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Guo F, Jing G, Lang Y, Liu Z, Yu S. Simultaneous sequencing of 102 Y-STRs on Ion Torrent ™ GeneStudio ™ S5 System. Forensic Sci Int Genet 2024; 71:103059. [PMID: 38749212 DOI: 10.1016/j.fsigen.2024.103059] [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: 07/31/2023] [Revised: 05/02/2024] [Accepted: 05/05/2024] [Indexed: 06/18/2024]
Abstract
The Precision ID NGS System from Thermo Fisher Scientific is a mainstream next-generation sequencing (NGS) platform used in forensic laboratories to detect almost all commonly used forensic markers, except for Y-chromosomal short tandem repeats (Y-STRs). This study aimed to: 1) develop a Y-STR panel compatible with the automatic workflow of the NGS system using Ion AmpliSeq Technology, 2) evaluate the panel performance following the SWGDAM guidelines, and 3) explore the possibility of using a combination workflow to detect autosomal STRs and Y-STRs (AY-STR NGS workflow). The GrandFiler Y-STR Panel was successfully designed using the 'separating' and 'merging' strategies, including 102 Y-STRs and Amelogenin with an average amplicon length of 133 bp. It is a mega Y-STR multiplex system in which up to 16 samples can be sequenced simultaneously on an Ion 530 ™ Chip. Developmental validation studies of the performance of the NGS platform, species specificity, reproducibility, concordance, sensitivity, degraded samples, case-type samples, and mixtures were conducted to unequivocally determine whether the GrandFiler Y-STR Panel is suitable for real scenarios. The newly developed Y-STR panel showed compelling run metrics and NGS performance, including 92.47% bases with ≥ Q20, 91.80% effective reads, 2106 × depth of coverage (DoC), and 97.09% inter-locus balance. Additionally, it showed high specificity for human males and 99.40% methodological and bioinformatical concordance, generated complete profiles at ≥ 0.1 ng input DNA, and recovered more genetic information from severely degraded and diverse case samples. Although the outcome when used on mixtures was not as expected, more genetic information was obtained compared to that from capillary electrophoresis (CE) methods. The AY-STR NGS workflow was established by combining the GrandFiler Y-STR Panel with the Precision ID GlobalFiler ™ NGS STR Panel v2 at a 2:1 concentration ratio. The combination workflow on NGS performance, reproducibility, concordance, and sensitivity was as stable as the single Y-STR NGS workflow, providing more options for forensic scientists when dealing with different case scenarios. Overall, the GrandFiler Y-STR Panel was confirmed as the first to effectively detect a large number of Y-STR markers on the Precision ID NGS System, which is compatible with 51 Y-STRs in commercial CE kits and 51 Y-STRs in commercial NGS kits and the STRBase. The panel is as robust, reliable, and sensitive as current CE/NGS kits, and is suitable for solving real cases, especially for severely degraded samples (degradation index > 10).
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Affiliation(s)
- Fei Guo
- Shenyang Medical College, Shenyang, Liaoning 110034, PR China; Key Laboratory of Human Ethnic Specificity and Phenomics of Critical Illness in Liaoning Province, Shenyang, Liaoning 110034, PR China; Key Laboratory of Phenomics in Shenyang City, Shenyang, Liaoning 110034, PR China.
| | - Guangxin Jing
- Heyuan Public Security Forensic Science Center, Heyuan, Guangdong 517000, PR China
| | - Yubo Lang
- School of Public Security Information Technology and Intelligence, Criminal Investigation Police University of China, Shenyang, Liaoning 110854, PR China
| | - Ze Liu
- DNA Laboratory of Forensic Science Center, Shenyang Public Security Bureau, Shenyang, Liaoning 110002, PR China
| | - Shaobo Yu
- DNA Laboratory of Forensic Science Center, Shenyang Public Security Bureau, Shenyang, Liaoning 110002, PR China.
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2
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Ma D, Lin Y, Zhang R, Wang S, Hu W, Ye M, Gao H, Wang L, Song Y, Guo H. Effect of uniparental disomy in parentage testing. Leg Med (Tokyo) 2024; 67:102381. [PMID: 38154315 DOI: 10.1016/j.legalmed.2023.102381] [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: 04/22/2023] [Revised: 11/21/2023] [Accepted: 12/20/2023] [Indexed: 12/30/2023]
Abstract
Uniparental disomy (UPD) is a rare type of chromosomal aberration that may hinder the analysis of kinship during forensic identification. Here, we investigated these genetic findings to avoid false exclusions during parentage testing. Thirty-nine fluorescently labeled, autosomal short tandem repeats (STR) were amplified in three cases, to detect parent-child relationships. Twenty-three fluorescently labeled Y-chromosome STRs were also employed. These were subjected to capillary electrophoresis. The parentage index was calculated by the bipartite or tripartite model. Single nucleotide polymorphism (SNP) microarrays were performed to further investigate the genetic mechanisms. The conclusions supported the biological mother-child relationship in three cases. However, in all cases, the alleged father and child had three autosomal STR markers, constrained to a single chromosome, which did not conform to Mendelian inheritance rules. The genotyping of 23 Y-chromosome STRs did not reveal any violations of Mendelian law. The combination of STR profiling and SNP microarrays suggested that two children had maternal UPD of chromosome 7, whilst one had UPD of chromosome 2. After excluding the three incompatible loci, the conclusions supported the biological father-child relationship in all cases. The same results were obtained when parentage testing of trios was used. Uniparental disomy may complicate the judgment of kinship in parentage testing. The possibility of UPD should be considered when incompatible STR loci are found on the same chromosome. Genetic evidence obtained through additional molecular techniques can provide better interpretation of kinship in the presence of UPD and avoid false exclusions of biological relationships.
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Affiliation(s)
- Di Ma
- Forensic Evidence Laboratory, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong 5180201, China
| | - YuMei Lin
- Forensic Evidence Laboratory, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong 5180201, China
| | - RuanZhang Zhang
- Forensic Evidence Laboratory, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong 5180201, China
| | - Shayan Wang
- Forensic Evidence Laboratory, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong 5180201, China
| | - Wenlong Hu
- Forensic Evidence Laboratory, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong 5180201, China
| | - Mei Ye
- Forensic Evidence Laboratory, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong 5180201, China
| | - Hui Gao
- Forensic Evidence Laboratory, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong 5180201, China
| | - Lijuan Wang
- Forensic Evidence Laboratory, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong 5180201, China
| | - Yaqin Song
- Forensic Evidence Laboratory, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong 5180201, China
| | - Hui Guo
- Forensic Evidence Laboratory, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong 5180201, China.
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3
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Yuan X, Wang X, Lan Q, Li S, Lin Y, Zhao M, Xu H, Lei F, Shen C, Zhu B. Using two self-developed InDel panels to explore forensic traits and ancestral components in the Hui group. Genomics 2024; 116:110756. [PMID: 38061479 DOI: 10.1016/j.ygeno.2023.110756] [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: 08/08/2023] [Revised: 11/05/2023] [Accepted: 12/03/2023] [Indexed: 12/30/2023]
Abstract
To address the challenges faced by forensic examiners in degraded DNA analysis, we have developed two different panels for various forensic applications, encompassing an AIM-InDel panel for ancestry inference and a Multi-InDel panel for individual identification, respectively. Herein, the efficiencies of these two panels were tested in the Chinese Hui group. By calculating forensic parameters and simulating family relationships, we verified that the Multi-InDel panel could be an effective tool for individual identification, paternity testing, and could assist in kinship identification in the Hui group. For full siblings, the true positive rate of kinship discrimination was 96.553%, when the threshold of log10LR was 1. The cumulative probability of matching as well as cumulative probability of exclusion were 3.8117 × 10-26 and 0.999999722, respectively. Meanwhile, we found that the AIM-InDel panel was effective for bio-geographic ancestry inference, with the vast majority of loci contributing significantly to distinguish East Asian, African, and European populations. By studying the population structure of the Hui ethnic minority, the genetic distance to the Beijing Han population was the closest among the 26 reference populations, which was similar to previous reports. In summary, we have developed two panels which can be effectively applied to the Hui group for individual identification, parentage testing and bio-geographic ancestry inference.
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Affiliation(s)
- Xi Yuan
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong, China
| | - Xi Wang
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong, China
| | - Qiong Lan
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong, China; Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Shuanglin Li
- Department of Anatomy and Histology, School of Basic Medical Sciences, Shenzhen University, Shenzhen 518060, China
| | - Yifeng Lin
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong, China
| | - Ming Zhao
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong, China
| | - Hui Xu
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong, China
| | - Fanzhang Lei
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong, China
| | - Chunmei Shen
- Department of Clinical Laboratory, Nanfang Hospital, Southern Medical University, Guangzhou 510515, Guangdong, China.
| | - Bofeng Zhu
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong, China; Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China; Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi, China.
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4
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Wei X, Song F, Wang X, Wang S, Jiang L, Zhang K, Zhou Y, Wang Z, Liao M, Zha L, Luo H. Validation of the AGCU Expressmarker 20 + 20Y Kit: A 6-dye multiplex assay for forensic application. Forensic Sci Int 2022; 336:111342. [DOI: 10.1016/j.forsciint.2022.111342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 04/15/2022] [Accepted: 05/07/2022] [Indexed: 11/04/2022]
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5
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Xia R, Tao R, Qu Y, Zhang X, Yu H, Yuan C, Zhang S, Li C. Development and Validation of a Novel and Fast Detection Method for Cannabis sativa: A 19-Plex Short Tandem Repeat Typing System. FRONTIERS IN PLANT SCIENCE 2022; 13:837945. [PMID: 35295633 PMCID: PMC8918947 DOI: 10.3389/fpls.2022.837945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 01/20/2022] [Indexed: 06/14/2023]
Abstract
In recent years, influenced by the legalization of Cannabis sativa in some countries and regions, the number of people who smoke or abuse C. sativa has continuously grown, cases of transnational C. sativa trafficking have also been increasing. Therefore, fast and accurate identification and source tracking of C. sativa have become urgent social needs. In this study, we developed a new 19-plex short tandem repeats (STRs) typing system for C. sativa, which includes 15 autosomal STRs (D02-CANN1, C11-CANN1, 4910, B01-CANN1, E07-CANN1, 9269, B05-CANN1, H06-CANN2, 5159, nH09, CS1, ANUCS 305, 3735, and ANUCS 302 and 9043), two X-chromosome STRs (ANUCS 501 and 1528), one sex-determining marker (DM016, on Y-chromosome), and a quality control marker (DM029, on autosome). The whole polymerase chain reaction (PCR) process could finish within 1 h, making the system suitable for fast detection. The PCR products were detected and separated with an Applied Biosystems 3500XL Genetic Analyser. Developmental validation studies indicated that the 19-plex typing system was accurate, reliable and sensitive, which could also deconvolute mixed C. sativa samples. Specifically, the sensitivity study showed that a full genotyping profile was obtainable with as low as 125 pg of C. sativa DNA. The species specificity study demonstrated that this multiplex has no cross-reactivity with common non C. sativa DNA. In the population study, a total of 162 alleles at 15 autosomal STRs and 14 alleles at two X-chromosome STRs were detected among 85 samples. The efficiency parameters, including the total discrimination power (TDP) and the combined power of exclusion (CPE) of the system, were calculated to exceed 0.999 999 999 999 988 and 0.998 455 889 684 078, respectively, further proving that the system could meet the needs of individual identification. To the extent of the known studies, this is the first study that included the C. sativa sex-determining marker. In conclusion, the developed new 19-plex STR typing system can successfully achieve the purposes of species identification, gender determination, and individual identification, which could be a powerful tool in tracing trade routes of particular drug syndicates or dealers or in linking certain C. sativa to a crime scene.
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Affiliation(s)
- Ruocheng Xia
- Academy of Forensic Sciences, Ministry of Justice, Shanghai, China
| | - Ruiyang Tao
- Academy of Forensic Sciences, Ministry of Justice, Shanghai, China
| | - Yiling Qu
- Academy of Forensic Sciences, Ministry of Justice, Shanghai, China
| | - Xiaochun Zhang
- Academy of Forensic Sciences, Ministry of Justice, Shanghai, China
| | - Huan Yu
- School of Forensic Medicine, Shanxi Medical University, Taiyuan, China
| | - Chunyan Yuan
- Academy of Forensic Sciences, Ministry of Justice, Shanghai, China
- Department of Forensic Medicine, Inner Mongolia Medical University, Hohhot, China
| | - Suhua Zhang
- Academy of Forensic Sciences, Ministry of Justice, Shanghai, China
| | - Chengtao Li
- Academy of Forensic Sciences, Ministry of Justice, Shanghai, China
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6
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Chen C, Lin Y, Yu H, Xue Y, Xu Q, Jiang L, Zhu R, Chen A, Yang Y, Xia R, Zhang X, Yang Q, Tao R, Zhu B, Li C, Zhang S. Establishing an integrated pipeline for automatic and efficient detection of trace DNA encountered in forensic applications. Sci Justice 2022; 62:50-59. [PMID: 35033328 DOI: 10.1016/j.scijus.2021.10.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 08/13/2021] [Accepted: 10/26/2021] [Indexed: 11/26/2022]
Abstract
The analysis of trace DNA is a crucial component in forensic applications. Biological materials containing low-level DNA collected at crime scenes, such as fingerprints, can be valuable as evidence. Automatic detection of biological samples has been largely embraced in forensic applications to meet the increasing throughput requirements. However, the amount of DNA automatically retrieved from trace evidence often tends to be small and unstable, ultimately resulting in poor detection of DNA profiles. Thus, in this work, we introduced a robust DNA extraction and purification platform named Bionewtech® BN3200 (Bionewtech®, Shanghai, China) with the goal of constructing a rapid automatic detection system for trace DNA. The establishment of automatic detection system for trace DNA mainly encompassed two parts: assessing the sensitivity of automatic extraction platform and screening the optimal short tandem repeat (STR) typing kit. The sensitivity of Bionewtech® BN3200 platform based on Ultra-sensitive DNA Extraction kit was initially estimated, demonstrating that this extraction platform might contain large potential in the trace DNA extraction. For the amplification part, three sets of commercial multiplex STR typing kits were selected as candidates, and the amplified products were further genotyped on the Applied Biosystems 3500xl Genetic Analyzer. After comparation, SiFa™ 23 Plex Kit was determined as the most suitable amplification system for trace DNA. Eventually, the newly exploited trace DNA detection system was successfully implemented in the detection of fingerprints derived from glass surfaces with the five-seconds contact time. As a result, the DNA recovered from the fingerprints fluctuated approximately from 57.60 pg to 18.05 ng, in addition, over 70% of the total STR loci were detected in 75% of the fingerprint samples.
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Affiliation(s)
- Chong Chen
- College of Forensic Medicine, Xi'an Jiaotong University Health Science Center, Xi'an 710061, China; Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai 200063, China
| | - Yuan Lin
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai 200063, China
| | - Huan Yu
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai 200063, China; Department of Forensic Science, Medical School of Soochow University, Suzhou 215123, China
| | - Yu Xue
- Bionewtech® Company., Ltd., Shanghai 201615, China
| | - Qiannan Xu
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai 200063, China; Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Lei Jiang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai 200063, China
| | - Ruxin Zhu
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai 200063, China
| | - Anqi Chen
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai 200063, China; Department of Forensic Medicine, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Yue Yang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai 200063, China; School of Basic Medicine, Inner Mongolia Medical University, Hohhot 010030, China
| | - Ruocheng Xia
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai 200063, China; Department of Forensic Medicine, School of Basic Medical Science, Wenzhou Medical University, Wenzhou 325035, China
| | - Xiaochun Zhang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai 200063, China; Department of Forensic Science, Medical School of Soochow University, Suzhou 215123, China
| | - Qi Yang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai 200063, China; Department of Forensic Science, Medical School of Soochow University, Suzhou 215123, China
| | - Ruiyang Tao
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai 200063, China
| | - Bofeng Zhu
- College of Forensic Medicine, Xi'an Jiaotong University Health Science Center, Xi'an 710061, China
| | - Chengtao Li
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai 200063, China.
| | - Suhua Zhang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai 200063, China.
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7
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Farhat Ullah M, Ali A, Majeed A, Ijaz A, Albastaki A, Ijaz Khan M, Ramzan Khan M, Ahmed Alghamdi H, Abdulrahman Alshahrani M. Population and Mutational Assessment of Novel Repeats in 13RM Y-STRs in Unrelated Males Born in Gilgit, Pakistan. Saudi J Biol Sci 2022; 29:3177-3183. [PMID: 35844379 PMCID: PMC9280172 DOI: 10.1016/j.sjbs.2022.01.055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 01/21/2022] [Accepted: 01/24/2022] [Indexed: 11/25/2022] Open
Abstract
Because they are totally transferred to the future generations until mutations occur, Y chromosome genetic markers are commonly utilised in forensics for the classification of male lineages for criminal justice purposes. The mutation rate of Rapidly Mutating Y-STRs (RM Y-STRs) markers is high. That is not seen in other Y-STRs markers, and they appear to be effective in distinguishing paternally related men. This study aimed to estimate the population and mutational parameters of 13 RM Y-STRs in 13 unrelated males born in Gilgit, Pakistan. Repeat there was no population substructure and strong discriminating capacity in the counts. In this population, there were higher mutation rates with the unusual structure of repeats. More research is needed to better characterize these loci in diverse Pakistani groups.
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8
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Shang S, Jiang R, Luo R, Jia S, Irwin DM, Wang Z, Zhang S. Development of a 19-plex short tandem repeat typing system for individual identification and parentage testing of horses (Equus caballus). Anim Genet 2021; 52:754-758. [PMID: 34268790 DOI: 10.1111/age.13119] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/25/2021] [Indexed: 12/01/2022]
Abstract
Individual identification of horses for pedigree verification and registration is important for the sustainable development of the horse industry. Horse individual identification and parentage tests commonly use the 17 short tandem repeats (STRs) recommended by the International Society for Animal Genetics (ISAG) and the locus LEX33. While many multiplex STR typing systems have been established for the horse, a sex determining marker is usually absent, and none of them can simultaneously detect all 17 ISAG recommended loci and the locus LEX33. Here, we present a 19-plex STR typing system that contains the 17 ISAG recommend loci, the locus LEX33 and amelogenin as sex determining loci. The results of our sensitivity, species specificity, stutter analysis and population data analysis, indicate that this system is a specific, sensitive, and robust tool for the identification of individuals, parentage testing and genetic research in the horse.
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Affiliation(s)
- S Shang
- Institute of Equine Sciences, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China
| | - R Jiang
- Institute of Equine Sciences, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China
| | - R Luo
- Institute of Equine Sciences, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China
| | - S Jia
- Institute of Equine Sciences, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China
| | - D M Irwin
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Z Wang
- Institute of Equine Sciences, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China
| | - S Zhang
- Institute of Equine Sciences, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China
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9
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Qu Y, Tao R, Yu H, Yang Q, Wang Z, Tan R, Zhang X, Xia R, Xiong L, Xi S, Wu J, Gao Y, Zhang S, Li C. Development and validation of a forensic six-dye multiplex assay with 29 STR loci. Electrophoresis 2021; 42:1419-1430. [PMID: 33864289 DOI: 10.1002/elps.202100019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 03/05/2021] [Accepted: 04/10/2021] [Indexed: 11/10/2022]
Abstract
This paper describes the development and validation of a novel 31-locus, six-dye STR multiplex system, which is designed to meet the needs of the rapidly growing Chinese forensic database. This new assay combines 20 extended-CODIS core loci (D3S1358, D5S818, TPOX, CSF1PO, TH01, vWA, D7S820, D21S11, D8S1179, D18S51, D16S539, D13S317, FGA, D1S1656, D2S441, D2S1338, D10S1248, D12S391, D19S433, and D22S1045), nine highly polymorphic loci in Chinese Han population (D3S3045, D6S1043, D6S477, D8S1132, D10S1435, D15S659, D19S253, Penta D, and Penta E), and two gender determining markers, amelogenin and Y-Indel, which could amplify DNA from extracts, as well as direct amplification from substrates. To demonstrate the suitability for forensic applications, this system was validated by precision and accuracy evaluation, concordance tests, case sample tests, sensitivity, species specificity, stability, stutter calculation, and DNA mixtures, according to the guidelines described by the Scientific Working Group on DNA Analysis Methods (SWGDAM) and regulations published by the China Ministry of Public Security. The validation results indicate the robustness and reliability of this new system, and it could be a potentially helpful tool for human identification and paternity testing in the Chinese population, as well as facilitating global forensic DNA data sharing.
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Affiliation(s)
- Yiling Qu
- Department of Forensic Science, Medical School of Soochow University, Suzhou, P. R. China.,Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, P. R. China
| | - RuiYang Tao
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, P. R. China
| | - Huan Yu
- Department of Forensic Science, Medical School of Soochow University, Suzhou, P. R. China.,Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, P. R. China
| | - Qi Yang
- Department of Forensic Science, Medical School of Soochow University, Suzhou, P. R. China.,Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, P. R. China
| | - Ziwei Wang
- Department of Forensic Science, Medical School of Soochow University, Suzhou, P. R. China.,Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, P. R. China
| | - Rui Tan
- Department of Forensic Science, Medical School of Soochow University, Suzhou, P. R. China.,Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, P. R. China
| | - Xiaochun Zhang
- Department of Forensic Science, Medical School of Soochow University, Suzhou, P. R. China.,Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, P. R. China
| | - Ruocheng Xia
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, P. R. China.,Department of Forensic Medicine, School of Basic Medical Science, Wenzhou Medical University, Wenzhou, P. R. China
| | - Lei Xiong
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, P. R. China.,School of Basic Medicine, Inner Mongolia Medical University, Hohhot, P. R. China
| | - Shihan Xi
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, P. R. China.,Clinical Medical School of Inner Mongolia University for the Nationalities, Tongliao, P. R. China
| | - Jun Wu
- PeopleSpot Inc., Beijing, P. R. China
| | - Yuzhen Gao
- Department of Forensic Science, Medical School of Soochow University, Suzhou, P. R. China
| | - Suhua Zhang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, P. R. China
| | - Chengtao Li
- Department of Forensic Science, Medical School of Soochow University, Suzhou, P. R. China.,Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, P. R. China
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10
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Wang S, Song F, Xie M, Zhang K, Xie B, Huang Z, Luo H. Evaluation of a six-dye multiplex composed of 27 markers for forensic analysis and databasing. Mol Genet Genomic Med 2020; 8:e1419. [PMID: 32677357 PMCID: PMC7507347 DOI: 10.1002/mgg3.1419] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 06/10/2020] [Accepted: 07/01/2020] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Short tandem repeat (STR) markers play a significant role in genetic applications and have proved to be effective for the personal identification in forensic medicine. In this study, a six-dye multiplex composed of 23 autosomal STR loci (TH01, D3S1358, Penta D, D6S1043, D21S11, TPOX, D1S1656, D12S391, Penta E, D10S1248, D22S1045, D19S433, D8S1179, D2S1338, D2S441, D18S51, vWA, FGA, D16S539, CSF1PO, D13S317, D5S818, D7S820), one Y chromosome STR (DYS391), two internal quality control markers (Quality Sensor QS1 and QS2), and Amelogenin was evaluated. METHODS Evaluation studies, including PCR-based studies, sensitivity studies, species specificity studies, stability studies, DNA mixture studies, concordance studies, and precision evaluations were performed according to the guidelines of "Validation Guidelines for Forensic DNA Analysis Methods (2016)" by the Scientific Working Group on DNA Analysis Methods (SWGDAM). In addition, the forensic characteristics of 357 unrelated male samples from Han and Hui populations in China were investigated using 27 markers. RESULTS Full STR profiles were obtained from different reaction volumes (5 ~ 25 μl), cycle numbers (28 ~ 34 cycles) and annealing temperatures (58 ~ 62°C). All STR profiles were obtained at humic acid concentration of up to 200 ng/μl and hematin concentration of up to 500 μM. No peaks were observed in most common animal samples except two innovative internal PCR controls (Quality Sensor QS1 and QS2). The six-dye multiplex showed a notably high value for the combined probability of exclusion (CPE), exhibiting values of with 0.99999999977688 in the Han population and 0.999999999583875 in the Hui population. The values of combined probability of discrimination (CPD) were 0.999999999999999999999999999997453 in the Han population and 0. 999999999999999999999999999994398 in the Hui population. In addition, concordance studies showed that there was no difference with the AGCU Express Marker 22 Kit. CONCLUSION The results indicated that the Investigator® 26plex QS Kit is a robust, reliable, and suitable tool for forensic analysis and databasing.
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Affiliation(s)
- Shuangshuang Wang
- Department of Forensic GeneticsWest China School of Basic Medical Sciences & Forensic MedicineSichuan UniversityChengduChina
| | - Feng Song
- Department of Forensic GeneticsWest China School of Basic Medical Sciences & Forensic MedicineSichuan UniversityChengduChina
| | - Mingkun Xie
- Department of ObstetricsXiangya HospitalCentral South UniversityChangshaChina
| | - Ke Zhang
- Department of Forensic GeneticsWest China School of Basic Medical Sciences & Forensic MedicineSichuan UniversityChengduChina
| | - Bowen Xie
- Department of Forensic GeneticsWest China School of Basic Medical Sciences & Forensic MedicineSichuan UniversityChengduChina
| | - Zhanglong Huang
- Department of Criminal Investigation Bureau of Sichuan Provincial Public SecurityChengduChina
| | - Haibo Luo
- Department of Forensic GeneticsWest China School of Basic Medical Sciences & Forensic MedicineSichuan UniversityChengduChina
- Key Laboratory of Sichuan Higher Education, Criminal Science and Technology LaboratorySichuan Police CollegeLuzhouChina
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11
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Zhang J, Zhang J, Tao R, Jiang L, Chen L, Li X, Li C, Zhang S. A newly devised multiplex assay of novel polymorphic non-CODIS STRs as a valuable tool for forensic application. Forensic Sci Int Genet 2020; 48:102341. [PMID: 32599549 DOI: 10.1016/j.fsigen.2020.102341] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 06/05/2020] [Accepted: 06/15/2020] [Indexed: 11/18/2022]
Abstract
DNA profiling that relies on sets of highly polymorphic autosomal STR markers is widely used in the forensic field for human identification and paternity testing. However, the number of markers that are included in the STR kits that are currently available is insufficient to conclusively prove or disprove a relationship between individuals, especially when complex family scenarios are suspected or indirect analyses are required. In these cases, it becomes necessary to increase the number of loci under analysis to reach an adequate likelihood ratio (LR). In this study, we discovered 18 new autosomal non-CODIS STR loci (D1S1616, D1S1608, D2S437, D3S2457, D4S2406, D4S3249, D5S2843, D5S2501, D6S1010, D8S1039, D12S1301, D14S586, D15S815, SHGC-145653, CHLC.GATA14D12, D1S1603, HUMUT7148, and CHLC.GATA84D07) by web scanning and experimental screening. On the basis of this discovery, we developed a novel multiplex typing system named the "SiFaSTR 21plex_NCII Typing System" comprising 1) the 18 non-CODIS autosomal STRs mentioned above, 2) a CODIS locus of D2S1338, and 3) Amelogenin and DYS391. A forensic developmental validation, including sensitivity, species specificity, concordance, reproducibility, sample suitability, testing stability, and mixture testing, was performed following SWGDAM. The results of the validation studies indicated that this system is accurate, reliable and suitable for human DNA profiling. The sensitivity study of the system demonstrated that a full profile was obtainable with DNA as low as 125 pg. Species specificity was proven by the lack of cross-reactivity with a series of common animal species. The stability study demonstrated that 1 ng of control DNA could be fully genotyped with concentrations of haematin ≤ 150 μM, indigotin ≤ 5000 ng/μl, urea ≤ 16000 ng/μl, nigrosine ≤ 100 ng/μl and humic acid ≤ 20 ng/μl. In the mixture test, all of the minor alleles could be called at mixed ratios of 1:1, 1:3 and 3:1. We also investigated the allelic frequencies and forensic parameters of the included markers in 259 Chinese Han individuals. The forensic efficiency parameters, including the total power of discrimination (TDP) and the combined exclusion power in duos (CPEduos) and in trios (CPEtrios) of the system were calculated to be greater than 0.9999999, 0.9997347 and 0.9999997, respectively. This result proved that the system is suitable for human identification and paternity testing. The 18 newly discovered non-CODIS STRs and the developed system will be a valuable supplementary tool for the forensic community and will help solve complex paternity cases, evolutionary studies and population investigations.
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Affiliation(s)
- Jiashuo Zhang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, 200063, PR China; Key Laboratory of Evidence Identification in Universities of Shandong Province, Shandong University of Political Science and Law, Jinan, 250014, PR China
| | - Jingyi Zhang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, 200063, PR China; Department of Forensic Science, Medical School of Soochow University, Suzhou, 215123, PR China
| | - Ruiyang Tao
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, 200063, PR China; Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, PR China
| | - Lei Jiang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, 200063, PR China
| | - Liqin Chen
- School of Basic Medicine, Inner Mongolia Medical University, Hohhot, 010030, PR China
| | - Xuebo Li
- Key Laboratory of Evidence Identification in Universities of Shandong Province, Shandong University of Political Science and Law, Jinan, 250014, PR China
| | - Chengtao Li
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, 200063, PR China.
| | - Suhua Zhang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, 200063, PR China.
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12
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Kasu M, Fraser M, Lesaoana M, D'Amato ME. Allelic ladder production for a 10 locus Y‐chromosome DNA profiling system. SEPARATION SCIENCE PLUS 2020. [DOI: 10.1002/sscp.201900085] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Mohaimin Kasu
- Forensic DNA LaboratoryDepartment of BiotechnologyUniversity of the Western Cape Bellville South Africa
| | - Mischa Fraser
- Inqaba Biotechnical Industries Muckleneuk Pretoria South Africa
| | - Mpasi Lesaoana
- Forensic DNA LaboratoryDepartment of BiotechnologyUniversity of the Western Cape Bellville South Africa
- Lesotho Mounted Police ServiceTechnical Support Services Maseru Lesotho
| | - Maria Eugenia D'Amato
- Forensic DNA LaboratoryDepartment of BiotechnologyUniversity of the Western Cape Bellville South Africa
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13
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Zhao X, Qiu Q, Li C, Fu D, Hu X, Gao S, Zhu Y, Mu H, Wang R, Yang H, Li B. Genome-based development of 15 microsatellite markers in fluorescent multiplexes for parentage testing in captive tigers. PeerJ 2020; 8:e8939. [PMID: 32411512 PMCID: PMC7210807 DOI: 10.7717/peerj.8939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 03/18/2020] [Indexed: 11/20/2022] Open
Abstract
As one of the most endangered species, tiger (Panthera tigris) inbreeding has become an urgent issue to address. Using a microsatellite (short tandem repeat, STR) identification system, paternity testing may be helpful to avoid inbreeding in captive breeding programs. In this study, we developed a genome-based identification system named tiger pedigree identification multiplex system (TPI-plex). By analyzing the entire tiger genome, 139,967 STR loci were identified and 12.76% of these displayed three to six alleles among three re-sequenced individual tiger genomes. A total of 204 candidate STRs were identified and screened with a reference population containing 31 unrelated captive tigers. Of these, 15 loci were chosen for inclusion in the multiplex panel. The mean allele number and mean expected heterozygosity (He) were 7.3333 and 0.7789, respectively. The cumulative probability of exclusion (CPE) and total probability of discrimination power (TDP) reached 0.999999472 and 0.999999999999995, respectively. The results showed that the TPI-plex system can be applied in routine pedigree identification for captive tigers. We also added a sex identification marker named TAMEL into the TPI-plex for sex determination.
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Affiliation(s)
- Xiao Zhao
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China.,Forensic Genomics International (FGI), BGI-Shenzhen, Shenzhen, China.,Shenzhen Key Laboratory of Forensics, BGI-Shenzhen, Shenzhen, China.,BGI-Shenzhen, Shenzhen, China
| | - Qiguan Qiu
- Changsha Ecological Zoo, Changsha, China
| | - Chang Li
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China.,BGI-Shenzhen, Shenzhen, China.,BGI-Qingdao, BGI-Shenzhen, Qingdao, China
| | - Dongke Fu
- Forensic Genomics International (FGI), BGI-Shenzhen, Shenzhen, China.,Shenzhen Key Laboratory of Forensics, BGI-Shenzhen, Shenzhen, China.,BGI-Shenzhen, Shenzhen, China
| | - Xuesong Hu
- Forensic Genomics International (FGI), BGI-Shenzhen, Shenzhen, China.,BGI-Shenzhen, Shenzhen, China
| | - Shengjie Gao
- Forensic Genomics International (FGI), BGI-Shenzhen, Shenzhen, China.,BGI-Shenzhen, Shenzhen, China
| | - Yugang Zhu
- Changsha Sanzhen Tiger Park, Changsha, China
| | - Haofang Mu
- Center of Forensic Sciences, BGI, Beijing, China
| | - Runping Wang
- BGI Shaanxi Xixian new area Institute of Forensic Science, Xi'an, China
| | - Huanming Yang
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China.,BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Bo Li
- BGI-Shenzhen, Shenzhen, China
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14
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Cui W, Jin X, Guo Y, Chen C, Zhang W, Kong T, Meng H, Zhu B. An innovative panel containing a set of insertion/deletion loci for individual identification and its forensic efficiency evaluations in Chinese Hui ethnic minority. Mol Genet Genomic Med 2020; 8:e1074. [PMID: 31865639 PMCID: PMC7005628 DOI: 10.1002/mgg3.1074] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 10/25/2019] [Accepted: 11/15/2019] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Individual identification is one of the most important tasks in the field of forensic genetics. Insertion/Deletion (InDel) polymorphism marker has been a promising marker for individual identification. However, a part of InDel loci in commonly used commercial kit show low polymorphisms in Chinese populations. METHODS We evaluated a panel of 35 InDel loci constructed previously for individual identifications in Hui group. Subsequently, population data of three Chinese populations from 1,000 Genomes Project database were used to evaluate individual identification performance of these 35 InDels. Forensic parameters, such as heterozygosity, power of exclusion, match probability and power of discrimination, were calculated to evaluate the forensic efficiency of these loci in Hui group. The heatmap of insertion allelic frequencies, Nei's genetic distances, pairwise fixation index values, principal component analyses and admixture analyses were used to analyze the genetic differentiations and structure between Hui group and other populations. RESULTS In studied Hui group, besides rs3054057, polymorphism information content values of the remaining loci were greater than 0.3. Values of expected heterozygosity of these loci were close to 0.5. The combined power of discrimination and power of exclusion values were 0.99999999999999659609 and 0.998682, respectively. Analyses of population genetics revealed that Chinese Hui group had closer genetic relationships with East Asian populations than other intercontinental populations. CONCLUSION The forensic statistical analyses revealed these loci showed relatively high genetic polymorphisms in Chinese Hui group, and could be served as a useful tool for individual identifications in Hui group. Population genetic evaluations indicated that Chinese Hui group had close genetic relationships with East Asian populations.
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Affiliation(s)
- Wei Cui
- Key laboratory of Shaanxi Province for Craniofacial Precision Medicine ResearchCollege of StomatologyXi’an Jiaotong UniversityXi’anChina
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial DiseasesCollege of StomatologyXi’an Jiaotong UniversityXi’anChina
- College of Medicine and ForensicsXi’an Jiaotong University Health Science CenterXi’anChina
| | - Xiaoye Jin
- Key laboratory of Shaanxi Province for Craniofacial Precision Medicine ResearchCollege of StomatologyXi’an Jiaotong UniversityXi’anChina
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial DiseasesCollege of StomatologyXi’an Jiaotong UniversityXi’anChina
- College of Medicine and ForensicsXi’an Jiaotong University Health Science CenterXi’anChina
| | - Yuxin Guo
- Key laboratory of Shaanxi Province for Craniofacial Precision Medicine ResearchCollege of StomatologyXi’an Jiaotong UniversityXi’anChina
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial DiseasesCollege of StomatologyXi’an Jiaotong UniversityXi’anChina
- College of Medicine and ForensicsXi’an Jiaotong University Health Science CenterXi’anChina
| | - Chong Chen
- Key laboratory of Shaanxi Province for Craniofacial Precision Medicine ResearchCollege of StomatologyXi’an Jiaotong UniversityXi’anChina
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial DiseasesCollege of StomatologyXi’an Jiaotong UniversityXi’anChina
- College of Medicine and ForensicsXi’an Jiaotong University Health Science CenterXi’anChina
| | - Wenqing Zhang
- Key laboratory of Shaanxi Province for Craniofacial Precision Medicine ResearchCollege of StomatologyXi’an Jiaotong UniversityXi’anChina
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial DiseasesCollege of StomatologyXi’an Jiaotong UniversityXi’anChina
| | - Tingting Kong
- Key laboratory of Shaanxi Province for Craniofacial Precision Medicine ResearchCollege of StomatologyXi’an Jiaotong UniversityXi’anChina
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial DiseasesCollege of StomatologyXi’an Jiaotong UniversityXi’anChina
| | - Haotian Meng
- Key laboratory of Shaanxi Province for Craniofacial Precision Medicine ResearchCollege of StomatologyXi’an Jiaotong UniversityXi’anChina
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial DiseasesCollege of StomatologyXi’an Jiaotong UniversityXi’anChina
| | - Bofeng Zhu
- Key laboratory of Shaanxi Province for Craniofacial Precision Medicine ResearchCollege of StomatologyXi’an Jiaotong UniversityXi’anChina
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial DiseasesCollege of StomatologyXi’an Jiaotong UniversityXi’anChina
- Department of Forensic GeneticsSchool of Forensic MedicineSouthern Medical UniversityGuangzhouChina
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15
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Tao R, Chen C, Sheng X, Xia R, Zhang X, Zhang J, Yang Z, Zhang S, Li C. Validation of the Investigator 24plex QS Kit: a 6-dye multiplex PCR assay for forensic application in the Chinese Han population. Forensic Sci Res 2019; 7:172-180. [PMID: 35784410 PMCID: PMC9246015 DOI: 10.1080/20961790.2019.1665160] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The Investigator 24plex QS Kit (QIAGEN, Hilden, Germany) is a 6-dye fluorescent chemistry short tandem repeat (STR) polymerase chain reaction (PCR) amplification system that simultaneously amplifies 20 of the expanded Combined DNA Index System (CODIS) core STR loci, SE33, DYS391, and the standard sex-determining locus, amelogenin, as well as two special internal performance quality sensor controls (QS1 and QS2), which are included in the primer mix to check the PCR performance. This study was designed to be a pilot evaluation of this STR-PCR kit in a Chinese Han population regarding the PCR conditions, sensitivity, precision, accuracy, repeatability, reproducibility, and concordance; tolerance to PCR inhibitors; applicability to real “forensic-type” samples; species specificity; mixture, balance and stutter analyses, and utility in a population investigation. The exhaustive validation studies demonstrated that the Investigator 24plex QS system is accurate, sensitive and robust for STR genotyping. In addition, these genetic markers in the population data in our study indicated that they can also be useful for forensic identification and paternity testing in the Chinese Han population.
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Affiliation(s)
- Ruiyang Tao
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, China
| | - Chong Chen
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, China
- College of Medicine and Forensics, Xi’an Jiaotong University Health Science Center, Xi’an, China
| | | | - Ruocheng Xia
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, China
- Department of Forensic Medicine, School of Basic Medical Science, Wenzhou Medical University, Wenzhou, China
| | - Xiaochun Zhang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, China
- Department of Forensic Science, Medical School of Soochow University, Suzhou, China
| | - Jingyi Zhang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, China
- Department of Forensic Science, Medical School of Soochow University, Suzhou, China
| | - Zihao Yang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, China
- Department of Forensic Medicine, School of Basic Medical Science, Wenzhou Medical University, Wenzhou, China
| | - Suhua Zhang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, China
| | - Chengtao Li
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, China
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16
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Dang W, Shang S, Zhang X, Yu Y, Irwin DM, Wang Z, Zhang S. A novel 13-plex STR typing system for individual identification and parentage testing of donkeys (Equus asinus). Equine Vet J 2019; 52:290-297. [PMID: 31398262 DOI: 10.1111/evj.13158] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 07/27/2019] [Indexed: 11/28/2022]
Abstract
BACKGROUND Previous studies investigating donkey parentage and genetic diversity used horse-specific multiplex systems. However, several mis-allele and null-allele issues were found with some of the horse primers when used in donkeys. In 2017, the International Society for Animal Genetics (ISAG) recommended 13 dinucleotide short tandem repeats (STRs) (AHT4, ASB23, HMS2, HMS3, HMS6, HMS7, HMS18, HTG7, HTG10, TKY297, TKY312, TKY337 and TKY343) as a core panel that should be used to identify individuals and to test for parentage in donkeys. To date, no single multiplex STR typing system containing all 13 donkey STRs recommended by the ISAG has been reported. OBJECTIVES To establish a novel and donkey-specific multiplex STR typing system containing all 13 recommended STRs. STUDY DESIGN Assay development and validation in field population. METHODS Primers for seven of the STRs were redesigned and conditions for polymerase chain reaction (PCR) were optimised. We analysed the allele sequences, sensitivity, species-specificity and stutter ratios of this new system. RESULTS A 13-plex STR typing system for donkey was established. A full profile could be generated from a single PCR reaction using as little as 5 ng of DNA template with the 13 pairs of primers labelled with fluorescent dyes. An allele ladder, containing 101 alleles from the 13 STRs, was generated. No full genotype profile was generated with these primers if DNA from humans, or 11 other commonly encountered animals, was used. Genotypes could be generated for the horse and horse-donkey hybrids (mule and hinny). Stutter ratios and population genetic parameters were calculated based on samples from 150 donkeys. The combined probabilities of paternity exclusion for this system were 0.988907326 (CPEduo) and 0.999665018 (CPEtrio). MAIN LIMITATIONS This system cannot detect sex. CONCLUSIONS Our results indicate that our donkey-specific 13-plex STR typing system is sensitive, species-specific and robust for individual identification, paternity testing and population genetic analysis in donkeys, and has potential forensic applications.
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Affiliation(s)
- W Dang
- Institute of Equine Sciences, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - S Shang
- Institute of Equine Sciences, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - X Zhang
- Liaoning Province Engineering Center of Modern Agricultural Production Base, Shenyang, China
| | - Y Yu
- Institute of Equine Sciences, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - D M Irwin
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Z Wang
- Institute of Equine Sciences, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - S Zhang
- Institute of Equine Sciences, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
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17
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Zheng H, Tao R, Zhang J, Zhang J, Wang S, Yang Z, Xu Q, Gao Y, Zhang S, Li C. Development and validation of a novel SiFaSTR
TM
23‐plex system. Electrophoresis 2019; 40:2644-2654. [DOI: 10.1002/elps.201900045] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 03/22/2019] [Accepted: 05/23/2019] [Indexed: 11/09/2022]
Affiliation(s)
- Hancheng Zheng
- Department of Forensic ScienceMedical School of Soochow University Suzhou P. R. China
- Shanghai Key Laboratory of Forensic MedicineShanghai Forensic Service PlatformAcademy of Forensic Sciences Shanghai P. R. China
| | - Ruiyang Tao
- Shanghai Key Laboratory of Forensic MedicineShanghai Forensic Service PlatformAcademy of Forensic Sciences Shanghai P. R. China
- Institute of Forensic MedicineWest China School of Basic Medical Sciences & Forensic MedicineSichuan University Chengdu P. R. China
| | - Jingyi Zhang
- Department of Forensic ScienceMedical School of Soochow University Suzhou P. R. China
- Shanghai Key Laboratory of Forensic MedicineShanghai Forensic Service PlatformAcademy of Forensic Sciences Shanghai P. R. China
| | - Jiashuo Zhang
- Department of Forensic ScienceMedical School of Soochow University Suzhou P. R. China
- Shanghai Key Laboratory of Forensic MedicineShanghai Forensic Service PlatformAcademy of Forensic Sciences Shanghai P. R. China
| | - Shouyu Wang
- Institute of Forensic MedicineWest China School of Basic Medical Sciences & Forensic MedicineSichuan University Chengdu P. R. China
| | - Zihao Yang
- Shanghai Key Laboratory of Forensic MedicineShanghai Forensic Service PlatformAcademy of Forensic Sciences Shanghai P. R. China
- Department of Forensic MedicineSchool of Basic Medical ScienceWenzhou Medical University Wenzhou P. R. China
| | - Qiannan Xu
- Shanghai Key Laboratory of Forensic MedicineShanghai Forensic Service PlatformAcademy of Forensic Sciences Shanghai P. R. China
- Department of Forensic MedicineSchool of Basic Medical ScienceWenzhou Medical University Wenzhou P. R. China
| | - Yuzhen Gao
- Department of Forensic ScienceMedical School of Soochow University Suzhou P. R. China
| | - Suhua Zhang
- Shanghai Key Laboratory of Forensic MedicineShanghai Forensic Service PlatformAcademy of Forensic Sciences Shanghai P. R. China
| | - Chengtao Li
- Department of Forensic ScienceMedical School of Soochow University Suzhou P. R. China
- Shanghai Key Laboratory of Forensic MedicineShanghai Forensic Service PlatformAcademy of Forensic Sciences Shanghai P. R. China
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18
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Bai X, Yao Y, Wang C, Li W, Wang Y, Song W, Mo X, Ma W, Ye J. Development of a new 25plex STRs typing system for forensic application. Electrophoresis 2019; 40:1662-1676. [PMID: 31012482 DOI: 10.1002/elps.201900021] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Revised: 03/21/2019] [Accepted: 04/06/2019] [Indexed: 11/11/2022]
Abstract
We have developed a novel STR 25-plex florescence multiplex-STR kit (DNATyper25) to genotype 23 autosomal and two sex-linked loci for forensic applications and paternity analysis. Of the 23 autosomal loci, 20 are non-CODIS. The sex-linked markers include a Y-STR locus (DYS391) and the Amelogenin gene. We present developmental validation studies to show that the DNATyper25 kit is reproducible, accurate, sensitive, and robust. Sensitivity testing showed that full profiles were achieved with as low as 125 pg of human DNA. Specificity testing demonstrated a lack of cross reactivity with a variety of commonly encountered non-human DNA contaminants. Stability testing showed that full profiles were obtained with humic acid concentration ≤60 ng/μL and hematin concentration <400 μM. For forensic evaluation, the 23 autosomal STRs followed the Hardy-Weinberg equilibrium. In an analysis of 509 Chinese (CN) Hans, we detected a combined total of 181 alleles at the 23 autosomal STR loci. Since these autosomal STRs are independent from one another, PM was 8.4528 × 10-22 , TDP was 0.999 999 999 999 999 999 999, CEP was 0.999 999 8395. The forensic efficiency parameters demonstrated that these autosomal STRs are highly polymorphic and informative in the Han population of China. We performed population comparisons and showed that the Northern CN Han has a close genetic relationship with the Luzhou Han, Tujia, and Bai populations. We propose that the DNATyper25 kit will be useful for cases where paternity analysis is difficult and for situations where DNA samples are limited in quantity and low in quality.
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Affiliation(s)
- Xue Bai
- Key Laboratory of Forensic Genetics, Institute of Forensic Science, Ministry of Public Security, Beijing, P. R. China
| | - Yiren Yao
- Key Laboratory of Forensic Genetics, Institute of Forensic Science, Ministry of Public Security, Beijing, P. R. China
| | - Changli Wang
- Chongqing Key Laboratory of Forensic Evidence Technology, Institute of Forensic Science, Chongqing of Public Security Bureau, Chongqing, P. R. China
| | - Wanshui Li
- Key Laboratory of Forensic Genetics, Institute of Forensic Science, Ministry of Public Security, Beijing, P. R. China
| | - Youzheng Wang
- Chongqing Key Laboratory of Forensic Evidence Technology, Institute of Forensic Science, Chongqing of Public Security Bureau, Chongqing, P. R. China
| | - Wen Song
- Key Laboratory of Forensic Genetics, Institute of Forensic Science, Ministry of Public Security, Beijing, P. R. China
| | - Xiaoting Mo
- Key Laboratory of Forensic Genetics, Institute of Forensic Science, Ministry of Public Security, Beijing, P. R. China
| | - Wenhua Ma
- Key Laboratory of Forensic Genetics, Institute of Forensic Science, Ministry of Public Security, Beijing, P. R. China
| | - Jian Ye
- Key Laboratory of Forensic Genetics, Institute of Forensic Science, Ministry of Public Security, Beijing, P. R. China
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19
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Tao R, Zhang J, Sheng X, Zhang J, Yang Z, Chen C, Bian Y, Liu X, Zhang S, Li C. Development and validation of a multiplex insertion/deletion marker panel, SifaInDel 45plex system. Forensic Sci Int Genet 2019; 41:128-136. [PMID: 31079022 DOI: 10.1016/j.fsigen.2019.04.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 04/22/2019] [Accepted: 04/29/2019] [Indexed: 01/08/2023]
Abstract
In addition to commonly used short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs), insertion and deletion polymorphisms (InDels) have considerable potential in the field of forensic genetics because they combine desirable characteristics of both STRs and SNPs. In the present study, the SifaInDel 45plex system was designed to amplify 45 InDel markers, including 27 autosomal InDels (A-InDels), 16 X chromosome InDels (X-InDels) and two Y chromosome InDels (Y-InDels), simultaneously in a single PCR procedure and then detect products by capillary electrophoresis (CE). We also optimized the PCR conditions for the novel panel and performed several validation studies including repeatability/reproducibility, concordance, accuracy, sensitivity, stability, species specificity and population genetics. The results confirmed that full profiles could be obtained from ≥62.5 pg of input DNA and from a series of challenging samples encountered in routine casework. The SifaInDel 45plex panel could tolerate different concentrations of inhibitors, such as ≤50 μM hematin, ≤20 ng/μL nigrosine and ≤8000 ng/μL urea. In a population investigation, for the 27 A-InDels, the combined power of discrimination (CPD) exceeded 0.999999, and the combined power of exclusion in duos (CPED) and trios (CPET) was 0.955118 and 0.997754, respectively. For the 16 X-InDels, the combined PDMale and PDFemale was computed as 0.999845 and 0.999998, respectively, and the combined mean exclusion chance in father/daughter or mother/son duos (MECDuo) and mean exclusion chance in standard trios involving daughters (MECTrio) was 0.976220 and 0.998163, respectively. In addition, the two Y-InDels could play a role in correctly determining gender. Overall, the established SifaInDel 45plex panel is a well-performing, reliable and robust multiplex system that stands out for combining a considerable number of A-indels, X-indels and Y-indels based on a CE platform. The population study results also demonstrated that the SifaInDel 45plex panel could be a valid complementary approach for human identification and complex kinship analysis.
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Affiliation(s)
- Ruiyang Tao
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, PR China; Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, 200063, PR China
| | - Jingyi Zhang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, 200063, PR China; Department of Forensic Science, Medical School of Soochow University, Suzhou, 215123, PR China
| | | | - Jiashuo Zhang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, 200063, PR China; Department of Forensic Science, Medical School of Soochow University, Suzhou, 215123, PR China
| | - Zihao Yang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, 200063, PR China; Department of Forensic Medicine, School of Basic Medical Science, Wenzhou Medical University, Wenzhou, 325035, PR China
| | - Chong Chen
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, 200063, PR China; College of Medicine and Forensics, Xi'an Jiaotong University Health Science Center, Xi'an, 710061, PR China
| | - Yingnan Bian
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, 200063, PR China
| | - Xiling Liu
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, 200063, PR China
| | - Suhua Zhang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, 200063, PR China.
| | - Chengtao Li
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, PR China; Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, 200063, PR China.
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20
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Shang S, Zhang M, Zhao Y, Dang W, Hua P, Zhang S, Wang Z. Development and validation of a novel 13‐plex
PCR
system for commonly used short tandem repeats in horses (
Equus caballus
). Equine Vet J 2018; 51:688-695. [DOI: 10.1111/evj.13047] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 11/13/2018] [Indexed: 11/30/2022]
Affiliation(s)
- S. Shang
- Institute of Equine Sciences College of Animal Science and Veterinary Medicine Shenyang Agricultural University Shenyang PR China
- College of Food Science Shenyang Agricultural University Shenyang PR China
| | - M. Zhang
- College of Economics and Management Shenyang Agricultural University Shenyang PR China
| | - Y. Zhao
- Institute of Equine Sciences College of Animal Science and Veterinary Medicine Shenyang Agricultural University Shenyang PR China
| | - W. Dang
- Institute of Equine Sciences College of Animal Science and Veterinary Medicine Shenyang Agricultural University Shenyang PR China
| | - P. Hua
- School of Ecological and Environmental Sciences East China Normal University Shanghai PR China
| | - S. Zhang
- Institute of Equine Sciences College of Animal Science and Veterinary Medicine Shenyang Agricultural University Shenyang PR China
| | - Z. Wang
- Institute of Equine Sciences College of Animal Science and Veterinary Medicine Shenyang Agricultural University Shenyang PR China
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21
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Sheng X, Wang Y, Zhang J, Chen L, Lin Y, Zhao Z, Li C, Zhang S. Forensic investigation of 23 autosomal STRs and application in Han and Mongolia ethnic groups. Forensic Sci Res 2018; 3:138-144. [PMID: 30483662 PMCID: PMC6197138 DOI: 10.1080/20961790.2018.1428782] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2017] [Accepted: 01/12/2018] [Indexed: 12/03/2022] Open
Abstract
A forensic validation study of the Early Access Huaxia™ Platinum Polymerase Chain Reaction (PCR) kit was completed to document the performance capabilities and limitations. The genotyping of DNA samples was consistent across a large range of template DNA concentrations, with complete profiles obtained at 0.125 ng; however, no more than 2 mm × 1.2 mm punches of samples would be recommended for direct amplification. The size precision and accuracy test revealed the genotyping ability; while consistent results were obtained when comparing the kit with other commercially available systems. In addition, the whole PCR amplification can finish within approximately 45 min, making the system suitable for fast-detection. However, only partial profiles may be obtained with challenging samples, including DNA stored on Foam-Tipped Applicators (FTA) cards or some case samples. For the forensic application in ethnic groups, a total of 282 and 229 alleles were obtained in Han and Mongolia, respectively. Since the 23 short tandem repeats were independent from each other, the cumulative power of exclusion in duos was 0.999 999 157 188 and the cumulative power of exclusion in trios was 0.999 999 999 859 in the Han group while the cumulative power of exclusion in duos (CPEduo) was 0.999 998 848 26 and cumulative power of exclusion in trios (CPEtrio) was 0.999 999 999 79 in the Mongolia group. And good internal consistency was found between the two investigated groups and the Sichuan Han, Hui, Tibetan and Uygur according to available reference data.
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Affiliation(s)
- Xiang Sheng
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Shanghai, China.,Department of Forensic Medicine, Medical College of Soochow University, Suzhou, China
| | - Yali Wang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Shanghai, China.,Department of Forensic Medicine, Inner Mongolia Medical University, Hohhot, China
| | - Jiashuo Zhang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Shanghai, China.,Department of Forensic Medicine, Medical College of Soochow University, Suzhou, China
| | - Liqin Chen
- Department of Forensic Medicine, Inner Mongolia Medical University, Hohhot, China
| | - Yuan Lin
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Shanghai, China
| | - Zhenmin Zhao
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Shanghai, China
| | - Chengtao Li
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Shanghai, China
| | - Suhua Zhang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Shanghai, China
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22
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Genetic diversity of 21 forensic autosomal STRs and DYS391 in the Han population from Shanghai, Eastern China. Forensic Sci Int Genet 2018; 37:e23-e25. [PMID: 30181102 DOI: 10.1016/j.fsigen.2018.08.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 08/13/2018] [Accepted: 08/26/2018] [Indexed: 01/11/2023]
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23
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Zhang S, Niu Y, Bian Y, Dong R, Liu X, Bao Y, Jin C, Zheng H, Li C. Sequence investigation of 34 forensic autosomal STRs with massively parallel sequencing. Sci Rep 2018; 8:6810. [PMID: 29717145 PMCID: PMC5931506 DOI: 10.1038/s41598-018-24495-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 04/05/2018] [Indexed: 12/18/2022] Open
Abstract
STRs vary not only in the length of the repeat units and the number of repeats but also in the region with which they conform to an incremental repeat pattern. Massively parallel sequencing (MPS) offers new possibilities in the analysis of STRs since they can simultaneously sequence multiple targets in a single reaction and capture potential internal sequence variations. Here, we sequenced 34 STRs applied in the forensic community of China with a custom-designed panel. MPS performance were evaluated from sequencing reads analysis, concordance study and sensitivity testing. High coverage sequencing data were obtained to determine the constitute ratios and heterozygous balance. No actual inconsistent genotypes were observed between capillary electrophoresis (CE) and MPS, demonstrating the reliability of the panel and the MPS technology. With the sequencing data from the 200 investigated individuals, 346 and 418 alleles were obtained via CE and MPS technologies at the 34 STRs, indicating MPS technology provides higher discrimination than CE detection. The whole study demonstrated that STR genotyping with the custom panel and MPS technology has the potential not only to reveal length and sequence variations but also to satisfy the demands of high throughput and high multiplexing with acceptable sensitivity.
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Affiliation(s)
- Suhua Zhang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, 200063, P.R. China
| | - Yong Niu
- Criminal Investigation Department, Ministry of Public Security, Beijing, 100741, P.R. China
| | - Yingnan Bian
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, 200063, P.R. China
| | - Rixia Dong
- The Affiliated Guangji Hospital of Soochow University, Suzhou, 215008, P.R. China
| | - Xiling Liu
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, 200063, P.R. China
| | - Yun Bao
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, 200063, P.R. China
| | - Chao Jin
- Shanghai OE Biotechnology Co, Ltd, Shanghai, 201114, P.R. China
| | - Hancheng Zheng
- Department of Forensic Medicine, Medical College of Soochow University, Suzhou, 215123, P.R. China
| | - Chengtao Li
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, 200063, P.R. China.
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24
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Genetic characteristics and phylogenetic analysis of three Chinese ethnic groups using the Huaxia Platinum System. Sci Rep 2018; 8:2429. [PMID: 29403025 PMCID: PMC5799253 DOI: 10.1038/s41598-018-20871-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 01/23/2018] [Indexed: 11/23/2022] Open
Abstract
Short tandem repeats (STRs) are attractive to genetic applications like forensic, anthropological and population genetics studies. The Huaxia Platinum System was specifically developed to allow co-amplification and detection of all markers in the expanded CODIS core loci and the Chinese National Database. In this study, in continuation to our previous validation study, 568 unrelated individuals were firstly genotyped to investigate the effectiveness of this novel assay in 3 main ethnic groups of China (Han, Tibetan and Yi). The combined power of discrimination (CPD) were 0.9999999999999999999999999992, 0.999999999999999999999999992, 0.999999999999999999999999998, respectively, and the combined power of exclusion (CPE) were 0.9999999999, 0.999999995, 0.999999998, respectively. Next, genetic relationships along administrative and ethnic divisions were analyzed using pairwise genetic distances, multidimensional scaling (MDS), principal component analysis (PCA) and phylogenetic analysis. The Han ethnicity showed a high genetic homogeneity all across China, and significant genetic differences existed between Han groups and some minority groups, most prominently for the Tibetans, the Uyghurs, the Kazakhs, the Miaos, the Zhuangs and the Dais. Aforementioned results suggested that the Huaxia Platinum System is polymorphic and informative, which provides an efficient tool not only for human forensics, but also for population genetics studies.
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25
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A review of bioinformatic methods for forensic DNA analyses. Forensic Sci Int Genet 2017; 33:117-128. [PMID: 29247928 DOI: 10.1016/j.fsigen.2017.12.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 11/30/2017] [Accepted: 12/10/2017] [Indexed: 12/20/2022]
Abstract
Short tandem repeats, single nucleotide polymorphisms, and whole mitochondrial analyses are three classes of markers which will play an important role in the future of forensic DNA typing. The arrival of massively parallel sequencing platforms in forensic science reveals new information such as insights into the complexity and variability of the markers that were previously unseen, along with amounts of data too immense for analyses by manual means. Along with the sequencing chemistries employed, bioinformatic methods are required to process and interpret this new and extensive data. As more is learnt about the use of these new technologies for forensic applications, development and standardization of efficient, favourable tools for each stage of data processing is being carried out, and faster, more accurate methods that improve on the original approaches have been developed. As forensic laboratories search for the optimal pipeline of tools, sequencer manufacturers have incorporated pipelines into sequencer software to make analyses convenient. This review explores the current state of bioinformatic methods and tools used for the analyses of forensic markers sequenced on the massively parallel sequencing (MPS) platforms currently most widely used.
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26
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Validation of the Microreader™ 23sp ID system: A new STR 23-plex system for forensic application. Forensic Sci Int Genet 2017; 27:67-73. [DOI: 10.1016/j.fsigen.2016.12.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 12/09/2016] [Accepted: 12/10/2016] [Indexed: 11/17/2022]
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27
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Zhang S, Bian Y, Chen A, Zheng H, Gao Y, Hou Y, Li C. Massively parallel sequencing of 231 autosomal SNPs with a custom panel: a SNP typing assay developed for human identification with Ion Torrent PGM. Forensic Sci Res 2017; 2:26-33. [PMID: 30483616 PMCID: PMC6197105 DOI: 10.1080/20961790.2017.1281011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 01/09/2017] [Indexed: 11/26/2022] Open
Abstract
The custom-designed single nucleotide polymorphism (SNP) panel amplified 231 autosomal SNPs in one PCR reaction and subsequently sequenced with massively parallel sequencing (MPS) technology and Ion Torrent personal genome machine (PGM). SNPs were chosen from SNPforID, IISNP, HapMap, dbSNP, and related published literatures. Full concordance was obtained between available MPS calling and Sanger sequencing with 9947A and 9948 controls. Ten SNPs (rs4606077, rs334355, rs430046, rs2920816, rs4530059, rs1478829, rs1498553, rs7141285, rs12714757 and rs2189011) with low coverage or heterozygote imbalance should be optimized or excluded from the panel. Sequence data had sufficiently high coverage and gave reliable SNP calling for the remaining 221 loci with the custom MPS–SNP panel. A default DNA input amount of 10 ng per reaction was recommended by Ampliseq technology but sensitivity testing revealed positive results from as little as 1 ng input DNA. Mixture testing with this panel is possible through analysis of the FMAR (frequency of major allele reads) values at most loci with enough high coverage depth and low level of sequencing noise. These results indicate the potential advantage of the custom MPS–SNP assays and Ion Torrent PGM platform for forensic study.
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Affiliation(s)
- Suhua Zhang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Institute of Forensic Sciences, Ministry of Justice, PRC, Shanghai, China
| | - Yingnan Bian
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Institute of Forensic Sciences, Ministry of Justice, PRC, Shanghai, China
| | - Anqi Chen
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Hancheng Zheng
- Department of Forensic Medicine, Medical College of Soochow University, Suzhou, China
| | - Yuzhen Gao
- Department of Forensic Medicine, Medical College of Soochow University, Suzhou, China
| | - Yiping Hou
- Department of Forensic Genetics, West China School of Preclinical and Forensic Medicine, Sichuan University, Chengdu, China
| | - Chengtao Li
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Institute of Forensic Sciences, Ministry of Justice, PRC, Shanghai, China
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28
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Developmental Validation of the Huaxia Platinum System and application in 3 main ethnic groups of China. Sci Rep 2016; 6:31075. [PMID: 27498550 PMCID: PMC4976323 DOI: 10.1038/srep31075] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 07/14/2016] [Indexed: 11/17/2022] Open
Abstract
STRs, scattered throughout the genome with higher mutation rate, are attractive to genetic application like forensic, anthropological and population genetics studies. STR profiling has now been applied in various aspects of human identification in forensic investigations. This work described the developmental validation of a novel and universal assay, the Huaxia Platinum System, which amplifies all markers in the expanded CODIS core loci and the Chinese National Database in one single PCR system. Developmental validation demonstrated that this novel assay is accurate, sensitive, reproducible and robust. No discordant calls were observed between the Huaxia Platinum System and other STR systems. Full genotypes could be achieved even with 250 pg of human DNA. Additionally, 402 unrelated individuals from 3 main ethnic groups of China (Han, Uygur and Tibetan) were genotyped to investigate the effectiveness of this novel assay. The CMP were 2.3094 × 10−27, 4.3791 × 10−28 and 6.9118 × 10−27, respectively, and the CPE were 0.99999999939059, 0.99999999989653 and 0.99999999976386, respectively. Aforementioned results suggested that the Huaxia Platinum System is polymorphic and informative, which provides efficient tool for national DNA database and facilitate international data sharing.
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29
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Development of new PCR multiplex system by the simultaneous detection of 10 miniSTRs, SE33, Penta E, Penta D, and four Y-STRs. Int J Legal Med 2016; 130:1409-1419. [DOI: 10.1007/s00414-016-1372-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 04/29/2016] [Indexed: 11/26/2022]
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