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Zhao Y, Cai L, Zhang X, Zhang H, Cai L, Zhou L, Huang B, Qian J. Hematoxylin and Eosin Staining Helps Reduce Maternal Contamination in Short Tandem Repeat Genotyping for Hydatidiform Mole Diagnosis. Int J Gynecol Pathol 2024; 43:253-263. [PMID: 37566880 PMCID: PMC11022989 DOI: 10.1097/pgp.0000000000000973] [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] [Indexed: 08/13/2023]
Abstract
Short tandem repeat (STR) genotyping provides parental origin information about aneuploidy pregnancy loss and has become the current gold standard for hydatidiform mole diagnosis. STR genotyping diagnostic support most commonly relies on formalin-fixed paraffin-embedded samples, but maternal contamination is one of the most common issues based on traditional unstained sections. To evaluate the influence of hematoxylin and eosin (H&E) staining on DNA quality and STR genotyping, DNA was isolated from unstained, deparaffinized hydrated, and H&E-stained tissue sections (i.e. 3 groups) from each of 6 formalin-fixed paraffin-embedded placentas. The macrodissected view field, DNA quality, and polymerase chain reaction amplification efficiency were compared among groups. STR genotyping analysis was performed in both the test cohort (n = 6) and the validation cohort (n = 149). H&E staining not only did not interfere with molecular DNA testing of formalin-fixed paraffin-embedded tissue but also had a clearer macrodissected field of vision. In the test cohort, H&E-stained sections were the only group that did not exhibit maternal miscellaneous peaks in STR genotyping results. In the validation cohort, 138 (92.62%) cases yielded satisfactory amplification results without maternal contamination. Thus, H&E staining helped to reduce maternal contamination in STR genotyping for hydatidiform mole diagnosis, suggesting that H&E-stained sections can be incorporated into the hydatidiform mole molecular diagnostic workflow.
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Zeid AM, Abdussalam A, Hanif S, Anjum S, Lou B, Xu G. Recent advances in microchip electrophoresis for analysis of pathogenic bacteria and viruses. Electrophoresis 2023; 44:15-34. [PMID: 35689426 DOI: 10.1002/elps.202200082] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 05/31/2022] [Accepted: 06/07/2022] [Indexed: 02/01/2023]
Abstract
Life-threatening diseases, such as hepatitis B, pneumonia, tuberculosis, and COVID-19, are widespread due to pathogenic bacteria and viruses. Therefore, the development of highly sensitive, rapid, portable, cost-effective, and selective methods for the analysis of such microorganisms is a great challenge. Microchip electrophoresis (ME) has been widely used in recent years for the analysis of bacterial and viral pathogens in biological and environmental samples owing to its portability, simplicity, cost-effectiveness, and rapid analysis. However, microbial enrichment and purification are critical steps for accurate and sensitive analysis of pathogenic bacteria and viruses in complex matrices. Therefore, we first discussed the advances in the sample preparation technologies associated with the accurate analysis of such microorganisms, especially the on-chip microfluidic-based sample preparations such as dielectrophoresis and microfluidic membrane filtration. Thereafter, we focused on the recent advances in the lab-on-a-chip electrophoretic analysis of pathogenic bacteria and viruses in different complex matrices. As the microbial analysis is mainly based on the analysis of nucleic acid of the microorganism, the integration of nucleic acid-based amplification techniques such as polymerase chain reaction (PCR), quantitative PCR, and multiplex PCR with ME will result in an accurate and sensitive analysis of microbial pathogens. Such analyses are very important for the point-of-care diagnosis of various infectious diseases.
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Affiliation(s)
- Abdallah M Zeid
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, P. R. China.,Department of Pharmaceutical Analytical Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
| | - Abubakar Abdussalam
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, P. R. China.,College of Natural and Pharmaceutical Sciences, Department of Chemistry, Bayero University, Kano, Nigeria.,School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, Anhui, P. R. China
| | - Saima Hanif
- Department of Biological Sciences, National University of Medical Sciences (NUMS), Punjab, Pakistan
| | - Saima Anjum
- Department of Chemistry, Govt. Sadiq College Women University, Bahawalpur, Pakistan
| | - Baohua Lou
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, P. R. China.,School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, Anhui, P. R. China
| | - Guobao Xu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, P. R. China.,School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, Anhui, P. R. China
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Jordan D, Mills D. Past, Present, and Future of DNA Typing for Analyzing Human and Non-Human Forensic Samples. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.646130] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Forensic DNA analysis has vastly evolved since the first forensic samples were evaluated by restriction fragment length polymorphism (RFLP). Methodologies advanced from gel electrophoresis techniques to capillary electrophoresis and now to next generation sequencing (NGS). Capillary electrophoresis was and still is the standard method used in forensic analysis. However, dependent upon the information needed, there are several different techniques that can be used to type a DNA fragment. Short tandem repeat (STR) fragment analysis, Sanger sequencing, SNapShot, and capillary electrophoresis-single strand conformation polymorphism (CE-SSCP) are a few of the techniques that have been used for the genetic analysis of DNA samples. NGS is the newest and most revolutionary technology and has the potential to be the next standard for genetic analysis. This review briefly encompasses many of the techniques and applications that have been utilized for the analysis of human and nonhuman DNA samples.
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Ragab MAA, El-Kimary EI. Recent Advances and Applications of Microfluidic Capillary Electrophoresis: A Comprehensive Review (2017-Mid 2019). Crit Rev Anal Chem 2020; 51:709-741. [PMID: 32447968 DOI: 10.1080/10408347.2020.1765729] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Microfluidic capillary electrophoresis (MCE) is the novel technique resulted from the CE mininaturization as planar separation and analysis device. This review presents and discusses various application fields of this advanced technology published in the period 2017 till mid-2019 in eight different sections including clinical, biological, single cell analysis, environmental, pharmaceuticals, food analysis, forensic and ion analysis. The need for miniaturization of CE and the consequence advantages achieved are also discussed including high-throughput, miniaturized detection, effective separation, portability and the need for micro- or even nano-volume of samples. Comprehensive tables for the MCE applications in the different studied fields are provided. Also, figure comparing the number of the published papers applying MCE in the eight discussed fields within the studied period is included. The future investigation should put into consideration the possibility of replacing conventional CE with the MCE after proper validation. Suitable validation parameters with their suitable accepted ranges should be tailored for analysis methods utilizing such unique technique (MCE).
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Affiliation(s)
- Marwa A A Ragab
- Faculty of Pharmacy, Department of Pharmaceutical Analytical Chemistry, Alexandria University, El-Messalah, Alexandria, Egypt
| | - Eman I El-Kimary
- Faculty of Pharmacy, Department of Pharmaceutical Analytical Chemistry, Alexandria University, El-Messalah, Alexandria, Egypt
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de Araujo WR, Cardoso TM, da Rocha RG, Santana MH, Muñoz RA, Richter EM, Paixão TR, Coltro WK. Portable analytical platforms for forensic chemistry: A review. Anal Chim Acta 2018; 1034:1-21. [DOI: 10.1016/j.aca.2018.06.014] [Citation(s) in RCA: 123] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2018] [Revised: 05/18/2018] [Accepted: 06/07/2018] [Indexed: 01/28/2023]
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Wuethrich A, Quirino JP. A decade of microchip electrophoresis for clinical diagnostics - A review of 2008-2017. Anal Chim Acta 2018; 1045:42-66. [PMID: 30454573 DOI: 10.1016/j.aca.2018.08.009] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 07/30/2018] [Accepted: 08/03/2018] [Indexed: 01/10/2023]
Abstract
A core element in clinical diagnostics is the data interpretation obtained through the analysis of patient samples. To obtain relevant and reliable information, a methodological approach of sample preparation, separation, and detection is required. Traditionally, these steps are performed independently and stepwise. Microchip capillary electrophoresis (MCE) can provide rapid and high-resolution separation with the capability to integrate a streamlined and complete diagnostic workflow suitable for the point-of-care setting. Whilst standard clinical diagnostics methods normally require hours to days to retrieve specific patient data, MCE can reduce the time to minutes, hastening the delivery of treatment options for the patients. This review covers the advances in MCE for disease detection from 2008 to 2017. Miniaturised diagnostic approaches that required an electrophoretic separation step prior to the detection of the biological samples are reviewed. In the two main sections, the discussion is focused on the technical set-up used to suit MCE for disease detection and on the strategies that have been applied to study various diseases. Throughout these discussions MCE is compared to other techniques to create context of the potential and challenges of MCE. A comprehensive table categorised based on the studied disease using MCE is provided. We also comment on future challenges that remain to be addressed.
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Affiliation(s)
- Alain Wuethrich
- Centre for Personalised Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), University of Queensland, Building 75, Brisbane, QLD, 4072, Australia
| | - Joselito P Quirino
- Australian Centre for Research on Separation Science (ACROSS), School of Physical Sciences-Chemistry, University of Tasmania, Private Bag 75, Hobart, TAS, 7001, Australia.
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Han J, Gan W, Zhuang B, Sun J, Zhao L, Ye J, Liu Y, Li CX, Liu P. A fully integrated microchip system for automated forensic short tandem repeat analysis. Analyst 2018; 142:2004-2012. [PMID: 28513665 DOI: 10.1039/c7an00295e] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We have successfully developed an integrated microsystem that combines two plastic microchips for DNA extraction and PCR amplification with a glass capillary array electrophoresis chip together in a compact control and detection instrument for automated forensic short tandem repeat (STR) analysis. DNA extraction followed by an "in situ PCR" was conducted in a single reaction chamber of the microchip based on a filter paper-based extraction methodology. PCR products were then mixed with sizing standards by an injection electrode and injected into the electrophoresis chip for four-color confocal fluorescence detection. The entire STR analysis can be completed in about two hours without any human intervention. Since the 15-plex STR system has a more stringent requirement for PCR efficiency, we optimized the structure of the plastic DNA extraction and amplification chip, in which the reaction chamber was formed by sandwiching a hollow structure layer with two blank cover layers, to reduce the adsorption of PCR reagents to the surfaces. In addition, PCR additives, bovine serum albumin, poly(ethylene glycol), and more magnesium chloride were included into the on-chip multiplex STR system. The limit-of-detection study demonstrated that our microsystem was able to produce full 15-plex STR profiles from 3.75 ng standard K562 DNA. Buccal swab and whole blood samples were also successfully typed by our system, validating the feasibility of performing rapid DNA typing in a "sample-in-answer-out" manner for on-site forensic human identification.
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Affiliation(s)
- Junping Han
- Department of Biomedical Engineering, School of Medicine, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Tsinghua University, Beijing, 100084, China.
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Tao R, Wang S, Zhang J, Zhang J, Yang Z, Sheng X, Hou Y, Zhang S, Li C. Separation/extraction, detection, and interpretation of DNA mixtures in forensic science (review). Int J Legal Med 2018; 132:1247-1261. [PMID: 29802461 DOI: 10.1007/s00414-018-1862-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 05/11/2018] [Indexed: 02/08/2023]
Abstract
Interpreting mixed DNA samples containing material from multiple contributors has long been considered a major challenge in forensic casework, especially when encountering low-template DNA (LT-DNA) or high-order mixtures that may involve missing alleles (dropout) and unrelated alleles (drop-in), among others. In the last decades, extraordinary progress has been made in the analysis of mixed DNA samples, which has led to increasing attention to this research field. The advent of new methods for the separation and extraction of DNA from mixtures, novel or jointly applied genetic markers for detection and reliable interpretation approaches for estimating the weight of evidence, as well as the powerful massively parallel sequencing (MPS) technology, has greatly extended the range of mixed samples that can be correctly analyzed. Here, we summarized the investigative approaches and progress in the field of forensic DNA mixture analysis, hoping to provide some assistance to forensic practitioners and to promote further development involving this issue.
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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, People's Republic of China.,Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Ministry of Justice, Academy of Forensic Sciences, Shanghai, 200063, People's Republic of China
| | - Shouyu Wang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, People's Republic of China
| | - Jiashuo Zhang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Ministry of Justice, Academy of Forensic Sciences, Shanghai, 200063, People's Republic of China.,Department of Forensic Science, Medical School of Soochow University, Suzhou, 215123, People's Republic of China
| | - Jingyi Zhang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Ministry of Justice, Academy of Forensic Sciences, Shanghai, 200063, People's Republic of China.,Department of Forensic Science, Medical School of Soochow University, Suzhou, 215123, People's Republic of China
| | - Zihao Yang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Ministry of Justice, Academy of Forensic Sciences, Shanghai, 200063, People's Republic of China.,Department of Forensic Medicine, School of Basic Medical Science, Wenzhou Medical University, Wenzhou, 325035, People's Republic of China
| | - Xiang Sheng
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Ministry of Justice, Academy of Forensic Sciences, Shanghai, 200063, People's Republic of China.,Department of Forensic Science, Medical School of Soochow University, Suzhou, 215123, People's Republic of China
| | - Yiping Hou
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, People's Republic of China
| | - Suhua Zhang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Ministry of Justice, Academy of Forensic Sciences, Shanghai, 200063, People's Republic of China.
| | - Chengtao Li
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, People's Republic of China. .,Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Ministry of Justice, Academy of Forensic Sciences, Shanghai, 200063, People's Republic of China.
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Anazawa T, Uchiho Y, Yokoi T, Chalkidis G, Yamazaki M. A simple and highly sensitive spectroscopic fluorescence-detection system for multi-channel plastic-microchip electrophoresis based on side-entry laser-beam zigzag irradiation. LAB ON A CHIP 2017; 17:2235-2242. [PMID: 28585967 DOI: 10.1039/c7lc00448f] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
A five-color fluorescence-detection system for eight-channel plastic-microchip electrophoresis was developed. In the eight channels (with effective electrophoretic lengths of 10 cm), single-stranded DNA fragments were separated (with single-base resolution up to 300 bases within 10 min), and seventeen-loci STR genotyping for forensic human identification was successfully demonstrated. In the system, a side-entry laser beam is passed through the eight channels (eight A channels), with alternately arrayed seven sacrificial channels (seven B channels), by a technique called "side-entry laser-beam zigzag irradiation." Laser-induced fluorescence from the eight A channels and Raman-scattered light from the seven B channels are then simultaneously, uniformly, and spectroscopically detected, in the direction perpendicular to the channel array plane, through a transmission grating and a CCD camera. The system is therefore simple and highly sensitive. Because the microchip is fabricated by plastic-injection molding, it is inexpensive and disposable and thus suitable for actual use in various fields.
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Affiliation(s)
| | | | | | | | - Motohiro Yamazaki
- Hitachi High-Technologies Corporation, Science & Medical Systems Business Group, Japan
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Gabriel EF, dos Santos RA, Lobo-Júnior EO, Rezende KC, Coltro WK. Hydrodynamic injection on electrophoresis microchips using an electronic micropipette. Talanta 2017; 162:19-23. [DOI: 10.1016/j.talanta.2016.09.046] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 09/16/2016] [Accepted: 09/17/2016] [Indexed: 01/06/2023]
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