-0397-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2009] [Accepted: 11/18/2009] [Indexed: 11/29/2022]
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Turrina S, Filippini G, De Leo D. Genetic studies of eight X-STRs in a Northeast Italian population. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2009. [DOI: 10.1016/j.fsigss.2009.08.146] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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50
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Luo HB, Ye Y, Wang YY, Liang WB, Yun LB, Liao M, Yan J, Wu J, Li YB, Hou YP. Characteristics of eight X-STR loci for forensic purposes in the Chinese population. Int J Legal Med 2009; 125:127-31. [DOI: 10.1007/s00414-009-0386-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2009] [Accepted: 10/23/2009] [Indexed: 10/20/2022]
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