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Han J, Zhuang B, Zou L, Wang D, Jiang L, Wei YL, Zhao L, Zhao L, Li C. A developmental validation of the Quick TargSeq 1.0 integrated system for automated DNA genotyping in forensic science for reference samples. Electrophoresis 2024; 45:814-828. [PMID: 38459798 DOI: 10.1002/elps.202300187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 02/07/2024] [Accepted: 02/21/2024] [Indexed: 03/10/2024]
Abstract
Analysis of short tandem repeats (STRs) is a global standard method for human identification. Insertion/Deletion polymorphisms (DIPs) can be used for biogeographical ancestry inference. Current DNA typing involves a trained forensic worker operating several specialized instruments in a controlled laboratory environment, which takes 6-8 h. We developed the Quick TargSeq 1.0 integrated system (hereinafter abbreviated to Quick TargSeq) for automated generation of STR and DIP profiles from buccal swab samples and blood stains. The system fully integrates the processes of DNA extraction, polymerase chain reaction (PCR) amplification, and electrophoresis separation using microfluidic biochip technology. Internal validation studies were performed using RTyper 21 or DIP 38 chip cartridges with single-source reference samples according to the Scientific Working Group for DNA Analysis Methods guidelines. These results indicated that the Quick TargSeq system can process reference samples and generate STR or DIP profiles in approximately 2 h, and the profiles were concordant with those determined using traditional STR or DIP analysis methods. Thus, reproducible and concordant DNA profiles were obtained from reference samples. Throughout the study, no lane-to-lane or run-to-run contamination was observed. The Quick TargSeq system produced full profiles from buccal swabs with at least eight swipes, dried blood spot cards with two 2-mm disks, or 10 ng of purified DNA. Potential PCR inhibitors (i.e., coffee, smoking tobacco, and chewing tobacco) did not appear to affect the amplification reactions of the instrument. The overall success rate and concordance rate of 153 samples were 94.12% and 93.44%, respectively, which is comparable to other commercially available rapid DNA instruments. A blind test initiated by a DNA expert group showed that the system can correctly produce DNA profiles with 97.29% genotype concordance with standard bench-processing methods, and the profiles can be uploaded into the national DNA database. These results demonstrated that the Quick TargSeq system can rapidly generate reliable DNA profiles in an automated manner and has the potential for use in the field and forensic laboratories.
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Affiliation(s)
- Junping Han
- Technology Department of Chaoyang Sub-bureau, Beijing Public Security Bureau, Beijing, P. R. China
- Key Laboratory of Forensic Genetics, Beijing Engineering Research Center of Crime Scene Evidence Examination, National Engineering Laboratory for Forensic Science, Institute of Forensic Science, Beijing, P. R. China
| | - Bin Zhuang
- Beijing CapitalBio Technology Ltd. Co., Beijing, P. R. China
| | - Lixin Zou
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, Jiangsu International Joint Center of Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, Jiangsu, P. R. China
| | - Daoyu Wang
- People's Public Security University of China, Beijing, P. R. China
| | - Li Jiang
- Key Laboratory of Forensic Genetics, Beijing Engineering Research Center of Crime Scene Evidence Examination, National Engineering Laboratory for Forensic Science, Institute of Forensic Science, Beijing, P. R. China
| | - Yi-Liang Wei
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, Jiangsu International Joint Center of Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, Jiangsu, P. R. China
| | - Lijian Zhao
- Beijing CapitalBio Technology Ltd. Co., Beijing, P. R. China
| | - Lei Zhao
- Key Laboratory of Forensic Genetics, Beijing Engineering Research Center of Crime Scene Evidence Examination, National Engineering Laboratory for Forensic Science, Institute of Forensic Science, Beijing, P. R. China
| | - Caixia Li
- Key Laboratory of Forensic Genetics, Beijing Engineering Research Center of Crime Scene Evidence Examination, National Engineering Laboratory for Forensic Science, Institute of Forensic Science, Beijing, P. R. China
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Liacini A, Tripathi G, McCollick A, Gravante C, Abdelmessieh P, Shestovska Y, Mathew L, Geier S. Chimerism Testing by Next Generation Sequencing for Detection of Engraftment and Early Disease Relapse in Allogeneic Hematopoietic Cell Transplantation and an Overview of NGS Chimerism Studies. Int J Mol Sci 2023; 24:11814. [PMID: 37511573 PMCID: PMC10380370 DOI: 10.3390/ijms241411814] [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: 06/29/2023] [Revised: 07/18/2023] [Accepted: 07/21/2023] [Indexed: 07/30/2023] Open
Abstract
Chimerism monitoring after allogenic Hematopoietic Cell Transplantation (allo-HCT) is critical to determine how well donor cells have engrafted and to detect relapse for early therapeutic intervention. The aim of this study was to establish and detect mixed chimerism and minimal residual disease using Next Generation Sequencing (NGS) testing for the evaluation of engraftment and the detection of early relapse after allo-HCT. Our secondary aim was to compare the data with the existing laboratory method based on Short Tandem Repeat (STR) analysis. One hundred and seventy-four DNA specimens from 46 individuals were assessed using a commercially available kit for NGS, AlloSeq HCT NGS (CareDx), and the STR-PCR assay. The sensitivity, precision, and quantitative accuracy of the assay were determined using artificially created chimeric constructs. The accuracy and linearity of the assays were evaluated in 46 post-transplant HCT samples consisting of 28 levels of mixed chimerism, which ranged from 0.3-99.7%. There was a 100% correlation between NGS and STR-PCR chimerism methods. In addition, 100% accuracy was attained for the two external proficiency testing surveys (ASHI EMO). The limit of detection or sensitivity of the NGS assay in artificially made chimerism mixtures was 0.3%. We conducted a review of all NGS chimerism studies published online, including ours, and concluded that NGS-based chimerism analysis using the AlloSeq HCT assay is a sensitive and accurate method for donor-recipient chimerism quantification and minimal residual disease relapse detection in patients after allo-HCT compared to STR-PCR assay.
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Affiliation(s)
- Abdelhamid Liacini
- Immunogenetics Laboratory, Pathology and Laboratory Medicine, Temple University and Hospital, Lewis Katz School of Medicine, 3401 N. Broad St., Office B242, Philadelphia, PA 19140, USA
| | - Gaurav Tripathi
- Immunogenetics Laboratory, Pathology and Laboratory Medicine, Temple University and Hospital, Lewis Katz School of Medicine, 3401 N. Broad St., Office B242, Philadelphia, PA 19140, USA
| | - Amanda McCollick
- Immunogenetics Laboratory, Pathology and Laboratory Medicine, Temple University and Hospital, Lewis Katz School of Medicine, 3401 N. Broad St., Office B242, Philadelphia, PA 19140, USA
| | - Christopher Gravante
- Immunogenetics Laboratory, Pathology and Laboratory Medicine, Temple University and Hospital, Lewis Katz School of Medicine, 3401 N. Broad St., Office B242, Philadelphia, PA 19140, USA
| | - Peter Abdelmessieh
- Fox Chase Cancer Center Medical Group, Temple Health, Philadelphia, PA 19140, USA
| | - Yuliya Shestovska
- Fox Chase Cancer Center Medical Group, Temple Health, Philadelphia, PA 19140, USA
| | - Leena Mathew
- Immunogenetics Laboratory, Pathology and Laboratory Medicine, Temple University and Hospital, Lewis Katz School of Medicine, 3401 N. Broad St., Office B242, Philadelphia, PA 19140, USA
| | - Steven Geier
- Immunogenetics Laboratory, Pathology and Laboratory Medicine, Temple University and Hospital, Lewis Katz School of Medicine, 3401 N. Broad St., Office B242, Philadelphia, PA 19140, USA
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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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Important factors in implementation of lineage-specific chimerism analysis for routine use. Bone Marrow Transplant 2020; 56:946-948. [PMID: 33082555 DOI: 10.1038/s41409-020-01089-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 09/09/2020] [Accepted: 10/07/2020] [Indexed: 11/08/2022]
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Qu S, Li H, Li Y, Lv M, Yang F, Zhu J, Yu Z, Liu Y, Chen C, Wang Y, Li Z, Zhang L, Liang W. Developmental validation of the Microreader™ 20A ID system. Electrophoresis 2019; 40:3099-3107. [PMID: 31596501 DOI: 10.1002/elps.201900221] [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: 06/20/2019] [Revised: 08/31/2019] [Accepted: 09/26/2019] [Indexed: 12/16/2022]
Abstract
The Microreader™ 20A ID system is designed for forensic applications such as personal identification, parentage testing, and research. It includes 13 combined DNA index system (CODIS) short tandem repeat (STR) loci (CSF1PO, FGA, TH01, TPOX, vWA, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, and D21S11), three expanded CODIS STR loci (D12S391, D19S433, and D2S1338), three non-CODIS STR loci (D6S1043, Penta D, and Penta E), and the amelogenin locus in one reaction with a six-dye fluorescent (FAM, HEX, TAMAR, ROX, PUR, and QD550) analysis system. In this study, the Microreader™ 20A ID system was validated according to the Scientific Working Group on DNA Analysis Methods validation guidelines for forensic DNA Analysis methods and Chinese national standard, including PCR-based studies, sensitivity study, precision, and accuracy evaluation, stutter calculation, inhibitor tests, species specificity, and DNA mixture studies. Our results suggest that the Microreader™ 20A ID system is a useful tool for personal identification and parentage testing.
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Affiliation(s)
- Shengqiu Qu
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, P. R. China
| | - Hang Li
- Criminal Investigation Team of Yueyang Public Security Bureau, Yueyang, Hunan, P. R. China
| | - Yifan Li
- Beijing Microread Genetics Co. Ltd, Beijing, P. R. China
| | - Meili Lv
- Department of Immunology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, P. R. China
| | - Fan Yang
- Suzhou Microread Genetics Co. Ltd, Suzhou, P. R. China
| | - Jing Zhu
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, P. R. China.,Department of Forensic Medicine, Sichuan Police College, Luzhou, Sichuan, P. R. China
| | - Zailiang Yu
- Suzhou Microread Genetics Co. Ltd, Suzhou, P. R. China
| | - Yuqing Liu
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, P. R. China
| | - Chuguang Chen
- Beijing Microread Genetics Co. Ltd, Beijing, P. R. China
| | - Yinji Wang
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, P. R. China
| | - Zhuo Li
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, China, Shanghai, P. R. China
| | - Lin Zhang
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, P. R. China
| | - Weibo Liang
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, P. R. China
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