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Zhang Y, Yu Z, Mo X, Zhao X, Li W, Liu H, Liu C, Wu R, Sun H. Development and validation of a new 18 X-STR typing assay for forensic applications. Electrophoresis 2021; 42:766-773. [PMID: 33415769 DOI: 10.1002/elps.202000168] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 11/30/2020] [Accepted: 12/10/2020] [Indexed: 11/08/2022]
Abstract
With a unique inheritance pattern compared to autosomal short tandem repeats (A-STRs), X chromosomal STRs (X-STRs) have special usage in forensic relationship testing. In this study, we designed a multiplex amplification system (named TYPER-X19 multiplex assay) consisting of 18 STR loci spreading from 7.837 to 149.460 Mb on the X chromosomes (DXS9895, DXS8378, DXS9902, DXS6810, DXS7132, DXS10079, DXS6789, DXS7424, DXS101, DXS6797, DXS7133, DXS6804, GATA165B12, DXS10103, HPRTB, GATA31E08, DXS8377, and DXS7423), and the amelogenin. PCR primers were marked with four kinds of fluorophores including FAM, HEX, TAMRA, and ROX. The multiplex system was optimized and tested for precision, concordance, reproducibility, sensitivity, stability, DNA mixture, and species specificity according to the conventional validation guidelines. The results indicated that the system was accurate, reliable, and sensitive enough, and was suitable for common forensic case-type samples. In the population genetic study, a total of 148 alleles were detected at the 18 X-STR loci in 398 Southern Han Chinese. Relatively high combined power of discrimination in male (PDm ), power of discrimination in female (PDf ), mean paternity exclusion chance in trios (MECtrio ), and mean paternity exclusion chance in duos (MECDuo ) by Desmarais were detected, and HPRTB-DXS10103 was in linkage disequilibrium. The results suggested that the TYPER-X19 multiplex assay was suitable for forensic applications.
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Affiliation(s)
- Yinming Zhang
- Institute of Forensic Science, Ministry of Public Security, Beijing, P. R. China.,Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, P. R. China.,Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, P. R. China
| | - Zhengliang Yu
- Institute of Forensic Science, Ministry of Public Security, Beijing, P. R. China
| | - Xiaoting Mo
- Institute of Forensic Science, Ministry of Public Security, Beijing, P. R. China
| | - Xingchun Zhao
- Institute of Forensic Science, Ministry of Public Security, Beijing, P. R. China
| | - Wanshui Li
- Institute of Forensic Science, Ministry of Public Security, Beijing, P. R. China
| | - Hong Liu
- Guangzhou Forensic Institute, Guangzhou, P. R. China
| | - Chao Liu
- Guangzhou Forensic Institute, Guangzhou, P. R. China
| | - Riga Wu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, P. R. China.,Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, P. R. China
| | - Hongyu Sun
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, P. R. China.,Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, P. R. China
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Yang X, Zhang X, Zhu J, Chen L, Liu C, Feng X, Chen L, Wang H, Liu C. Genetic analysis of 19 X chromosome STR loci for forensic purposes in four Chinese ethnic groups. Sci Rep 2017; 7:42782. [PMID: 28211539 PMCID: PMC5314363 DOI: 10.1038/srep42782] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 01/16/2017] [Indexed: 12/13/2022] Open
Abstract
A new 19 X- short tandem repeat (STR) multiplex PCR system has recently been developed, though its applicability in forensic studies has not been thoroughly assessed. In this study, 932 unrelated individuals from four Chinese ethnic groups (Han, Tibet, Uighur and Hui) were successfully genotyped using this new multiplex PCR system. Our results showed significant linkage disequilibrium between markers DXS10103 and DXS10101 in all four ethnic groups; markers DXS10159 and DXS10162, DXS6809 and DXS6789, and HPRTB and DXS10101 in Tibetan populations; and markers DXS10074 and DXS10075 in Uighur populations. The combined powers of discrimination in males and females were calculated according to haplotype frequencies from allele distributions rather than haplotype counts in the relevant population and were high in four ethnic groups. The cumulative powers of discrimination of the tested X-STR loci were 1.000000000000000 and 0.999999999997940 in females and males, respectively. All 19 X-STR loci are highly polymorphic. The highest Reynolds genetic distances were observed for the Tibet-Uighur pairwise comparisons. This study represents an extensive report on X-STR marker variation in minor Chinese populations and a comprehensive analysis of the diversity of these 19 X STR markers in four Chinese ethnic groups.
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Affiliation(s)
- Xingyi Yang
- Department of Forensic Medicine, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong Province 510515, P.R. China.,Guangzhou Forensic Science Institute, Guangdong Province Key Laboratory of Forensic Genetics, Guangzhou 510030, P.R. China
| | - Xiaofang Zhang
- Department of Forensic Medicine, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong Province 510515, P.R. China.,Guangzhou Forensic Science Institute, Guangdong Province Key Laboratory of Forensic Genetics, Guangzhou 510030, P.R. China
| | - Junyong Zhu
- Guangzhou Forensic Science Institute, Guangdong Province Key Laboratory of Forensic Genetics, Guangzhou 510030, P.R. China
| | - Linli Chen
- AGCU ScienTech Incorporation, Wuxi 214174, P.R. China
| | - Changhui Liu
- Guangzhou Forensic Science Institute, Guangdong Province Key Laboratory of Forensic Genetics, Guangzhou 510030, P.R. China
| | - Xingling Feng
- Department of Forensic Medicine, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong Province 510515, P.R. China.,Guangzhou Forensic Science Institute, Guangdong Province Key Laboratory of Forensic Genetics, Guangzhou 510030, P.R. China
| | - Ling Chen
- Department of Forensic Medicine, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong Province 510515, P.R. China
| | - Huijun Wang
- Department of Forensic Medicine, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong Province 510515, P.R. China
| | - Chao Liu
- Department of Forensic Medicine, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong Province 510515, P.R. China.,Guangzhou Forensic Science Institute, Guangdong Province Key Laboratory of Forensic Genetics, Guangzhou 510030, P.R. China
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Crnjac J, Ozretić P, Merkaš S, Ratko M, Lozančić M, Korolija M, Popović M, Mršić G. Investigator Argus X-12 study on the population of northern Croatia. Genet Mol Biol 2017; 40:80-83. [PMID: 27768154 PMCID: PMC5409765 DOI: 10.1590/1678-4685-gmb-2015-0261] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 02/03/2016] [Indexed: 02/08/2023] Open
Abstract
X chromosome STR typing has emerged recently as a powerful tool, complementary to autosomal STR typing, in solving complex forensic and missing person cases. Investigator® Argus X-12 is a commercial product that allows co-amplification of 12 X chromosomal markers belonging to four linkage groups (LGs). In this study, we analyzed by capillary electrophoresis blood samples from 100 females and 102 males from a population of northern Croatia. Statistical analysis included calculation of allele and haplotype frequencies, as well as forensic parameters. The most informative marker for the northern Croatia population was DXS10135 with PIC=0.9211 and a total of 27 alleles. The least polymorphic marker was DXS8378 with 6 alleles. The proportion of observed haplotypes from the number of possible haplotypes varied from 2.74-8.57% across all LGs, with LG1 being the most informative. Of the 11 tested world populations compared to the population of northern Croatia, significant differences in genetic distance (FST) were found for Greenlandic and all non-European populations. We found that all tested markers are in HWE and can thus be used for match probability calculation. Because of high combined power of discrimination in both men and women, Investigator® Argus X-12 is applicable for the northern Croatia population in routine forensic casework.
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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
| | - Martina Ratko
- Forensic Science Centre "Ivan Vučetić", Zagreb, Croatia
| | | | | | - Maja Popović
- Faculty of Veterinary Medicine, University of Zagreb, Zagreb, Croatia
| | - Gordan Mršić
- Forensic Science Centre "Ivan Vučetić", Zagreb, Croatia
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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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Chen MY, Ho CW, Pu CE, Wu FC. Genetic polymorphisms of 12 X-chromosomal STR loci in Taiwanese individuals and likelihood ratio calculations applied to case studies of blood relationships. Electrophoresis 2014; 35:1912-20. [DOI: 10.1002/elps.201300645] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Revised: 03/10/2014] [Accepted: 03/10/2014] [Indexed: 11/09/2022]
Affiliation(s)
- Meng-Yi Chen
- Department of Forensic Science; Investigation Bureau, Ministry of Justice; New Taipei City Taiwan Republic of China
- Department of Bioengineering; Tatung University; Taipei City Taiwan Republic of China
| | - Chin-Wen Ho
- Department of Bioengineering; Tatung University; Taipei City Taiwan Republic of China
| | - Chang-En Pu
- Department of Forensic Science; Investigation Bureau, Ministry of Justice; New Taipei City Taiwan Republic of China
| | - Fang-Chin Wu
- Department of Forensic Science; Investigation Bureau, Ministry of Justice; New Taipei City Taiwan Republic of China
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Elakkary S, Hoffmeister-Ullerich S, Schulze C, Seif E, Sheta A, Hering S, Edelmann J, Augustin C. Genetic polymorphisms of twelve X-STRs of the investigator Argus X-12 kit and additional six X-STR centromere region loci in an Egyptian population sample. Forensic Sci Int Genet 2014; 11:26-30. [PMID: 24632058 DOI: 10.1016/j.fsigen.2014.02.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Revised: 02/12/2014] [Accepted: 02/15/2014] [Indexed: 11/19/2022]
Abstract
Recently, many researchers have focused on analysis of different X-chromosomal STRs as they bear the potential to efficiently complement the analysis of autosomal and Y-chromosomal STRs in solving special complex kinship deficiency cases. In the current study we examined a sample of 250 unrelated Egyptian males with the Investigator Argus X-12 kit (Qiagen GmbH, Hilden, Germany) which detects 12 X-STR markers distributed over the entire X-chromosome as four closely linked clusters. Microvariant off ladder alleles as well as null alleles have been detected in some loci. Furthermore, discordant results were observed between the Investigator Argus X-12 and the Mentype(®) Argus X-8 kits (Biotype AG, Dresden, Germany). New primers were designed for loci DXS10101, DXS10146 and DXS10148 to correct the allele drop outs observed in these loci with the Investigator Argus X-12 kit. Additionally, DNA sequence analysis revealed the polymorphisms responsible for the allele drop outs. Furthermore, six additional X-STRs (DXS10161, DXS10159, DXS10162, DXS10163, DXS10164 and DXS10165) located in the centromere region at Xp11.21-Xq11.1 were examined in a single multiplex reaction. Allele and haplotype frequencies as well as different forensic statistical parameters of the 18 X-STR loci tested indicated that they are highly informative in different forensic applications in the Egyptian population. However, some modifications still need to be performed on the Investigator Argus X-12 kit before its use in forensic casework is validated.
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Affiliation(s)
- S Elakkary
- Institute of Legal Medicine, University Hospital Hamburg-Eppendorf, Butenfeld 34, 22529 Hamburg, Germany; Forensic Medicine and Clinical Toxicology Department, Faculty of Medicine, University of Alexandria, Champollion Street, El-khartoum Square, Azarita Medical Campus, Alexandria, Egypt.
| | - S Hoffmeister-Ullerich
- Centre of Molecular Neurobiology, University Hospital Hamburg-Eppendorf, Falkenried 94, 20251 Hamburg, Germany
| | - C Schulze
- Centre of Molecular Neurobiology, University Hospital Hamburg-Eppendorf, Falkenried 94, 20251 Hamburg, Germany
| | - E Seif
- Forensic Medicine and Clinical Toxicology Department, Faculty of Medicine, University of Alexandria, Champollion Street, El-khartoum Square, Azarita Medical Campus, Alexandria, Egypt
| | - A Sheta
- Forensic Medicine and Clinical Toxicology Department, Faculty of Medicine, University of Alexandria, Champollion Street, El-khartoum Square, Azarita Medical Campus, Alexandria, Egypt
| | - S Hering
- Institute of Legal Medicine, University of Dresden, Fetscherstrasse 74, 01307 Dresden, Germany
| | - J Edelmann
- Institute of Legal Medicine, University of Leipzig, Johannisallee 28, 04103 Leipzig, Germany
| | - C Augustin
- Institute of Legal Medicine, University Hospital Hamburg-Eppendorf, Butenfeld 34, 22529 Hamburg, Germany
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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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Samejima M, Nakamura Y, Nambiar P, Minaguchi K. Genetic study of 12 X-STRs in Malay population living in and around Kuala Lumpur using Investigator Argus X-12 kit. Int J Legal Med 2012; 126:677-83. [DOI: 10.1007/s00414-012-0705-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2012] [Accepted: 04/26/2012] [Indexed: 11/30/2022]
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X-chromosomal haplotype frequencies of four linkage groups using the Investigator Argus X-12 Kit. Forensic Sci Int Genet 2012; 6:e24-34. [DOI: 10.1016/j.fsigen.2011.01.001] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2010] [Revised: 12/23/2010] [Accepted: 01/05/2011] [Indexed: 11/24/2022]
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Samejima M, Nakamura Y, Minaguchi K. Population genetic study of six closely linked groups of X-STRs in a Japanese population. Int J Legal Med 2011; 125:895-900. [PMID: 21918845 DOI: 10.1007/s00414-011-0618-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2011] [Accepted: 08/29/2011] [Indexed: 10/17/2022]
Abstract
X chromosome STR (X-STR) polymorphisms are a useful tool in the fields of human population genetics and personal identification and are quite informative in the investigation of complex kinship or deficiency cases, especially where it is necessary to determine relationships with second-generation offspring in which the same X chromosome may have been inherited. We investigated eight X-STR systems using the Mentype Argus X-8 kit and further developed decaplex PCR for the DXS10148, DXS10161, DXS10160, DXS10159, DXS10079, DXS10075, DXS6799, DXS10102, DXS10106, and DXS10146 loci with the aim of constructing closely linked groups on the X chromosome. The studied population comprised 569 Japanese individuals (390 males and 179 females). Heterozygosity among the present 18 X-STRs showed a distribution of from 54.2% to 90.5%. We constructed six closely linked groups, each comprising three to five X-STRs: DXS10148- DXS10135-DXS8378, DXS10161- DXS10160-DXS10159, DXS7132-DXS10079-DXS10074-DXS10075-DXS981, DXS6809-DXS6789-DXS6799, DXS10102-HPRTB-DXS10101-DXS10106, and DXS8377-DXS10146-DXS10134-DXS7423. The forensic utility of these groups as haplotypes was then evaluated. Haplotype diversity values showed a distribution of from 0.9699 to 0.9959. Analysis of the present closely linked haplotypes will contribute to solving complex kinship cases involving X chromosome inheritance.
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Affiliation(s)
- Michinaga Samejima
- Department of Forensic Odontology, Tokyo Dental College, 1-2-2 Masago, Mihama-ku, Chiba City, Japan
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