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Huang Q, Zhang Y, Hu W, Chen K, Zhang J, Luo Z, Lu C. Characterization of Heat-labile Uracil-DNA Glycosylase from Oncorhynchus mykiss and its Application for Carry-over Contamination Control in RT-qPCR. Protein Pept Lett 2024; 31:169-177. [PMID: 38343045 DOI: 10.2174/0109298665283737240122105923] [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: 10/23/2023] [Revised: 12/07/2023] [Accepted: 12/08/2023] [Indexed: 06/14/2024]
Abstract
BACKGROUND Heat-labile uracil-DNA glycosylase (HL-UDG) is commonly employed to eliminate carry-over contamination in DNA amplifications. However, the prevailing HL-UDG is markedly inactivated at 50°C, rendering it unsuitable for specific one-step RT-qPCR protocols utilizing reverse transcriptase at an optimal temperature of 42°C. OBJECTIVE This study aimed to explore novel HL-UDG with lower inactivation temperature and for recombinant expression. METHODS The gene encoding an HL-UDG was cloned from the cold-water fish rainbow trout (Oncorhynchus mykiss) and expressed in Escherichia coli with high yield. The thermostability of this enzyme and other enzymatic characteristics were thoroughly examined. The novel HL-UDG was then applied for controlling carry-over contamination in one-step RT-qPCR. RESULTS This recombinantly expressed truncated HL-UDG of rainbow trout (OmUDG) exhibited high amino acids similarity (84.1% identity) to recombinant Atlantic cod UDG (rcUDG) and was easily denatured at 40°C. The optimal pH of OmUDG was 8.0, and the optimal concentrations of both Na+ and K+ were 10 mM. Since its inactivation temperature was lower than that of rcUDG, the OmUDG could be used to eliminate carry-over contamination in one-step RT-qPCR with moderate reverse transcription temperature. CONCLUSION We successfully identified and recombinantly expressed a novel HL-UDG with an inactivation temperature of 40°C. It is suitable for eliminating carry-over contamination in one-step RT-qPCR.
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Affiliation(s)
- Qingyuan Huang
- Jiangsu Key Laboratory of Marine Biological Resources and Environment, Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Jiangsu Ocean University, Lianyungang, 222005, China
- Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang, 222005, China
| | - Yaqi Zhang
- Jiangsu Key Laboratory of Marine Biological Resources and Environment, Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Jiangsu Ocean University, Lianyungang, 222005, China
- Jiangsu Food & Pharmaceutical Science College, Huai'an 223023, China
| | - Wenhao Hu
- Jiangsu Key Laboratory of Marine Biological Resources and Environment, Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Jiangsu Ocean University, Lianyungang, 222005, China
- Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang, 222005, China
| | - Keqi Chen
- Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang, 222005, China
- Jiangsu Best Enzymes Biotech Co., Ltd., Lianyungang, 222005, China
| | - Jian Zhang
- Jiangsu Key Laboratory of Marine Biological Resources and Environment, Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Jiangsu Ocean University, Lianyungang, 222005, China
- Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang, 222005, China
| | - Zhidan Luo
- Jiangsu Key Laboratory of Marine Biological Resources and Environment, Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Jiangsu Ocean University, Lianyungang, 222005, China
- Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang, 222005, China
| | - Chen Lu
- Jiangsu Key Laboratory of Marine Biological Resources and Environment, Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Jiangsu Ocean University, Lianyungang, 222005, China
- Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang, 222005, China
- Jiangsu Best Enzymes Biotech Co., Ltd., Lianyungang, 222005, China
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Gao L, Li L, Fang B, Fang Z, Xiang Y, Zhang M, Zhou J, Song H, Chen L, Li T, Xiao H, Wan R, Jiang Y, Peng H. Carryover Contamination-Controlled Amplicon Sequencing Workflow for Accurate Qualitative and Quantitative Detection of Pathogens: a Case Study on SARS-CoV-2. Microbiol Spectr 2023; 11:e0020623. [PMID: 37098913 PMCID: PMC10269707 DOI: 10.1128/spectrum.00206-23] [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: 01/13/2023] [Accepted: 04/02/2023] [Indexed: 04/27/2023] Open
Abstract
Carryover contamination during amplicon sequencing workflow (AMP-Seq) put the accuracy of the high-throughput detection for pathogens at risk. The purpose of this study is to develop a carryover contaminations-controlled AMP-Seq (ccAMP-Seq) workflow to enable accurate qualitative and quantitative detection for pathogens. By using the AMP-Seq workflow to detect SARS-CoV-2, Aerosols, reagents and pipettes were identified as potential sources of contaminations and ccAMP-Seq was then developed. ccAMP-Seq used filter tips and physically isolation of experimental steps to avoid cross contamination, synthetic DNA spike-ins to compete with contaminations and quantify SARS-CoV-2, dUTP/uracil DNA glycosylase system to digest the carryover contaminations, and a new data analysis procedure to remove the sequencing reads from contaminations. Compared to AMP-Seq, the contamination level of ccAMP-Seq was at least 22-folds lower and the detection limit was also about an order of magnitude lower-as low as one copy/reaction. By testing the dilution series of SARS-CoV-2 nucleic acid standard, ccAMP-Seq showed 100% sensitivity and specificity. The high sensitivity of ccAMP-Seq was further confirmed by the detection of SARS-CoV-2 from 62 clinical samples. The consistency between qPCR and ccAMP-Seq was 100% for all the 53 qPCR-positive clinical samples. Seven qPCR-negative clinical samples were found to be positive by ccAMP-Seq, which was confirmed by extra qPCR tests on subsequent samples from the same patients. This study presents a carryover contamination-controlled, accurate qualitative and quantitative amplicon sequencing workflow that addresses the critical problem of pathogen detection for infectious diseases. IMPORTANCE Accuracy, a key indicator of pathogen detection technology, is compromised by carryover contamination in the amplicon sequencing workflow. Taking the detection of SARS-CoV-2 as case, this study presents a new carryover contamination-controlled amplicon sequencing workflow. The new workflow significantly reduces the degree of contamination in the workflow, thereby significantly improving the accuracy and sensitivity of the SARS-CoV-2 detection and empowering the ability of quantitative detection. More importantly, the use of the new workflow is simple and economical. Therefore, the results of this study can be easily applied to other microorganism, which has great significance for improving the detection level of microorganism.
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Affiliation(s)
- Lifen Gao
- Institute for Systems Biology, Jianghan University, Wuhan, Hubei, People’s Republic of China
| | - Lun Li
- Institute for Systems Biology, Jianghan University, Wuhan, Hubei, People’s Republic of China
| | - Bin Fang
- Hubei Provincial Centers for Disease Control and Prevention, Wuhan, Hubei, People’s Republic of China
| | - Zhiwei Fang
- Institute for Systems Biology, Jianghan University, Wuhan, Hubei, People’s Republic of China
| | - Yanghai Xiang
- Yueyang Central Hospital, Yueyang, Hunan, People’s Republic of China
| | - Min Zhang
- Yueyang Central Hospital, Yueyang, Hunan, People’s Republic of China
| | - Junfei Zhou
- Institute for Systems Biology, Jianghan University, Wuhan, Hubei, People’s Republic of China
| | - Huiyin Song
- Institute for Systems Biology, Jianghan University, Wuhan, Hubei, People’s Republic of China
| | - Lihong Chen
- Institute for Systems Biology, Jianghan University, Wuhan, Hubei, People’s Republic of China
| | - Tiantian Li
- Institute for Systems Biology, Jianghan University, Wuhan, Hubei, People’s Republic of China
| | - Huafeng Xiao
- Institute for Systems Biology, Jianghan University, Wuhan, Hubei, People’s Republic of China
| | - Renjing Wan
- Institute for Systems Biology, Jianghan University, Wuhan, Hubei, People’s Republic of China
| | - Yongzhong Jiang
- Hubei Provincial Centers for Disease Control and Prevention, Wuhan, Hubei, People’s Republic of China
| | - Hai Peng
- Institute for Systems Biology, Jianghan University, Wuhan, Hubei, People’s Republic of China
- Mingliao Biotechnology Co., Ltd., Wuhan, Hubei, People’s Republic of China
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Protocol and Matters for Consideration for the Treatment of Polymerase Chain Reaction Contamination in Next-Generation Sequencing Laboratories. REV ROMANA MED LAB 2022. [DOI: 10.2478/rrlm-2022-0038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Abstract
Objective: The contamination of polymerase chain reaction (PCR) samples in molecular diagnostic laboratories can cause serious consequences. Internal quality control efforts are often inadequate, especially in clinical next-generation sequencing (NGS) laboratories.
Methods: In this study, we retrospectively investigated an incidence of PCR contamination and its decontamination process in a clinical laboratory. We performed a series of measures for decontamination. Taqman fluorescence quantification was carried out to determine the presence of contaminating DNA. SYBR-Green PCR was conducted to evaluate the effect of chlorine disinfectant on NGS library preparation.
Results: Through a series of elimination measures undertaken over 8 weeks, the decontamination process was verified as reliable. Almost no contamination was detected. Chlorine disinfectant should be forbidden in Illumina NGS laboratories because it may cause the failure of library preparation.
Conclusion: Our prevention and decontamination strategies could effectively eliminate PCR amplicons. Chlorine disinfectants should not be used in Illumina NGS laboratories.
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Yang J, Li D, Wang J, Zhang R, Li J. Design, optimization, and application of multiplex rRT-PCR in the detection of respiratory viruses. Crit Rev Clin Lab Sci 2022:1-18. [PMID: 35559711 DOI: 10.1080/10408363.2022.2072467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Viral respiratory infections are common and serious diseases. Because there is no effective treatment method or vaccine for respiratory tract infection, early diagnosis is vital to identify the pathogen so as to determine the infectivity of the patient and to quickly take measures to curb the spread of the virus, if warranted, to avoid serious public health problems. Real-time reverse transcriptase PCR (rRT-PCR), which has high sensitivity and specificity, is the best approach for early diagnosis. Among rRT-PCR methods, multiplex rRT-PCR can resolve issues arising from various types of viruses, high mutation frequency, coinfection, and low concentrations of virus. However, the design, optimization, and validation of multiplex rRT-PCR are more complicated than singleplex rRT-PCR, and comprehensive research on multiplex rRT-PCR methodology is lacking. This review summarizes recent progress in multiplex rRT-PCR methodology, outlines the principles of design, optimization and validation, and describes a scheme to help diagnostic companies to design and optimize their multiplex rRT-PCR detection panel and to assist laboratory staff to solve problems in their daily work. In addition, the analytical validity, clinical validity and clinical utility of multiplex rRT-PCR in viral respiratory tract infection diagnosis are assessed to provide theoretical guidance and useful information for physicians to understand the test results.
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Affiliation(s)
- Jing Yang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/ National Center of Gerontology, P.R. China.,Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, P.R. China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P.R. China
| | - Dandan Li
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/ National Center of Gerontology, P.R. China.,Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, P.R. China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P.R. China
| | - Jie Wang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/ National Center of Gerontology, P.R. China.,Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, P.R. China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P.R. China
| | - Rui Zhang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/ National Center of Gerontology, P.R. China.,Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, P.R. China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P.R. China
| | - Jinming Li
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/ National Center of Gerontology, P.R. China.,Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, P.R. China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P.R. China
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Naranbat D, Schneider L, Kantor R, Beckwith CG, Bazerman L, Gillani F, Sahu S, Rapoza K, Sam S, Novitsky V, Shin J, Hipolito E, Diaz I, Carnevale D, Tripathi A. DirectDetect SARS-CoV-2 Direct Real-Time RT-PCR Study Using Patient Samples. ACS OMEGA 2022; 7:4945-4955. [PMID: 35187313 PMCID: PMC8845437 DOI: 10.1021/acsomega.1c05595] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 01/28/2022] [Indexed: 05/09/2023]
Abstract
COVID-19 is an infectious disease that caused a global pandemic affecting people worldwide. As disease detection and vaccine rollout continue to progress, there is still a need for efficient diagnostic tools to satisfy continued testing needs. This preliminary study evaluated a novel SARS-CoV-2 diagnostic test called DirectDetect SARS-CoV-2 Direct Real-time reverse transcriptase polymerase chain reaction (RT-PCR) based on a limited sample size of 24 respiratory samples from 14 SARS-CoV-2-positive patients. The test is advantageous compared to others on the market since it does not require viral transport medium or viral RNA extraction prior to nucleic acid amplification and detection. This capability transforms the hours-long sample preparation time into a minutes-long procedure while also eliminating the need for many costly reagents which may be difficult to obtain during the surge in nucleic acid-based testing during the pandemic. The results show a positive agreement of 94.7, 100, and 94.7% between dry sample swabs, treated samples, and untreated samples tested using the DirectDetect SARS-CoV-2 Direct Real-time RT-PCR compared to tests used in a clinical laboratory, respectively. The findings indicate that DirectDetect can be used for multiple different sample types while reducing the number of reagents and time needed for diagnosis. Although this study shows promising results using the DirectDetect results, further validation of this test using a larger sample set is required to assess the true performance of this test.
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Affiliation(s)
- Dulguunnaran Naranbat
- Center for Biomedical Engineering, School of Engineering, Brown University, Providence, Rhode Island 02912, United States
| | - Lindsay Schneider
- Center for Biomedical Engineering, School of Engineering, Brown University, Providence, Rhode Island 02912, United States
| | - Rami Kantor
- Division of Infectious Diseases, Brown University Alpert Medical School, Providence, Rhode Island 02912, United States
- The Miriam Hospital, Providence, Rhode Island 02906, United States
| | - Curt G Beckwith
- Division of Infectious Diseases, Brown University Alpert Medical School, Providence, Rhode Island 02912, United States
- The Miriam Hospital, Providence, Rhode Island 02906, United States
| | - Lauri Bazerman
- The Miriam Hospital, Providence, Rhode Island 02906, United States
| | - Fizza Gillani
- Division of Infectious Diseases, Brown University Alpert Medical School, Providence, Rhode Island 02912, United States
- The Miriam Hospital, Providence, Rhode Island 02906, United States
| | - Sujata Sahu
- The Miriam Hospital, Providence, Rhode Island 02906, United States
| | - Kim Rapoza
- The Miriam Hospital, Providence, Rhode Island 02906, United States
| | - Soya Sam
- Division of Infectious Diseases, Brown University Alpert Medical School, Providence, Rhode Island 02912, United States
- The Miriam Hospital, Providence, Rhode Island 02906, United States
| | - Vlad Novitsky
- Division of Infectious Diseases, Brown University Alpert Medical School, Providence, Rhode Island 02912, United States
- The Miriam Hospital, Providence, Rhode Island 02906, United States
| | - Jimin Shin
- The Miriam Hospital, Providence, Rhode Island 02906, United States
| | - Evelyn Hipolito
- Rhode Island Hospital, Providence, Rhode Island 02903, United States
| | - Isabella Diaz
- Rhode Island Hospital, Providence, Rhode Island 02903, United States
| | | | - Anubhav Tripathi
- Center for Biomedical Engineering, School of Engineering, Brown University, Providence, Rhode Island 02912, United States
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Rapid and highly sensitive approach for multiplexed somatic fusion detection. Mod Pathol 2022; 35:1022-1033. [PMID: 35347250 PMCID: PMC9314249 DOI: 10.1038/s41379-022-01058-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 02/14/2022] [Accepted: 02/14/2022] [Indexed: 11/28/2022]
Abstract
Somatic gene translocations are key to making an accurate diagnosis in many cancers including many pediatric sarcomas. Currently available molecular diagnostic approaches to identifying somatic pathognomonic translocations have limitations such as minimal multiplexing, high cost, complex computational requirements, or slow turnaround times. We sought to develop a new fusion-detection assay optimized to mitigate these challenges. To accomplish this goal, we developed a highly sensitive multiplexed digital PCR-based approach that can identify the gene partners of multiple somatic fusion transcripts. This assay was validated for specificity with cell lines and synthetized DNA fragments. Assay sensitivity was optimized using a tiered amplification approach for fusion detection from low input and/or degraded RNA. The assay was then tested for the potential application of fusion detection from FFPE tissue and liquid biopsy samples. We found that this multiplexed PCR approach was able to accurately identify the presence of seven different targeted fusion transcripts with a turnaround time of 1 to 2 days. The addition of a tiered amplification step allowed the detection of targeted fusions from as little as 1 pg of RNA input. We also identified fusions from as little as two unstained slides of FFPE tumor biopsy tissue, from circulating tumor cells collected from tumor-bearing mice, and from liquid biopsy samples from patients with known fusion-positive cancers. We also demonstrated that the assay could be easily adapted for additional fusion targets. In summary, this novel assay detects multiple somatic fusion partners in biologic samples with low tumor content and low-quality RNA in less than two days. The assay is inexpensive and could be applied to surgical and liquid biopsies, particularly in places with inadequate resources for more expensive and expertise-dependent assays such as next-generation sequencing.
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