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Jiang B, Qu W, Wang F, Zhang L, Rong H, Li J, Wen D, Zeye MMJ, He W, Wang C, Xing H, Zhang T, Jin C, Chen L, Liu Y, Cai J, Zha L. Development and validation of novel 8-dye short tandem repeat multiplex system for forensic applications. Int J Legal Med 2021; 135:2263-2274. [PMID: 34550443 DOI: 10.1007/s00414-021-02695-9] [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: 06/22/2021] [Accepted: 08/25/2021] [Indexed: 11/30/2022]
Abstract
DNA profiling of short tandem repeats (STRs) is the primary method for genotyping forensic samples. However, degraded DNA and trace samples are still major problems for commercial 5- or 6-dye STR kits. In order to improve the performance of this method, we developed a novel 8-dye STR multiplex system containing 18 autosomal loci (D3S1358, D1S1656, TPOX, D16S539, vWA, D6S1043, D2S1338, CSF1PO, D19S433, D7S820, FGA, D8S1179, D5S818, D13S317, TH01, D21S11, D12S391, and PentaD) and the sex-determining locus Amelogenin, with all fragments smaller than 330 bases. Validation was carried out as recommended by the Scientific Working Group on DNA Analysis Methods. The results showed that complete profiles were obtainable when the input DNA was as low as 0.0625 ng. Full profiles were obtained even in the presence of inhibitors such as humic acid (< 300 ng/μl), hematin (< 100 μM), and indigo (0.01%). The 8-dye STR multiplex system also showed good performance in the detection degraded DNA samples. These results indicate that the 8-dye STR multiplex system is suitable for human DNA genotyping, including for difficult forensic materials.
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Affiliation(s)
- Bowei Jiang
- The First Research Institute of the Ministry of Public Security of P.R.C, Haidian District, No.1. Shouti South Road, Beijing, 100044, China
| | - Weifeng Qu
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Hunan Province, No. 172. Tongzipo Road, Changsha, 410013, China
| | - Feng Wang
- The First Research Institute of the Ministry of Public Security of P.R.C, Haidian District, No.1. Shouti South Road, Beijing, 100044, China
| | - Liming Zhang
- The First Research Institute of the Ministry of Public Security of P.R.C, Haidian District, No.1. Shouti South Road, Beijing, 100044, China
| | - Haibo Rong
- The First Research Institute of the Ministry of Public Security of P.R.C, Haidian District, No.1. Shouti South Road, Beijing, 100044, China
| | - Jienan Li
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Hunan Province, No. 172. Tongzipo Road, Changsha, 410013, China
| | - Dan Wen
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Hunan Province, No. 172. Tongzipo Road, Changsha, 410013, China
| | - Moutanou Modeste Judes Zeye
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Hunan Province, No. 172. Tongzipo Road, Changsha, 410013, China
| | - Wei He
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Hunan Province, No. 172. Tongzipo Road, Changsha, 410013, China
| | - Chudong Wang
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Hunan Province, No. 172. Tongzipo Road, Changsha, 410013, China
| | - Hao Xing
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Hunan Province, No. 172. Tongzipo Road, Changsha, 410013, China
| | - Tao Zhang
- The First Research Institute of the Ministry of Public Security of P.R.C, Haidian District, No.1. Shouti South Road, Beijing, 100044, China
| | - Chuan Jin
- The First Research Institute of the Ministry of Public Security of P.R.C, Haidian District, No.1. Shouti South Road, Beijing, 100044, China
| | - Li Chen
- The First Research Institute of the Ministry of Public Security of P.R.C, Haidian District, No.1. Shouti South Road, Beijing, 100044, China
| | - Ying Liu
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Hunan Province, No. 172. Tongzipo Road, Changsha, 410013, China
| | - Jifeng Cai
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Hunan Province, No. 172. Tongzipo Road, Changsha, 410013, China
| | - Lagabaiyila Zha
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Hunan Province, No. 172. Tongzipo Road, Changsha, 410013, China.
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Alsafiah HM, Aljanabi AA, Hadi S, Alturayeif SS, Goodwin W. An evaluation of the SureID 23comp Human Identification Kit for kinship testing. Sci Rep 2019; 9:16859. [PMID: 31727926 PMCID: PMC6856129 DOI: 10.1038/s41598-019-52838-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 10/21/2019] [Indexed: 01/16/2023] Open
Abstract
Short tandem repeat (STR) profiling has been routinely used in kinship testing since the introduction of commercial kits in the mid-1990s. While 15 to 23 STR loci normally give definitive results in simple kinship testing, additional loci are sometimes required to resolve complex cases. The SureID 23comp Human Identification Kit, recently released by Health Gene Technologies (China), multiplexes amelogenin and 22 autosomal STRs, 17 of which are non-CODIS STRs. This enables the profiling of 38–40 loci when used in conjunction with widely used commercial kits. In this study, the kit was evaluated for kinship applications as a supplementary STR kit following the minimum criteria for validation recommended by the European Network of Forensic Science Institutes (ENFSI) and the Scientific Working Group on DNA Analysis Methods (SWGDAM) using 500 samples. Performance was comparable with other commercial kits demonstrating: repeatability and reproducibility; precision (maximum s.d. 0.1048 nt); accuracy, all alleles were within ±0.41 nt compared to the actual sizes; heterozygous peak balances at all loci >68%; stutter ratios ranged from 3.8% to 16.15%; full profiles were generated with 125 pg DNA (95.12% of alleles at 62 pg),; and we found 100% concordance over 5 common STRs with the GlobalFiler kit.
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Affiliation(s)
- Hussain M Alsafiah
- School of Forensic and Applied Sciences, University of Central Lancashire, Preston, United Kingdom. .,Forensic Genetics Laboratory, General Administration of Criminal Evidences, Public Security, Ministry of Interior, Riyadh, Saudi Arabia.
| | - Ali A Aljanabi
- School of Forensic and Applied Sciences, University of Central Lancashire, Preston, United Kingdom
| | - Sibte Hadi
- School of Forensic and Applied Sciences, University of Central Lancashire, Preston, United Kingdom
| | - Saleh S Alturayeif
- Forensic Genetics Laboratory, General Administration of Criminal Evidences, Public Security, Ministry of Interior, Riyadh, Saudi Arabia
| | - William Goodwin
- School of Forensic and Applied Sciences, University of Central Lancashire, Preston, United Kingdom.
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Liu QL, Huang KK, Wu YD, Zhao H, Li CT, Lu DJ. Genetic polymorphism of 13 non-CODIS STR loci in three national populations from China. Electrophoresis 2014; 35:3395-401. [DOI: 10.1002/elps.201400290] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Revised: 07/24/2014] [Accepted: 07/29/2014] [Indexed: 11/12/2022]
Affiliation(s)
- Qiu-Ling Liu
- Shanghai Key Laboratory of Forensic Medicine; Institute of Forensic Sciences; Ministry of Justice Shanghai P. R. China
- Faculty of Forensic Medicine, Zhongshan School of Medicine; Sun Yat-Sen University; Guangzhou P. R. China
| | - Kai-Kai Huang
- Faculty of Forensic Medicine, Zhongshan School of Medicine; Sun Yat-Sen University; Guangzhou P. R. China
| | - Ye-Da Wu
- Faculty of Forensic Medicine, Zhongshan School of Medicine; Sun Yat-Sen University; Guangzhou P. R. China
| | - Hu Zhao
- Faculty of Forensic Medicine, Zhongshan School of Medicine; Sun Yat-Sen University; Guangzhou P. R. China
| | - Cheng-tao Li
- Shanghai Key Laboratory of Forensic Medicine; Institute of Forensic Sciences; Ministry of Justice Shanghai P. R. China
| | - De-Jian Lu
- Faculty of Forensic Medicine, Zhongshan School of Medicine; Sun Yat-Sen University; Guangzhou P. R. China
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Phillips C, Gelabert-Besada M, Fernandez-Formoso L, García-Magariños M, Santos C, Fondevila M, Ballard D, Syndercombe Court D, Carracedo Á, Victoria Lareu M. “New turns from old STaRs”: Enhancing the capabilities of forensic short tandem repeat analysis. Electrophoresis 2014; 35:3173-87. [DOI: 10.1002/elps.201400095] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Revised: 04/25/2014] [Accepted: 05/15/2014] [Indexed: 02/01/2023]
Affiliation(s)
- Christopher Phillips
- Forensic Genetics Unit, Institute of Legal Medicine; University of Santiago de Compostela; Santiago de Compostela Spain
| | - Miguel Gelabert-Besada
- Forensic Genetics Unit, Institute of Legal Medicine; University of Santiago de Compostela; Santiago de Compostela Spain
| | - Luis Fernandez-Formoso
- Forensic Genetics Unit, Institute of Legal Medicine; University of Santiago de Compostela; Santiago de Compostela Spain
| | | | - Carla Santos
- Forensic Genetics Unit, Institute of Legal Medicine; University of Santiago de Compostela; Santiago de Compostela Spain
| | - Manuel Fondevila
- Forensic Genetics Unit, Institute of Legal Medicine; University of Santiago de Compostela; Santiago de Compostela Spain
| | - David Ballard
- Department of Forensic and Analytical Science; King's College London; London UK
| | | | - Ángel Carracedo
- Forensic Genetics Unit, Institute of Legal Medicine; University of Santiago de Compostela; Santiago de Compostela Spain
- Center of Excellence in Genomic Medicine Research; King Abdulaziz University; Jeddah Saudi Arabia
| | - Maria Victoria Lareu
- Forensic Genetics Unit, Institute of Legal Medicine; University of Santiago de Compostela; Santiago de Compostela Spain
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Wu W, Hao H, Liu Q, Han X, Wu Y, Cheng J, Lu D. Analysis of linkage and linkage disequilibrium for syntenic STRs on 12 chromosomes. Int J Legal Med 2014; 128:735-9. [PMID: 24929640 DOI: 10.1007/s00414-014-1032-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2014] [Accepted: 06/02/2014] [Indexed: 11/30/2022]
Abstract
The purpose of this study is to evaluate allelic association and linkage of 18 adjacent syntenic short tandem repeat (STR) pairs form out of 30 markers located on 12 different autosomes. Linkage disequilibrium was tested by using the unknown gametic phase genotypes and phased haplotypes from 290 unrelated individuals from Chinese Han population. Genetic linkage analysis between syntenic STRs was performed based on 145 two-generation families which involved 628 meioses. The results showed no significant linkage disequilibrium at any STR pairs and independent inheritance between syntenic STR pairs was indicated. Significant linkage (maximum logarithm of odd (LOD) scores >3.0) was found in 6 out of the 18 adjacent syntenic STR pairs (D1S1627-D1S1677, CSF1PO-D5S818, D6S1017-D6S1043, D6S1043-D6S474, D12S391-vWA, and D19S253-D19S433). These significant linkage marker pairs had a genetic distance ranged from 11.94 to 41.33 cM deduced from HapMap. When recombination fractions determined in families were compared to those derived from Kosambi mapping function based on HapMap data, the latter may have an overestimation. In summary, our results demonstrated that product rule included syntenic STRs can be used for unrelated individual profile probability and the recombination fraction based on family data was superior to the estimation from HapMap for kinship analysis.
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Affiliation(s)
- Weiwei Wu
- Department of Criminal Investigation of Zhejiang Provincial Public Security Bureau, 66#, Minsheng Road, 310009, Hangzhou, People's Republic of China
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