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Dong L, Zhang Y, Fu B, Swart C, Jiang H, Liu Y, Huggett J, Wielgosz R, Niu C, Li Q, Zhang Y, Park SR, Sui Z, Yu L, Liu Y, Xie Q, Zhang H, Yang Y, Dai X, Shi L, Yin Y, Fang X. Reliable biological and multi-omics research through biometrology. Anal Bioanal Chem 2024; 416:3645-3663. [PMID: 38507042 DOI: 10.1007/s00216-024-05239-3] [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: 01/12/2024] [Revised: 02/28/2024] [Accepted: 03/04/2024] [Indexed: 03/22/2024]
Abstract
Metrology is the science of measurement and its applications, whereas biometrology is the science of biological measurement and its applications. Biometrology aims to achieve accuracy and consistency of biological measurements by focusing on the development of metrological traceability, biological reference measurement procedures, and reference materials. Irreproducibility of biological and multi-omics research results from different laboratories, platforms, and analysis methods is hampering the translation of research into clinical uses and can often be attributed to the lack of biologists' attention to the general principles of metrology. In this paper, the progresses of biometrology including metrology on nucleic acid, protein, and cell measurements and its impacts on the improvement of reliability and comparability in biological research are reviewed. Challenges in obtaining more reliable biological and multi-omics measurements due to the lack of primary reference measurement procedures and new standards for biological reference materials faced by biometrology are discussed. In the future, in addition to establishing reliable reference measurement procedures, developing reference materials from single or multiple parameters to multi-omics scale should be emphasized. Thinking in way of biometrology is warranted for facilitating the translation of high-throughput omics research into clinical practices.
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Affiliation(s)
- Lianhua Dong
- Center for Advanced Measurement of Science, National Institute of Metrology, Beijing, 100029, China.
| | - Yu Zhang
- Center for Advanced Measurement of Science, National Institute of Metrology, Beijing, 100029, China
| | - Boqiang Fu
- Center for Advanced Measurement of Science, National Institute of Metrology, Beijing, 100029, China
| | - Claudia Swart
- Physikalisch-Technische Bundesanstalt, 38116, Braunschweig, Germany
| | | | - Yahui Liu
- Center for Advanced Measurement of Science, National Institute of Metrology, Beijing, 100029, China
| | - Jim Huggett
- National Measurement Laboratory at LGC (NML), Teddington, Middlesex, UK
| | - Robert Wielgosz
- Bureau International Des Poids Et Mesures (BIPM), Pavillon de Breteuil, 92312, Sèvres Cedex, France
| | - Chunyan Niu
- Center for Advanced Measurement of Science, National Institute of Metrology, Beijing, 100029, China
| | - Qianyi Li
- BGI, BGI-Shenzhen, Shenzhen, 518083, China
| | - Yongzhuo Zhang
- Center for Advanced Measurement of Science, National Institute of Metrology, Beijing, 100029, China
| | - Sang-Ryoul Park
- Korea Research Institute of Standards and Science, Daejeon, Republic of Korea
| | - Zhiwei Sui
- Center for Advanced Measurement of Science, National Institute of Metrology, Beijing, 100029, China
| | - Lianchao Yu
- Center for Advanced Measurement of Science, National Institute of Metrology, Beijing, 100029, China
| | | | - Qing Xie
- BGI, BGI-Shenzhen, Shenzhen, 518083, China
| | - Hongfu Zhang
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | | | - Xinhua Dai
- Center for Advanced Measurement of Science, National Institute of Metrology, Beijing, 100029, China.
| | - Leming Shi
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, 200438, China
| | - Ye Yin
- BGI, BGI-Shenzhen, Shenzhen, 518083, China.
| | - Xiang Fang
- Center for Advanced Measurement of Science, National Institute of Metrology, Beijing, 100029, China.
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2
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Shin JC, Jeong JY, Son SG, Choi SH, Nam HC, Yoon TH, Kim HJ, Choi DG, Lee H, Lee U, Yang SM, Kang I, Jung DY, Lee HW, Lee MK, Lee TJ, Kim G, Park HO, Lee SW. Developing centrifugal force real-time digital PCR for detecting extremely low DNA concentration. Sci Rep 2024; 14:11522. [PMID: 38769102 DOI: 10.1038/s41598-024-62199-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Accepted: 05/14/2024] [Indexed: 05/22/2024] Open
Abstract
Digital PCR (dPCR) is a technique for absolute quantification of nucleic acid molecules. To develop a dPCR technique that enables more accurate nucleic acid detection and quantification, we established a novel dPCR apparatus known as centrifugal force real-time dPCR (crdPCR). This system is efficient than other systems with only 2.14% liquid loss by dispensing samples using centrifugal force. Moreover, we applied a technique for analyzing the real-time graph of the each micro-wells and distinguishing true/false positives using artificial intelligence to mitigate the rain, a persistent issue with dPCR. The limits of detection and quantification were 1.38 and 4.19 copies/μL, respectively, showing a two-fold higher sensitivity than that of other comparable devices. With the integration of this new technology, crdPCR will significantly contribute to research on next-generation PCR targeting absolute micro-analysis.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Ukyeol Lee
- RevoSketch Inc., Daejeon, Republic of Korea
| | | | - Il Kang
- RevoSketch Inc., Daejeon, Republic of Korea
| | | | | | - Moon-Keun Lee
- Center for Nano Bio Development, National NanoFab Center (NNFC), Daejeon, Republic of Korea
| | - Tae Jae Lee
- Center for Nano Bio Development, National NanoFab Center (NNFC), Daejeon, Republic of Korea
| | - Geehong Kim
- Nano-Convergence Systems Research Division, Korea Institute of Machinery & Materials, Daejeon, Republic of Korea
| | - Han-Oh Park
- Bioneer Corporation, Daejeon, Republic of Korea
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Johnson FE, Lerch RN, Motavalli PP, Veum KS, Scharf PC. Comparative analysis of three next-generation sequencing techniques to measure nosZ gene abundance in Missouri claypan soils. ENVIRONMENTAL RESEARCH 2024; 249:118346. [PMID: 38311204 DOI: 10.1016/j.envres.2024.118346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 01/16/2024] [Accepted: 01/27/2024] [Indexed: 02/10/2024]
Abstract
Quantitative next-generation sequencing techniques have been critical in gaining a better understanding of microbial ecosystems. In soils, denitrifying microorganisms are responsible for dinitrogen (N2) production. The nosZ gene codes for nitrous oxide reductase, the enzyme facilitating the reduction of nitrous oxide (N2O) to N2. The objectives of this research were to: 1) understand how soil depth influences RNA concentration and nosZ gene abundance; 2) assess the spatial dependence of nosZ gene abundance in two claypan soil fields; and 3) compare and evaluate multiple RNA-based sequencing methods for quantifying nosZ gene abundance in soils in relation to dinitrogen (N2) production. Research sites consisted of two intensively studied claypan soil fields in Central Missouri, USA. Soil cores were collected from two landscape transects across both fields and analyzed for extractable soil RNA at two depths (0-15 cm and 15-30 cm). Measurements of nosZ gene abundance were obtained using real-time quantitative polymerase chain reaction (RT-qPCR), droplet digital polymerase chain reaction (ddPCR), and nanostring sequencing (NS). In both fields, soil RNA concentrations were significantly greater at 0-15 cm depth compared to 15-30 cm. These data indicated low overall soil microbial activity below 15 cm. Due to low quantities of extractable soil RNA in the subsoil, nosZ gene abundance was only determined in the 0-15 cm depth. Sequencing method comparisons of average nosZ gene abundance showed that NS results were constrained to a narrow range and were 10-20-fold lower than ddPCR and RT-qPCR at each landscape position within each field. Droplet digital PCR appears to be the most promising method, as it reflected changes in N2 production across landscape position.
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Affiliation(s)
- Frank E Johnson
- School of Natural Resources, University of Missouri, Columbia, MO, USA; Now at Water Quality and Ecology Research Unit, USDA-ARS, Oxford, MS, USA.
| | - Robert N Lerch
- Cropping Systems and Water Quality Research Unit, USDA-ARS, Columbia, MO, USA
| | - Peter P Motavalli
- School of Natural Resources, University of Missouri, Columbia, MO, USA
| | - Kristen S Veum
- Cropping Systems and Water Quality Research Unit, USDA-ARS, Columbia, MO, USA
| | - Peter C Scharf
- Division of Plant Sciences and Technology, University of Missouri, Columbia, MO, USA
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4
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Song J, Zhou D, Wu L, Wang Z, Jiang X, Su P, Yang Y. A potential primary method for peptide purity analysis by gas chromatography-isotope dilution infrared spectrometry. Anal Bioanal Chem 2023:10.1007/s00216-023-04772-x. [PMID: 37291250 DOI: 10.1007/s00216-023-04772-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 05/12/2023] [Accepted: 05/22/2023] [Indexed: 06/10/2023]
Abstract
Here we proposed a method for peptide purity analysis using gas chromatography-isotope dilution infrared spectroscopy. The principle and feasibility of the proposed measurement method were investigated. The derivatization, separation, and infrared detection conditions for amino acids were optimized, and the performance of the method was investigated. Then, the proposed method was used for assessment of [Glu1]-fibrinopeptide B purity, and the results were compared with those obtained by high performance liquid chromatography-isotope dilution mass spectrometry. The average purity of six sub-samples using the proposed method was (0.755 ± 0.017) g/g, which agreed well with that obtained by isotope dilution mass spectrometry (0.754 ± 0.012) g/g. The repeatability of the proposed method was 2.2%, which was similar to that of isotope dilution mass spectrometry (1.7%). The proposed method has a similar principle and had similar accuracy, precision, and linearity to isotope dilution mass spectrometry; however, the developed method had higher limit of detection (LOD) and limit of quantitation (LOQ) values because of the low sensitivity of infrared detection. The results were also Système International d'Unités (SI) traceable. The developed method has the advantage of lower cost compared with isotope dilution mass spectrometry because only one isotope-labeled atom in an analog is required, and several infrared spectra can be extracted, averaged, and used for an amino acid calculation during one run, potentially leading to higher accuracy. This method could be easily expanded to the accurate quantitation of other organic compounds, including proteins. It is expected that the proposed method will be widely used in chemical and biological measurements as a new primary method.
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Affiliation(s)
- Jiayi Song
- Beijing Key Laboratory of Environmentally Harmful Chemical Analysis, College of Chemistry, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Dongmei Zhou
- Beijing Key Laboratory of Environmentally Harmful Chemical Analysis, College of Chemistry, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Liqing Wu
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing, 100029, China
| | - Ziliang Wang
- China National Accreditation Service for Conformity Assessment, Beijing, 100062, China
| | - Xue Jiang
- Beijing Key Laboratory of Environmentally Harmful Chemical Analysis, College of Chemistry, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Ping Su
- Beijing Key Laboratory of Environmentally Harmful Chemical Analysis, College of Chemistry, Beijing University of Chemical Technology, Beijing, 100029, China.
| | - Yi Yang
- Beijing Key Laboratory of Environmentally Harmful Chemical Analysis, College of Chemistry, Beijing University of Chemical Technology, Beijing, 100029, China.
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Liu S, Wang Z, Wang M, Meng T, Zhang Y, Zhang W, Sui Z. Evaluation of volume-based flow cytometry as a potential primary method for quantification of bacterial reference material. Talanta 2023; 255:124197. [PMID: 36571974 DOI: 10.1016/j.talanta.2022.124197] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 12/11/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022]
Abstract
Bacterial reference materials (RMs) play a crucial role in many analytical processes of microbiological detection. Currently, bacteria are typically counted using the traditional plate-based approach, which results in a higher uncertainty of bacterial RMs unfortunately. Therefore, novel methods are urgently required for the value assignment of RMs in the field of microbiology to derive measurement traceability and accuracy. A potential primary method for microbiological quantification based on flow cytometry (FCM) is described in this study using Escherichia coli O157 (E. coli O157) as an example. The proposed method was applied to determine the number of viable E. coli O157 cells in the RMs with a result of (5.48 ± 0.27) × 108 cells mL-1, which was in good agreement with the result obtained using the plate-based method (En = 0.47). Additionally, this method could be entirely described and understood by equations, and provides formal traceability to the SI for counts of viable bacterial cells, while the associated relative expanded uncertainty (4.93%, k = 2) was significantly lower in comparison to the plate-based method. Therefore, the FCM-based method might be a potential primary method for characterizing bacterial RMs. To our knowledge, this is the first description of FCM as a potential primary method for accurate and traceable quantification of viable bacterial cells with a comprehensive uncertainty statement in microbiological metrology.
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Affiliation(s)
- Siyuan Liu
- College of Food Science and Technology, Hebei Agricultural University, Baoding, 071001, China; Center for Advanced Measurement Science, National Institute of Metrology, Beijing, 100029, China; Hebei Key Laboratory of Analysis and Control for Zoonotic Pathogenic Microorganism, Hebei Agricultural University, Baoding, 071001, China
| | - Ziquan Wang
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing, 100029, China
| | - Meng Wang
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing, 100029, China
| | - Tao Meng
- Division of Thermophysics Metrology, National Institute of Metrology, Beijing, 100029, China
| | - Yunzhe Zhang
- College of Food Science and Technology, Hebei Agricultural University, Baoding, 071001, China; Hebei Key Laboratory of Analysis and Control for Zoonotic Pathogenic Microorganism, Hebei Agricultural University, Baoding, 071001, China
| | - Wei Zhang
- College of Food Science and Technology, Hebei Agricultural University, Baoding, 071001, China; Hebei Key Laboratory of Analysis and Control for Zoonotic Pathogenic Microorganism, Hebei Agricultural University, Baoding, 071001, China.
| | - Zhiwei Sui
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing, 100029, China.
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Establishment and evaluation of digital PCR methods for HER2 copy number variation in breast cancer. Anal Bioanal Chem 2023; 415:725-733. [PMID: 36571590 DOI: 10.1007/s00216-022-04466-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 11/20/2022] [Accepted: 11/24/2022] [Indexed: 12/27/2022]
Abstract
Accurate measurement of human epidermal growth factor receptor 2 (HER2) copy number variation (CNV) is very important for guiding the tumor target therapy in breast cancer. Digital PCR (dPCR) is a sensitive and an absolute quantitative method, which can be used to detect HER2 CNV. Three HER2 exon-specific digital PCR assays along with three new reference genes assays (homo sapiens ribonuclease P RNA component H1 (RPPH1), glucose-6-phosphate isomerase (GPI), and chromosome 1 open reading frame 43 (C1ORF43), on different chromosomes) were established and validated by using standard reference material, 8 different cell lines and 110 clinical Formalin-fixed and paraffin-embedded (FFPE) samples. DPCR can achieve precise quantification of HER2 CNV by calculating the ratio of HER2/reference gene. The positive and negative coincidence rates were 98% (53/54) and 95% (53/56), respectively, compared with fluorescence in situ hybridization (FISH) diagnostic result 110 of FFPE samples. The common reference gene CEP17 used for FISH diagnostic was not suitable as single reference gene for HER2 CNV measurements by dPCR. The best practice of HER2 CNV determination by dPCR is to conduct the three duplex assays of H1 (HER2 exon 4) with the proposed three new reference genes, with a positive cut-off value of H1/RPPH1 ≥ 2.0 or H1/averaged reference gene ≥ 2.0. The proposed dPCR method in our study can accurately provide absolute copy number of HER2 and reference gene on an alternative chromosome, thus avoiding false negative caused by polysomy of chromosome 17. The improved molecular typing and diagnosis of breast cancer will better guide clinical medication.
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Hartman LM, Blackall LL, van Oppen MJH. Antibiotics reduce bacterial load in Exaiptasia diaphana, but biofilms hinder its development as a gnotobiotic coral model. Access Microbiol 2022; 4:000314. [PMID: 35252752 PMCID: PMC8895603 DOI: 10.1099/acmi.0.000314] [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: 06/16/2021] [Accepted: 12/07/2021] [Indexed: 12/02/2022] Open
Abstract
Coral reefs are declining due to anthropogenic disturbances, including climate change. Therefore, improving our understanding of coral ecosystems is vital, and the influence of bacteria on coral health has attracted particular interest. However, a gnotobiotic coral model that could enhance studies of coral–bacteria interactions is absent. To address this gap, we tested the ability of treatment with seven antibiotics for 3 weeks to deplete bacteria in Exaiptasia diaphana, a sea anemone widely used as a coral model. Digital droplet PCR (ddPCR) targeting anemone Ef1-α and bacterial 16S rRNA genes was used to quantify bacterial load, which was found to decrease six-fold. However, metabarcoding of bacterial 16S rRNA genes showed that alpha and beta diversity of the anemone-associated bacterial communities increased significantly. Therefore, gnotobiotic E. diaphana with simplified, uniform bacterial communities were not generated, with biofilm formation in the culture vessels most likely impeding efforts to eliminate bacteria. Despite this outcome, our work will inform future efforts to create a much needed gnotobiotic coral model.
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Affiliation(s)
- Leon M. Hartman
- School of BioSciences, The University of Melbourne, Melbourne, VIC, Australia
- Swinburne University of Technology, Hawthorn, VIC, Australia
- Monash University, Clayton, VIC, Australia
| | - Linda L. Blackall
- School of BioSciences, The University of Melbourne, Melbourne, VIC, Australia
| | - Madeleine J. H. van Oppen
- Australian Institute of Marine Science, Townsville, QLD, Australia
- School of BioSciences, The University of Melbourne, Melbourne, VIC, Australia
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Guo J, Zhou Y, Guo H, Min W. Saline and alkaline stresses alter soil properties and composition and structure of gene-based nitrifier and denitrifier communities in a calcareous desert soil. BMC Microbiol 2021; 21:246. [PMID: 34521348 PMCID: PMC8442331 DOI: 10.1186/s12866-021-02313-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 09/06/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Saline and alkaline stresses damages the health of soil systems. Meanwhile, little is known about how saline or alkaline stress affects soil nitrifier and denitrifier communities. Therefore, we compared the responses of gene-based nitrifier and denitrifier communities to chloride (CS), sulfate (SS), and alkaline (AS) stresses with those in a no-stress control (CK) in pots with a calcareous desert soil. RESULTS Compared with CK, saline and alkaline stress decreased potential nitrification rate (PNR) and NO3-N; increased pH, salinity, water content, and NH4-N; and decreased copy numbers of amoA-AOA and amoA-AOB genes but increased those of denitrifier nirS and nosZ genes. Copies of nirK increased in SS and AS but decreased in CS. There were more copies of amoA-AOB than of amoA-AOA and of nirS than of nirK or nosZ. Compared with CK, SS and AS decreased operational taxonomic units (OTUs) of amoA-AOB but increased those of nirS and nosZ, whereas CS decreased nirK OTUs but increased those of nosZ. The numbers of OTUs and amoA-AOB genes were greater than those of amoA-AOA. There were positive linear relations between PNR and amoA-AOA and amoA-AOB copies. Compared with CK, the Chao 1 index of amoA-AOA and amoA-AOB decreased in AS, that of nirK increased in CS and SS, but that of nirS and nosZ increased in all treatments. The Shannon index of amoA-AOB decreased but that of nirS increased in CS and SS, whereas the index of nirK decreased in all treatments. Saline and alkaline stress greatly affected the structure of nitrifier and denitrifier communities and decreased potential biomarkers of nirS-type; however, AS increased those of nirK- and nosZ-type, and SS decreased those of nosZ-type. Soil water content, pH, and salinity were important in shaping amoA-AOA and denitrifier communities, whereas soil water and pH were important to amoA-AOB communities. CONCLUSION These results indicate that the nitrifier and denitrifier communities respond to saline and alkaline stresses conditions. Communities of amoA-AOA and amoA-AOB contribute to nitrification in alluvial gray desert soil, and those of nirS are more important in denitrification than those of nirK or nosZ.
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Affiliation(s)
- Jiaxin Guo
- Department of Resources and Environmental Science, Agriculture College, Shihezi University, Box #425, Shihezi, Xinjiang, 832003, People's Republic of China
| | - Yongxue Zhou
- Department of Resources and Environmental Science, Agriculture College, Shihezi University, Box #425, Shihezi, Xinjiang, 832003, People's Republic of China
| | - Huijuan Guo
- Department of Resources and Environmental Science, Agriculture College, Shihezi University, Box #425, Shihezi, Xinjiang, 832003, People's Republic of China
| | - Wei Min
- Department of Resources and Environmental Science, Agriculture College, Shihezi University, Box #425, Shihezi, Xinjiang, 832003, People's Republic of China.
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Chen X, Ji Y, Li K, Wang X, Peng C, Xu X, Pei X, Xu J, Li L. Development of a Duck Genomic Reference Material by Digital PCR Platforms for the Detection of Meat Adulteration. Foods 2021; 10:foods10081890. [PMID: 34441667 PMCID: PMC8394454 DOI: 10.3390/foods10081890] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/12/2021] [Accepted: 08/13/2021] [Indexed: 11/16/2022] Open
Abstract
Low-cost meat, such as duck, is frequently used to adulterate more expensive foods like lamb or beef in many countries. However, the lack of DNA-based reference materials has limited the quality control and detection of adulterants. Here, we report the development and validation of duck genomic DNA certified reference materials (CRMs) through the detection of the duck interleukin 2 (IL2) gene by digital PCR (dPCR) for the identification of duck meat in food products. The certified value of IL2 in CRMs was 5.78 ± 0.51 × 103 copies/μL with extended uncertainty (coverage factor k = 2) based on IL2 quantification by eight independent collaborating laboratories. Quantification of the mitochondrial gene cytb revealed a concentration of 2.0 × 106 copies/μL, as an information value. The CRMs were also used to determine the limit of detection (LOD) for six commercial testing kits, which confirmed that these kits meet or exceed their claimed sensitivity and are reliable for duck detection.
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Affiliation(s)
- Xiaoyun Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (X.C.); (Y.J.); (X.W.); (C.P.); (X.X.)
| | - Yi Ji
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (X.C.); (Y.J.); (X.W.); (C.P.); (X.X.)
| | - Kai Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (K.L.); (X.P.)
| | - Xiaofu Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (X.C.); (Y.J.); (X.W.); (C.P.); (X.X.)
| | - Cheng Peng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (X.C.); (Y.J.); (X.W.); (C.P.); (X.X.)
| | - Xiaoli Xu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (X.C.); (Y.J.); (X.W.); (C.P.); (X.X.)
| | - Xinwu Pei
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (K.L.); (X.P.)
| | - Junfeng Xu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (X.C.); (Y.J.); (X.W.); (C.P.); (X.X.)
- Correspondence: (J.X.); (L.L.)
| | - Liang Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (K.L.); (X.P.)
- Correspondence: (J.X.); (L.L.)
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10
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Kojabad AA, Farzanehpour M, Galeh HEG, Dorostkar R, Jafarpour A, Bolandian M, Nodooshan MM. Droplet digital PCR of viral DNA/RNA, current progress, challenges, and future perspectives. J Med Virol 2021; 93:4182-4197. [PMID: 33538349 PMCID: PMC8013307 DOI: 10.1002/jmv.26846] [Citation(s) in RCA: 105] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 02/01/2021] [Indexed: 12/18/2022]
Abstract
High-throughput droplet-based digital PCR (ddPCR) is a refinement of the conventional polymerase chain reaction (PCR) methods. In ddPCR, DNA/RNA is encapsulated stochastically inside the microdroplets as reaction chambers. A small percentage of the reaction chamber contains one or fewer copies of the DNA or RNA. After PCR amplification, concentrations are determined based on the proportion of nonfluorescent partitions through the Poisson distribution. Some of the main features of ddPCR include high sensitivity and specificity, absolute quantification without a standard curve, high reproducibility, good tolerance to PCR inhibitor, and high efficacy compared to conventional molecular methods. These advantages make ddPCR a valuable addition to the virologist's toolbox. The following review outlines the recent technological advances in ddPCR methods and their applications in viral identification.
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Affiliation(s)
- Amir Asri Kojabad
- Applied Virology Research CenterBaqiyatallah University of Medical SciencesTehranIran
| | - Mahdieh Farzanehpour
- Applied Virology Research CenterBaqiyatallah University of Medical SciencesTehranIran
| | | | - Ruhollah Dorostkar
- Applied Virology Research CenterBaqiyatallah University of Medical SciencesTehranIran
| | - Ali Jafarpour
- Research Center for Clinical VirologyTehran University of Medical SciencesTehranIran
| | - Masoumeh Bolandian
- Applied Virology Research CenterBaqiyatallah University of Medical SciencesTehranIran
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Wang X, Zhang Y, Niu C, Wang S, Li L, Guo Y, Zhu L, Jin X, Gao H, Xu W, Zhu P, Lan Q, Du M, Cheng X, Gao Y, Dong L. Establishment of primary reference measurement procedures and reference materials for EGFR variant detection in non-small cell lung cancer. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2021; 13:2114-2123. [PMID: 33870958 DOI: 10.1039/d1ay00328c] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Circulating tumor DNA (ctDNA)-based mutation detection is promising to change the clinical practice of genotype-directed therapy for cancer. A growing number of non-invasive tests for cancer screening and monitoring that involve the detection of ctDNA have been commercialized. Primary reference measurement procedures (PRMPs) and reference materials (RMs) are urgently needed to assess the non-invasive tests. In this study, a PRMP based on digital PCR (dPCR) and ctDNA RMs for quantification of the frequently occurring variant in epidermal growth factor receptor (EGFR L858R, T790M, and 19Del) in non-small cell lung cancer (NSCLC) were established. The candidate dPCR PRMP showed high specificity (false positive rate 0-0.003%), good repeatability (coefficient of variance (CV), 2-3% for 104 copies/reaction), and high interlaboratory reproducibility (3-10%). A good linearity (0.97 < slope < 1.03, R2 ≥ 0.9999) between the measured mutant (MU) value and prepared value was observed for all assays over the fractional abundance (FA) range, between 25% and 0.05%. The limit of quantification (LoQ) was determined to be 34 L858R, 23 T790M, and 34 19Del copies/reaction, corresponding to a FA of 0.2%. An inter-laboratory study of using the EGFR ctDNA RMs and dPCR assays demonstrated that the participating laboratories produced consistent concentrations of MU and wild-type (WT), as well as FA. This study demonstrates that dPCR can act as a potential PRMP for EGFR mutation for validation of NSCLC genotyping tests and ctDNA quantitative tests. The PRMP and RMs established here could improve interlaboratory repeatability and reproducibility, which supports rapid translation and application of non-invasive tests into clinical practice.
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Affiliation(s)
- Xia Wang
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing 100029, People's Republic of China.
| | - Yongzhuo Zhang
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing 100029, People's Republic of China.
| | - Chunyan Niu
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing 100029, People's Republic of China.
| | - Shangjun Wang
- Nanjing Institute of Measurement and Testing Technology, Nanjing 210049, People's Republic of China
| | - Liang Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, People's Republic of China
| | - Yong Guo
- Department of Biomedical Engineering, School of Medicine, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Tsinghua University, Beijing 100084, People's Republic of China
| | - Lingxiang Zhu
- Human Genetic Resource Center, National Research Institute for Health and Family Planning, Beijing 100081, People's Republic of China
| | - Xiaohua Jin
- Human Genetic Resource Center, National Research Institute for Health and Family Planning, Beijing 100081, People's Republic of China
| | - Huafang Gao
- Human Genetic Resource Center, National Research Institute for Health and Family Planning, Beijing 100081, People's Republic of China
| | - Wentao Xu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, People's Republic of China
| | - Pengyu Zhu
- Chinese Academy of Inspection and Quarantine, Beijing 100176, People's Republic of China
| | - Qingkuo Lan
- Tianjin Institute of Agricultural Quality Standard and Testing Technology, Tianjin Academy of Agricultural Sciences, Tianjin 300381, People's Republic of China
| | - Meihong Du
- Beijing Engineering Technology Research Centre of Gene Sequencing and Gene Function Analysis, Beijing Center for Physical & Chemical Analysis, Beijing 100093, People's Republic of China
| | - Xiaoyan Cheng
- Beijing Engineering Technology Research Centre of Gene Sequencing and Gene Function Analysis, Beijing Center for Physical & Chemical Analysis, Beijing 100093, People's Republic of China
| | - Yunhua Gao
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing 100029, People's Republic of China.
| | - Lianhua Dong
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing 100029, People's Republic of China.
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12
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Wu X, Tay JK, Goh CK, Chan C, Lee YH, Springs SL, Wang DY, Loh KS, Lu TK, Yu H. Digital CRISPR-based method for the rapid detection and absolute quantification of nucleic acids. Biomaterials 2021; 274:120876. [PMID: 34034027 DOI: 10.1016/j.biomaterials.2021.120876] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 04/23/2021] [Accepted: 05/02/2021] [Indexed: 12/23/2022]
Abstract
Rapid diagnostics of adventitious agents in biopharmaceutical/cell manufacturing release testing and the fight against viral infection have become critical. Quantitative real-time PCR and CRISPR-based methods rapidly detect DNA/RNA in 1 h but suffer from inter-site variability. Absolute quantification of DNA/RNA by methods such as digital PCR reduce this variability but are currently too slow for wider application. Here, we report a RApid DIgital Crispr Approach (RADICA) for absolute quantification of nucleic acids in 40-60 min. Using SARS-CoV-2 as a proof-of-concept target, RADICA allows for absolute quantification with a linear dynamic range of 0.6-2027 copies/μL (R2 value > 0.99), high accuracy and low variability, no cross-reactivity to similar targets, and high tolerance to human background DNA. RADICA's versatility is validated against other targets such as Epstein-Barr virus (EBV) from human B cells and patients' serum. RADICA can accurately detect and absolutely quantify EBV DNA with similar dynamic range of 0.5-2100 copies/μL (R2 value > 0.98) in 1 h without thermal cycling, providing a 4-fold faster alternative to digital PCR-based detection. RADICA therefore enables rapid and sensitive absolute quantification of nucleic acids which can be widely applied across clinical, research, and biomanufacturing areas.
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Affiliation(s)
- Xiaolin Wu
- Critical Analytics for Manufacturing Personalized Medicine Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, 138602, Singapore
| | - Joshua K Tay
- Department of Otolaryngology-Head and Neck Surgery, National University of Singapore, Singapore
| | - Chuan Keng Goh
- Department of Otolaryngology-Head and Neck Surgery, National University of Singapore, Singapore
| | - Cheryl Chan
- Critical Analytics for Manufacturing Personalized Medicine Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, 138602, Singapore
| | - Yie Hou Lee
- Critical Analytics for Manufacturing Personalized Medicine Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, 138602, Singapore
| | - Stacy L Springs
- Critical Analytics for Manufacturing Personalized Medicine Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, 138602, Singapore; Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - De Yun Wang
- Department of Otolaryngology-Head and Neck Surgery, National University of Singapore, Singapore
| | - Kwok Seng Loh
- Department of Otolaryngology-Head and Neck Surgery, National University of Singapore, Singapore
| | - Timothy K Lu
- Critical Analytics for Manufacturing Personalized Medicine Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, 138602, Singapore; Synthetic Biology Center, Massachusetts Institute of Technology (MIT), Cambridge, MA, 02139, USA; Synthetic Biology Group, Research Laboratory of Electronics, Massachusetts Institute of Technology (MIT), Cambridge, MA, 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA; Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology (MIT), Cambridge, MA, 02142, USA; Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA, 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA, 02142, USA.
| | - Hanry Yu
- Critical Analytics for Manufacturing Personalized Medicine Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, 138602, Singapore; Institute of Bioengineering and Bioimaging, A*STAR, The Nanos, #04-01, 31, Biopolis Way, 138669, Singapore; Mechanobiology Institute, National University of Singapore, T-Lab, #05-01, 5A Engineering Drive 1, 117411, Singapore; Department of Physiology & the Institute for Digital Medicine (WisDM), Yong Loo Lin School of Medicine, MD9-04-11, 2 Medical Drive, 117593, Singapore.
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13
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Zhou H, Liu D, Ma L, Ma T, Xu T, Ren L, Li L, Xu S. A SARS-CoV-2 Reference Standard Quantified by Multiple Digital PCR Platforms for Quality Assessment of Molecular Tests. Anal Chem 2021; 93:715-721. [PMID: 33289545 PMCID: PMC7737535 DOI: 10.1021/acs.analchem.0c03996] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 11/24/2020] [Indexed: 01/03/2023]
Abstract
The outbreak of novel coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread worldwide. To meet the urgent and massive demand for the screening and diagnosis of infected individuals, many in vitro diagnostic assays using nucleic acid tests (NATs) have been urgently authorized by regulators worldwide. A reference standard with a well-characterized concentration or titer is of the utmost importance for the study of limit of detection (LoD), which is a crucial feature for a diagnostic assay. Although several reference standards of plasmids or synthetic RNA have already been announced, a reference standard for inactivated virus particles with an accurate concentration is still needed to evaluate the complete procedure. Here, we performed a collaborative study to estimate the NAT-detectable units as a viral genomic equivalent quantity (GEQ) of an inactivated whole-virus SARS-CoV-2 reference standard candidate using digital PCR (dPCR) on multiple commercialized platforms. The median of the quantification results (4.6 × 105 ± 6.5 × 104 GEQ/mL) was treated as the consensus true value of GEQ of virus particles in the reference standard. This reference standard was then used to challenge the LoDs of six officially approved diagnostic assays. Our study demonstrates that an inactivated whole virus quantified by dPCR can serve as a reference standard and provides a unified solution for assay development, quality control, and regulatory surveillance.
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Affiliation(s)
- Haiwei Zhou
- Division II of In Vitro Diagnostics for Infectious
Diseases, Institute for In Vitro Diagnostics Control, National Institutes for
Food and Drug Control, Beijing 100050, China
| | - Donglai Liu
- Division II of In Vitro Diagnostics for Infectious
Diseases, Institute for In Vitro Diagnostics Control, National Institutes for
Food and Drug Control, Beijing 100050, China
| | - Liang Ma
- Department of Biomedical Devices, Bioland
Laboratory (Guangzhou Regenerative Medicine and Health Guangdong
Laboratory), Guangzhou 510320, China
| | - Tingting Ma
- Division II of In Vitro Diagnostics for Infectious
Diseases, Institute for In Vitro Diagnostics Control, National Institutes for
Food and Drug Control, Beijing 100050, China
| | - Tingying Xu
- Division II of In Vitro Diagnostics for Infectious
Diseases, Institute for In Vitro Diagnostics Control, National Institutes for
Food and Drug Control, Beijing 100050, China
| | - Lili Ren
- Institute of Pathogen Biology, Chinese
Academy of Medical Sciences & Peking Union Medical College, Beijing
100730, China
| | - Liang Li
- Biotechnology Research Institute, Chinese
Academy of Agricultural Sciences, Beijing 100081,
China
| | - Sihong Xu
- Division II of In Vitro Diagnostics for Infectious
Diseases, Institute for In Vitro Diagnostics Control, National Institutes for
Food and Drug Control, Beijing 100050, China
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14
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Rotondo JC, Oton-Gonzalez L, Mazziotta C, Lanzillotti C, Iaquinta MR, Tognon M, Martini F. Simultaneous Detection and Viral DNA Load Quantification of Different Human Papillomavirus Types in Clinical Specimens by the High Analytical Droplet Digital PCR Method. Front Microbiol 2020; 11:591452. [PMID: 33329471 PMCID: PMC7710522 DOI: 10.3389/fmicb.2020.591452] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 10/19/2020] [Indexed: 12/31/2022] Open
Abstract
Human papillomaviruses (HPVs) are small DNA tumor viruses that mainly infect mucosal epithelia of anogenital and upper respiratory tracts. There has been progressive demand for more analytical assays for HPV DNA quantification. A novel droplet digital PCR (ddPCR) method was developed to simultaneously detect and quantify HPV DNA from different HPV types. DdPCR was initially tested for assay sensitivity, accuracy, specificity as well as intra- and inter-run assay variation employing four recombinant plasmids containing HPV16, HPV18, HPV11, and HPV45 DNAs. The assay was extended to investigate/quantify HPV DNA in Cervical Intraepithelial Neoplasia (CIN, n = 45) specimens and human cell lines (n = 4). DdPCR and qPCR data from clinical samples were compared. The assay showed high accuracy, sensitivity and specificity, with low intra-/inter- run variations, in detecting/quantifying HPV16/18/11/45 DNAs. HPV DNA was detected in 51.1% (23/45) CIN DNA samples by ddPCR, whereas 40% (18/45) CIN tested HPV-positive by qPCR. Five CIN, tested positive by ddPCR, were found to be negative by qPCR. In CIN specimens, the mean HPV DNA loads determined by ddPCR were 3.81 copy/cell (range 0.002-51.02 copy/cell), whereas 8.04 copy/cell (range 0.003-78.73 copy/cell) by qPCR. DdPCR and qPCR concordantly detected HPV DNA in SiHa, CaSki and Hela cells, whereas HaCaT tested HPV-negative. The correlation between HPV DNA loads simultaneously detected by ddPCR/qPCR in CINs/cell lines was good (R 2 = 0.9706, p < 0.0001). Our data indicate that ddPCR is a valuable technique in quantifying HPV DNA load in CIN specimens and human cell lines, thereby improving clinical applications, such as patient management after primary diagnosis of HPV-related lesions with HPV-type specific assays.
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Affiliation(s)
| | | | | | | | | | - Mauro Tognon
- Laboratories of Cell Biology and Molecular Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Fernanda Martini
- Laboratories of Cell Biology and Molecular Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
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15
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Voegel TM, Larrabee MM, Nelson LM. Development of droplet digital PCR assays to quantify genes involved in nitrification and denitrification, comparison with quantitative real-time PCR and validation of assays in vineyard soil. Can J Microbiol 2020; 67:174-187. [PMID: 32910858 DOI: 10.1139/cjm-2020-0033] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Quantifying genes in soil is important to relate the abundance of soil bacteria to biogeochemical cycles. Quantitative real-time PCR is widely used for quantification, but its use with environmental samples is limited by poor reaction efficiencies or by PCR inhibition through co-purified soil substances. Droplet digital PCR (ddPCR) is a technology for absolute, sensitive quantification of genes. This study optimized eight ddPCR assays to quantify total bacteria and archaea as well as the nitrification (bacterial and archaeal amoA) and denitrification (nirS, nirK, nosZI, nosZII) genes involved in the generation or reduction of the greenhouse gas nitrous oxide. Detection and quantification thresholds were compared with those of quantitative real-time PCR and were equal to, or improved, in ddPCR. To validate the assays using environmental samples, soil DNA was isolated from two vineyards in the Okanagan valley in British Columbia, Canada, over the 2017 growing season. Soil properties related to the observed gene abundances were determined. Total bacteria, nirK, and nosZII increased with time and the soil C/N ratio and NH4+-N concentration affected total archaea and archaeal amoA negatively. The results, compared with those of other studies, showed that ddPCR is a valid alternative to qPCR to quantify genes involved in nitrification or denitrification.
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Affiliation(s)
- Tanja M Voegel
- Irving K. Barber Faculty of Science, Department of Biology, University of British Columbia Okanagan, 1177 Research Road, Kelowna, BC V1V 1V7, Canada.,Irving K. Barber Faculty of Science, Department of Biology, University of British Columbia Okanagan, 1177 Research Road, Kelowna, BC V1V 1V7, Canada
| | - Melissa M Larrabee
- Irving K. Barber Faculty of Science, Department of Biology, University of British Columbia Okanagan, 1177 Research Road, Kelowna, BC V1V 1V7, Canada.,Irving K. Barber Faculty of Science, Department of Biology, University of British Columbia Okanagan, 1177 Research Road, Kelowna, BC V1V 1V7, Canada
| | - Louise M Nelson
- Irving K. Barber Faculty of Science, Department of Biology, University of British Columbia Okanagan, 1177 Research Road, Kelowna, BC V1V 1V7, Canada.,Irving K. Barber Faculty of Science, Department of Biology, University of British Columbia Okanagan, 1177 Research Road, Kelowna, BC V1V 1V7, Canada
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16
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A Chip Digital PCR Assay for Quantification of Common Wheat Contamination in Pasta Production Chain. Foods 2020; 9:foods9070911. [PMID: 32664323 PMCID: PMC7404985 DOI: 10.3390/foods9070911] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 07/06/2020] [Accepted: 07/07/2020] [Indexed: 02/06/2023] Open
Abstract
Pasta, the Italian product par excellence, is made of pure durum wheat. The use of Triticum durum derived semolina is in fact mandatory for Italian pasta, in which Triticum aestivum species is considered a contamination that must not exceed the 3% maximum level. Over the last 50 years, various electrophoretic, chemical, and immuno-chemical methods have been proposed aimed to track the possible presence of common wheat in semolina and pasta. More recently, a new generation of methods, based on DNA (DeoxyriboNucleic Acid) analysis, has been developed to this aim. Species traceability can be now enforced by a new technology, namely digital Polymerase Chain Reaction (dPCR) which quantify the number of target sequence present in a sample, using limiting dilutions, PCR, and Poisson statistics. In our work we have developed a duplex chip digital PCR (cdPCR) assay able to quantify common wheat presence along pasta production chain, from raw materials to final products. The assay was verified on reference samples at known level of common wheat contamination and applied to commercial pastas sampled in the Italian market.
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17
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Cao Y, Yu M, Dong G, Chen B, Zhang B. Digital PCR as an Emerging Tool for Monitoring of Microbial Biodegradation. Molecules 2020; 25:E706. [PMID: 32041334 PMCID: PMC7037809 DOI: 10.3390/molecules25030706] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 02/03/2020] [Accepted: 02/04/2020] [Indexed: 11/16/2022] Open
Abstract
Biodegradation of contaminants is extremely complicated due to unpredictable microbial behaviors. Monitoring of microbial biodegradation drives us to determine (1) the amounts of specific degrading microbes, (2) the abundance, and (3) expression level of relevant functional genes. To this endeavor, the cultivation independent polymerase chain reaction (PCR)-based monitoring technique develops from endpoint PCR, real-time quantitative PCR, and then into novel digital PCR. In this review, we introduce these three categories of PCR techniques and summarize the timely applications of digital PCR and its superiorities than qPCR for biodegradation monitoring. Digital PCR technique, emerging as the most accurately absolute quantification method, can serve as the most promising and robust tool for monitoring of microbial biodegradation.
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Affiliation(s)
| | | | | | - Bing Chen
- The Northern Region Persistent Organic Pollution (NRPOP) Control Laboratory, Faculty of Engineering and Applied Science, Memorial University of Newfoundland, St. John’s, NL A1B 3X5, Canada; (Y.C.); (M.Y.); (G.D.)
| | - Baiyu Zhang
- The Northern Region Persistent Organic Pollution (NRPOP) Control Laboratory, Faculty of Engineering and Applied Science, Memorial University of Newfoundland, St. John’s, NL A1B 3X5, Canada; (Y.C.); (M.Y.); (G.D.)
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18
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Dong L, Wang X, Wang S, Du M, Niu C, Yang J, Li L, Zhang G, Fu B, Gao Y, Wang J. Interlaboratory assessment of droplet digital PCR for quantification of BRAF V600E mutation using a novel DNA reference material. Talanta 2019; 207:120293. [PMID: 31594564 DOI: 10.1016/j.talanta.2019.120293] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 08/19/2019] [Accepted: 08/20/2019] [Indexed: 12/13/2022]
Abstract
Droplet digital PCR (ddPCR) has attracted much attention in the detection of genetic signatures of cancer present at low levels in circulating tumor DNA (ctDNA) in blood. A growing number of laboratory-developed liquid biopsy tests based on such technology have become commercially available for clinical settings. To obtain consistent and comparable results, an international standard is necessary for validation of the analytical performance. In this study, a novel and SI-traceable "ctDNA" reference material (RM) carrying BRAF V600E was prepared by gravimetrically mixing a 152 bp PCR amplicon and sonicated wild-type genomic DNA. The ddPCR performance was evaluated by analyzing serial "ctDNA" dilutions using a competitive MGB assay. The mutant frequency concordance (k) between ddPCR and the gravimetrical value was 1.03 in the range from 53.9% to 0.1%. The limit of blank (LoB), detection (LoD) and quantification (LoQ) of ddPCR assay were determined to be 0.01%, 0.02% and 0.1%, respectively. Results from the interlaboratory study, using challenging low levels of BRAF V600E ctDNA RMs, demonstrated that the participating laboratories had the appropriate technical competency to perform accurate ddPCR-based low level of ratio measurements. However, a systematic error caused by uncorrected droplet volume in Naica Crystal ddPCR platform was found by using the ctDNA RM. Between-laboratory consistency in copy number measurement was greatly improved when a correct droplet volume was applied for the ddPCR measurement by using the ctDNA RM. This confirms that the "ctDNA" RM is fit for the validation of ddPCR systems for ctDNA quantification. This would also support translation of tests for circulating tumor DNA by ddPCR into routine use.
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Affiliation(s)
- Lianhua Dong
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing, 100013, PR China.
| | - Xia Wang
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing, 100013, PR China
| | - Shangjun Wang
- Nanjing Institute of Measurement and Testing Technology, Nanjing, 210049, PR China
| | - Meihong Du
- Beijing Engineering Technology Research Centre of Gene Sequencing and Gene Function Analysis, Beijing Center for Physical & Chemical Analysis, Beijing, 100093, PR China
| | - Chunyan Niu
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing, 100013, PR China
| | - Jiayi Yang
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing, 100013, PR China
| | - Liang Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China
| | - Ganlin Zhang
- Oncology Department, Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing, 100069, PR China
| | - Boqiang Fu
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing, 100013, PR China
| | - Yunhua Gao
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing, 100013, PR China
| | - Jing Wang
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing, 100013, PR China.
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19
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Development of certified reference material NMIJ CRM 6205-a for the validation of DNA quantification methods: accurate mass concentrations of 600-bp DNA solutions having artificial sequences. Anal Bioanal Chem 2019; 411:6091-6100. [PMID: 31289897 DOI: 10.1007/s00216-019-01992-y] [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: 03/26/2019] [Revised: 06/03/2019] [Accepted: 06/18/2019] [Indexed: 10/26/2022]
Abstract
Two 600-bp DNA solutions (DNA600-G and DNA600-T) were developed as certified reference material, NMIJ CRM 6205-a, for the validation of DNA quantification methods. Both DNA600-G and DNA600-T are ideal as "spike-in control" because these materials have artificial nucleic acid sequences. The certified values were determined as the mass concentration of total DNA (whole DNA materials in sample solution regardless of sequence) at 25 °C by formic acid hydrolysis/liquid chromatography-isotope dilution mass spectrometry (LC-IDMS) and inductively coupled plasma-mass spectrometry (ICP-MS) based on the amount of phosphorus. DNAs were synthesized, and plasmids including the synthesized DNAs were cloned into Escherichia coli DH5α. The amplified plasmids were digested with a restriction enzyme and highly purified. Then, the purified DNAs were diluted with water to approximately 1 ng/μL. By using the CRM-validated methods in fields where DNA quantification is required, the reliability of DNA quantification could be improved. Graphical abstract.
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20
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Dong L, Wang S, Fu B, Wang J. Evaluation of droplet digital PCR and next generation sequencing for characterizing DNA reference material for KRAS mutation detection. Sci Rep 2018; 8:9650. [PMID: 30504843 PMCID: PMC6269532 DOI: 10.1038/s41598-018-27368-3] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 05/23/2018] [Indexed: 01/05/2023] Open
Abstract
KRAS gene mutations are predictive markers of non-response to anti-epidermal growth factor receptor. An increasing number of techniques are being developed to detect KRAS mutations. To obtain consistent and comparable results, a traceable reference material (RM) is necessary for validation the routinely used method. However, a lack of reference methods is a main impediment for deriving traceability and measurement comparability. In this study, droplet digital PCR (ddPCR) and next generation sequencing (NGS) were evaluated. No cross- reactivity was detected with any of the probe by ddPCR. The measured fraction of KRAS mutant allele by ddPCR and NGS agreed with the prepared value by gravimetrical dilution (concordance (k) >0.95 and >0.93 for ddPCR and NGS, respectively). The reliable limit of quantification (LOQ) was 0.1% and 1% for ddPCR and NGS, respectively. In conclusion, the validated ddPCR and NGS are suitable to characterize the KRAS RM due to the high specificity and accuracy. Verification of the LOD of three commercial kits by using the NIM-KRAS-8 RM showed that the LOD was inconsistent with the claimed LOD of the kits (1%) for some assays. This indicates a traceable RM was important for setting up the criteria regarding the LOD for the commercial kit.
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Affiliation(s)
- Lianhua Dong
- National Institute of Metrology, Beijing, 100013, P. R. China.
| | - Shangjun Wang
- Nanjing Institute of Measurement and Testing Technology, Nanjing, 210049, P. R. China
| | - Boqiang Fu
- National Institute of Metrology, Beijing, 100013, P. R. China
| | - Jing Wang
- National Institute of Metrology, Beijing, 100013, P. R. China
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21
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Happel E, Bartl I, Voss M, Riemann L. Extensive nitrification and active ammonia oxidizers in two contrasting coastal systems of the Baltic Sea. Environ Microbiol 2018; 20:2913-2926. [PMID: 29921003 DOI: 10.1111/1462-2920.14293] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 04/30/2018] [Accepted: 05/16/2018] [Indexed: 11/27/2022]
Abstract
Nitrification is important in nitrogen (N) cycling of aquatic environments, but knowledge about its regulation and importance is sparse. Here we examined nitrification and ammonia oxidizers in the Baltic Sea. We investigated two sites with different catchment characteristics (agricultural and forest), the Bay of Gdánsk (south) and the Öre Estuary (north), and measured pelagic nitrification rates and abundance, composition and expression of ammonia monooxygenase (amoA) genes. Highest nitrification rates were found in the nutrient rich Bay of Gdańsk. Interestingly, abundances of ammonia-oxidizing archaea (AOA) and bacteria (AOB) were orders of magnitude lower than reported from other sites. Although AOA were most abundant at both sites, the highest expression levels were from AOB. Interestingly, few AOA and AOB taxa dominated amoA gene expression, with a Nitrosomarinus related phylotype showing widespread expression. AOA and AOB communities differed between sites and depths, respectively, with the composition in rivers being distinct. A storm event, causing an even depth distribution of nitrification and particles in the Bay of Gdańsk, indicated that the presence of particles stimulate nitrification. The study highlights coastal regions as dynamic sites of extensive pelagic nitrification, which may affect local food web dynamics and loss of N mediated by denitrification.
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Affiliation(s)
- Elisabeth Happel
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
| | - Ines Bartl
- Department of Biological Oceanography, Leibniz Institute for Baltic Sea Research (IOW), Rostock, Germany
| | - Maren Voss
- Department of Biological Oceanography, Leibniz Institute for Baltic Sea Research (IOW), Rostock, Germany
| | - Lasse Riemann
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
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Leguizamón Guerrero JE, Vela Rojas AF, Arias Cortés MM, Cifuentes Fernández LF. Panorama general de los organismos genéticamente modificados en Colombia y en el mundo: Capacidad nacional de detección. REVISTA COLOMBIANA DE BIOTECNOLOGÍA 2018. [DOI: 10.15446/rev.colomb.biote.v20n2.77080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Los organismos genéticamente modificados (OGM) y en particular los cultivos genéticamente modificados (GM), son el resultado de la modificación de la información genética de una especie a partir del uso de la biotecnología moderna para proporcionar nuevas características que su contraparte no modificada no posee, tales como resistencia a insectos, tolerancia a herbicidas, contenido de nutrientes entre otros. La mayor parte de estos cultivos se concentran en cuatro productos: soya (Glycine max), maíz (Zea Mays), canola (Brassica napus) y algodón (Gossypium hirsutum); y los principales productores son Estados Unidos, Brasil, Argentina, India y Canadá. Por su parte, Colombia ocupa el puesto 18 con cultivos de maíz, algodón y claveles azules. La introducción de estas especies en cualquier mercado está limitada por la legislación propia del país destino, así como por los estudios que permiten establecer su efecto sobre el medio ambiente, la salud humana y animal; en este sentido, la precisión y confianza de las técnicas analíticas empleadas en la evaluación del contenido de OGM son un elemento importante para la toma de decisiones basadas en evidencias objetivas, especialmente frente al debate en torno a su uso. Este documento presenta una revisión de las tecnologías de análisis más importantes disponibles a nivel mundial, frente a las capacidades nacionales para su detección.
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Whale AS, Jones GM, Pavšič J, Dreo T, Redshaw N, Akyürek S, Akgöz M, Divieto C, Sassi MP, He HJ, Cole KD, Bae YK, Park SR, Deprez L, Corbisier P, Garrigou S, Taly V, Larios R, Cowen S, O'Sullivan DM, Bushell CA, Goenaga-Infante H, Foy CA, Woolford AJ, Parkes H, Huggett JF, Devonshire AS. Assessment of Digital PCR as a Primary Reference Measurement Procedure to Support Advances in Precision Medicine. Clin Chem 2018; 64:1296-1307. [PMID: 29903874 DOI: 10.1373/clinchem.2017.285478] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 05/24/2018] [Indexed: 11/06/2022]
Abstract
BACKGROUND Genetic testing of tumor tissue and circulating cell-free DNA for somatic variants guides patient treatment of many cancers. Such measurements will be fundamental in the future support of precision medicine. However, there are currently no primary reference measurement procedures available for nucleic acid quantification that would support translation of tests for circulating tumor DNA into routine use. METHODS We assessed the accuracy of digital PCR (dPCR) for copy number quantification of a frequently occurring single-nucleotide variant in colorectal cancer (KRAS c.35G>A, p.Gly12Asp, from hereon termed G12D) by evaluating potential sources of uncertainty that influence dPCR measurement. RESULTS Concentration values for samples of KRAS G12D and wild-type plasmid templates varied by <1.2-fold when measured using 5 different assays with varying detection chemistry (hydrolysis, scorpion probes, and intercalating dyes) and <1.3-fold with 4 commercial dPCR platforms. Measurement trueness of a selected dPCR assay and platform was validated by comparison with an orthogonal method (inductively coupled plasma mass spectrometry). The candidate dPCR reference measurement procedure showed linear quantification over a wide range of copies per reaction and high repeatability and interlaboratory reproducibility (CV, 2%-8% and 5%-10%, respectively). CONCLUSIONS This work validates dPCR as an SI-traceable reference measurement procedure based on enumeration and demonstrates how it can be applied for assignment of copy number concentration and fractional abundance values to DNA reference materials in an aqueous solution. High-accuracy measurements using dPCR will support the implementation and traceable standardization of molecular diagnostic procedures needed for advancements in precision medicine.
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Affiliation(s)
| | - Gerwyn M Jones
- Molecular and Cell Biology Team, LGC, Teddington, Middlesex, UK
| | - Jernej Pavšič
- National Institute of Biology, Department of Biotechnology and Systems Biology, Ljubljana, Slovenia.,Jožef Stefan International Postgraduate School, Ljubljana, Slovenia
| | - Tanja Dreo
- National Institute of Biology, Department of Biotechnology and Systems Biology, Ljubljana, Slovenia
| | | | - Sema Akyürek
- TUBITAK National Metrology Institute (TUBITAK UME), Bioanalysis Laboratory, Gebze, Kocaeli, Turkey
| | - Müslüm Akgöz
- TUBITAK National Metrology Institute (TUBITAK UME), Bioanalysis Laboratory, Gebze, Kocaeli, Turkey
| | - Carla Divieto
- INRIM Istituto Nazionale di Ricerca Metrologica, Turin, Italy
| | | | - Hua-Jun He
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD
| | - Kenneth D Cole
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD
| | - Young-Kyung Bae
- Center for Bioanalysis, KRISS, Yuseong-gu, Daejeon, Republic of Korea
| | - Sang-Ryoul Park
- Center for Bioanalysis, KRISS, Yuseong-gu, Daejeon, Republic of Korea
| | - Liesbet Deprez
- Directorate for Health, Consumers and Reference Materials, Joint Research Centre (JRC), European Commission, Geel, Belgium
| | - Philippe Corbisier
- Directorate for Health, Consumers and Reference Materials, Joint Research Centre (JRC), European Commission, Geel, Belgium
| | - Sonia Garrigou
- INSERM UMR-S1147, CNRS SNC5014, Equipe labellisée Ligue Nationale contre le cancer, Paris Descartes University, Paris, France
| | - Valérie Taly
- INSERM UMR-S1147, CNRS SNC5014, Equipe labellisée Ligue Nationale contre le cancer, Paris Descartes University, Paris, France
| | - Raquel Larios
- Inorganic Analysis Team, LGC, Teddington, Middlesex, UK
| | - Simon Cowen
- Statistics Team, LGC, Teddington, Middlesex, UK
| | | | | | | | - Carole A Foy
- Molecular and Cell Biology Team, LGC, Teddington, Middlesex, UK
| | | | - Helen Parkes
- Molecular and Cell Biology Team, LGC, Teddington, Middlesex, UK
| | - Jim F Huggett
- Molecular and Cell Biology Team, LGC, Teddington, Middlesex, UK; .,School of Biosciences and Medicine, Faculty of Health and Medical Science, University of Surrey, Guildford, UK
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Vynck M, Thas O. Reducing Bias in Digital PCR Quantification Experiments: The Importance of Appropriately Modeling Volume Variability. Anal Chem 2018; 90:6540-6547. [DOI: 10.1021/acs.analchem.8b00115] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Matthijs Vynck
- Department of Data Analysis and Mathematical Modelling, Ghent University, Ghent 9000, Belgium
| | - Olivier Thas
- Department of Data Analysis and Mathematical Modelling, Ghent University, Ghent 9000, Belgium
- National Institute for Applied Statistics Research Australia (NIASRA), University of Wollongong, Wollongong, NSW 2522, Australia
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Jia P, Purcell MK, Pan G, Wang J, Kan S, Liu Y, Zheng X, Shi X, He J, Yu L, Hua Q, Lu T, Lan W, Winton JR, Jin N, Liu H. Analytical validation of a reverse transcriptase droplet digital PCR (RT-ddPCR) for quantitative detection of infectious hematopoietic necrosis virus. J Virol Methods 2017; 245:73-80. [PMID: 28347708 DOI: 10.1016/j.jviromet.2017.03.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 03/23/2017] [Accepted: 03/23/2017] [Indexed: 12/14/2022]
Abstract
Infectious hematopoietic necrosis virus (IHNV) is an important pathogen of salmonid fishes. A validated universal reverse transcriptase quantitative PCR (RT-qPCR) assay that can quantify levels of IHNV in fish tissues has been previously reported. In the present study, we adapted the published set of IHNV primers and probe for use in a reverse-transcriptase droplet digital PCR (RT-ddPCR) assay for quantification of the virus in fish tissue samples. The RT-ddPCR and RT-qPCR assays detected 13 phylogenetically diverse IHNV strains, but neither assay produced detectable amplification when RNA from other fish viruses was used. The RT-ddPCR assay had a limit of detection (LOD) equating to 2.2 plaque forming units (PFU)/μl while the LOD for the RT-qPCR was 0.2 PFU/μl. Good agreement (69.4-100%) between assays was observed when used to detect IHNV RNA in cell culture supernatant and tissues from IHNV infected rainbow trout (Oncorhynchus mykiss) and arctic char (Salvelinus alpinus). Estimates of RNA copy number produced by the two assays were significantly correlated but the RT-qPCR consistently produced higher estimates than the RT-ddPCR. The analytical properties of the N gene RT-ddPCR test indicated that this method may be useful to assess IHNV RNA copy number for research and diagnostic purposes. Future work is needed to establish the within and between laboratory diagnostic performance of the RT-ddPCR assay.
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Affiliation(s)
- Peng Jia
- Shenzhen Entry-exit Inspection and Quarantine Bureau, Shenzhen, 518045, People's Republic of China; Shenzhen Academy of Inspection and Quarantine Sciences, Shenzhen, 518045, People's Republic of China; Institute of Military Veterinary Medicine, Academy of Military Medical Sciences of PLA, Jilin, 130117, People's Republic of China
| | - Maureen K Purcell
- US Geological Survey, Western Fisheries Research Center, 6505 Northeast 65th Street, Seattle, WA 98115, USA
| | - Guang Pan
- Shenzhen Entry-exit Inspection and Quarantine Bureau, Shenzhen, 518045, People's Republic of China; Shenzhen Academy of Inspection and Quarantine Sciences, Shenzhen, 518045, People's Republic of China
| | - Jinjin Wang
- Shenzhen Entry-exit Inspection and Quarantine Bureau, Shenzhen, 518045, People's Republic of China; Shenzhen Academy of Inspection and Quarantine Sciences, Shenzhen, 518045, People's Republic of China
| | - Shifu Kan
- Shenzhen Supervision and Testing Center for Quality and Safety of Agri-products, Shenzhen, 518005, People's Republic of China
| | - Yin Liu
- Shenzhen Entry-exit Inspection and Quarantine Bureau, Shenzhen, 518045, People's Republic of China; Shenzhen Academy of Inspection and Quarantine Sciences, Shenzhen, 518045, People's Republic of China
| | - Xiaocong Zheng
- Shenzhen Entry-exit Inspection and Quarantine Bureau, Shenzhen, 518045, People's Republic of China; Shenzhen Academy of Inspection and Quarantine Sciences, Shenzhen, 518045, People's Republic of China
| | - Xiujie Shi
- Shenzhen Entry-exit Inspection and Quarantine Bureau, Shenzhen, 518045, People's Republic of China; Shenzhen Academy of Inspection and Quarantine Sciences, Shenzhen, 518045, People's Republic of China
| | - Junqiang He
- Shenzhen Entry-exit Inspection and Quarantine Bureau, Shenzhen, 518045, People's Republic of China; Shenzhen Academy of Inspection and Quarantine Sciences, Shenzhen, 518045, People's Republic of China
| | - Li Yu
- Shenzhen Entry-exit Inspection and Quarantine Bureau, Shenzhen, 518045, People's Republic of China; Shenzhen Academy of Inspection and Quarantine Sciences, Shenzhen, 518045, People's Republic of China
| | - Qunyi Hua
- Shenzhen Entry-exit Inspection and Quarantine Bureau, Shenzhen, 518045, People's Republic of China; Shenzhen Academy of Inspection and Quarantine Sciences, Shenzhen, 518045, People's Republic of China
| | - Tikang Lu
- Shenzhen Entry-exit Inspection and Quarantine Bureau, Shenzhen, 518045, People's Republic of China; Shenzhen Academy of Inspection and Quarantine Sciences, Shenzhen, 518045, People's Republic of China
| | - Wensheng Lan
- Shenzhen Entry-exit Inspection and Quarantine Bureau, Shenzhen, 518045, People's Republic of China; Shenzhen Academy of Inspection and Quarantine Sciences, Shenzhen, 518045, People's Republic of China
| | - James R Winton
- US Geological Survey, Western Fisheries Research Center, 6505 Northeast 65th Street, Seattle, WA 98115, USA
| | - Ningyi Jin
- Institute of Military Veterinary Medicine, Academy of Military Medical Sciences of PLA, Jilin, 130117, People's Republic of China
| | - Hong Liu
- Shenzhen Entry-exit Inspection and Quarantine Bureau, Shenzhen, 518045, People's Republic of China; Shenzhen Academy of Inspection and Quarantine Sciences, Shenzhen, 518045, People's Republic of China.
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Witte AK, Mester P, Fister S, Witte M, Schoder D, Rossmanith P. A Systematic Investigation of Parameters Influencing Droplet Rain in the Listeria monocytogenes prfA Assay - Reduction of Ambiguous Results in ddPCR. PLoS One 2016; 11:e0168179. [PMID: 27992475 PMCID: PMC5167268 DOI: 10.1371/journal.pone.0168179] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 11/25/2016] [Indexed: 11/18/2022] Open
Abstract
The droplet digital polymerase chain reaction (ddPCR) determines DNA amounts based upon the pattern of positive and negative droplets, according to Poisson distribution, without the use of external standards. However, division into positive and negative droplets is often not clear because a part of the droplets has intermediate fluorescence values, appearing as “rain” in the plot. Despite the droplet rain, absolute quantification with ddPCR is possible, as shown previously for the prfA assay in quantifying Listeria monocytogenes. Nevertheless, reducing the rain, and thus ambiguous results, promotes the accuracy and credibility of ddPCR. In this study, we extensively investigated chemical and physical parameters for optimizing the prfA assay for ddPCR. While differences in the concentration of all chemicals and the dye, quencher and supplier of the probe did not alter the droplet pattern, changes in the PCR cycling program, such as prolonged times and increased cycle numbers, improved the assay.
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Affiliation(s)
- Anna Kristina Witte
- Christian Doppler Laboratory for Monitoring of Microbial Contaminants, Institute of Milk Hygiene, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
| | - Patrick Mester
- Christian Doppler Laboratory for Monitoring of Microbial Contaminants, Institute of Milk Hygiene, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
| | - Susanne Fister
- Christian Doppler Laboratory for Monitoring of Microbial Contaminants, Institute of Milk Hygiene, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
| | - Matthias Witte
- Department of Psychology, University of Graz, Graz, Austria
| | - Dagmar Schoder
- Christian Doppler Laboratory for Monitoring of Microbial Contaminants, Institute of Milk Hygiene, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
- Institute of Milk Hygiene, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
| | - Peter Rossmanith
- Christian Doppler Laboratory for Monitoring of Microbial Contaminants, Institute of Milk Hygiene, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
- Institute of Milk Hygiene, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
- * E-mail:
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27
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Cavé L, Brothier E, Abrouk D, Bouda PS, Hien E, Nazaret S. Efficiency and sensitivity of the digital droplet PCR for the quantification of antibiotic resistance genes in soils and organic residues. Appl Microbiol Biotechnol 2016; 100:10597-10608. [DOI: 10.1007/s00253-016-7950-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 10/12/2016] [Accepted: 10/20/2016] [Indexed: 11/28/2022]
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28
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Devonshire AS, O'Sullivan DM, Honeyborne I, Jones G, Karczmarczyk M, Pavšič J, Gutteridge A, Milavec M, Mendoza P, Schimmel H, Van Heuverswyn F, Gorton R, Cirillo DM, Borroni E, Harris K, Barnard M, Heydenrych A, Ndusilo N, Wallis CL, Pillay K, Barry T, Reddington K, Richter E, Mozioğlu E, Akyürek S, Yalçınkaya B, Akgoz M, Žel J, Foy CA, McHugh TD, Huggett JF. The use of digital PCR to improve the application of quantitative molecular diagnostic methods for tuberculosis. BMC Infect Dis 2016; 16:366. [PMID: 27487852 PMCID: PMC4971652 DOI: 10.1186/s12879-016-1696-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 07/06/2016] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Real-time PCR (qPCR) based methods, such as the Xpert MTB/RIF, are increasingly being used to diagnose tuberculosis (TB). While qualitative methods are adequate for diagnosis, the therapeutic monitoring of TB patients requires quantitative methods currently performed using smear microscopy. The potential use of quantitative molecular measurements for therapeutic monitoring has been investigated but findings have been variable and inconclusive. The lack of an adequate reference method and reference materials is a barrier to understanding the source of such disagreement. Digital PCR (dPCR) offers the potential for an accurate method for quantification of specific DNA sequences in reference materials which can be used to evaluate quantitative molecular methods for TB treatment monitoring. METHODS To assess a novel approach for the development of quality assurance materials we used dPCR to quantify specific DNA sequences in a range of prototype reference materials and evaluated accuracy between different laboratories and instruments. The materials were then also used to evaluate the quantitative performance of qPCR and Xpert MTB/RIF in eight clinical testing laboratories. RESULTS dPCR was found to provide results in good agreement with the other methods tested and to be highly reproducible between laboratories without calibration even when using different instruments. When the reference materials were analysed with qPCR and Xpert MTB/RIF by clinical laboratories, all laboratories were able to correctly rank the reference materials according to concentration, however there was a marked difference in the measured magnitude. CONCLUSIONS TB is a disease where the quantification of the pathogen could lead to better patient management and qPCR methods offer the potential to rapidly perform such analysis. However, our findings suggest that when precisely characterised materials are used to evaluate qPCR methods, the measurement result variation is too high to determine whether molecular quantification of Mycobacterium tuberculosis would provide a clinically useful readout. The methods described in this study provide a means by which the technical performance of quantitative molecular methods can be evaluated independently of clinical variability to improve accuracy of measurement results. These will assist in ultimately increasing the likelihood that such approaches could be used to improve patient management of TB.
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Affiliation(s)
| | | | - Isobella Honeyborne
- Centre for Clinical Microbiology, Department of Infection, University College London, Royal Free Campus, London, UK
| | - Gerwyn Jones
- Molecular and Cell Biology, LGC, Queens Road, Teddington, TW11 0LY, UK
| | - Maria Karczmarczyk
- European Commission, Joint Research Centre (JRC), Institute for Reference Materials and Measurements (IRMM), Geel, Belgium
| | - Jernej Pavšič
- National Institute of Biology, Večna pot 111, 1000, Ljubljana, Slovenia
| | - Alice Gutteridge
- Molecular and Cell Biology, LGC, Queens Road, Teddington, TW11 0LY, UK
| | - Mojca Milavec
- National Institute of Biology, Večna pot 111, 1000, Ljubljana, Slovenia
| | - Pablo Mendoza
- Vircell S.L. Molecular Diagnostic Department, The Technology Park of Health Sciences, Granada, Spain
| | - Heinz Schimmel
- European Commission, Joint Research Centre (JRC), Institute for Reference Materials and Measurements (IRMM), Geel, Belgium
| | - Fran Van Heuverswyn
- European Commission, Joint Research Centre (JRC), Institute for Reference Materials and Measurements (IRMM), Geel, Belgium
| | - Rebecca Gorton
- Centre for Clinical Microbiology, Department of Infection, University College London, Royal Free Campus, London, UK
| | - Daniela Maria Cirillo
- TB Supranational Reference Laboratory, San Raffaele Scientific Institute, Milan, Italy
| | - Emanuele Borroni
- TB Supranational Reference Laboratory, San Raffaele Scientific Institute, Milan, Italy
| | - Kathryn Harris
- Microbiology, Virology and Infection Control, Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - Marinus Barnard
- Centre for Clinical Tuberculosis Research, TASK Applied Science, Cape Town, South Africa
- SA MRC Centre for TB Research, DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences - Stellenbosch University, Francie van Zijl Drive, Tygerberg 7505, PO Box 241, Cape Town, 8000, South Africa
| | - Anthenette Heydenrych
- Centre for Clinical Tuberculosis Research, TASK Applied Science, Cape Town, South Africa
- SA MRC Centre for TB Research, DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences - Stellenbosch University, Francie van Zijl Drive, Tygerberg 7505, PO Box 241, Cape Town, 8000, South Africa
| | | | - Carole L Wallis
- BARC-SA and Mycobacteriology Department, Lancet Laboratories, Johannesburg, South Africa
| | - Keshree Pillay
- BARC-SA and Mycobacteriology Department, Lancet Laboratories, Johannesburg, South Africa
| | - Thomas Barry
- Nucleic Acid Diagnostics Research Laboratory (NADRL), Microbiology, School of Natural Sciences, National University of Ireland, Galway, Ireland
| | - Kate Reddington
- Nucleic Acid Diagnostics Research Laboratory (NADRL), Microbiology, School of Natural Sciences, National University of Ireland, Galway, Ireland
| | - Elvira Richter
- Forschungszentrum Borstel, National Reference Centre for Mycobacteria, Borstel, D-23845, Germany
| | | | - Sema Akyürek
- UME, Ulusal Metroloji Enstitüsü, Gebze, Kocaeli, Turkey
| | | | - Muslum Akgoz
- UME, Ulusal Metroloji Enstitüsü, Gebze, Kocaeli, Turkey
| | - Jana Žel
- National Institute of Biology, Večna pot 111, 1000, Ljubljana, Slovenia
| | - Carole A Foy
- Molecular and Cell Biology, LGC, Queens Road, Teddington, TW11 0LY, UK
| | - Timothy D McHugh
- Centre for Clinical Microbiology, Department of Infection, University College London, Royal Free Campus, London, UK
| | - Jim F Huggett
- Molecular and Cell Biology, LGC, Queens Road, Teddington, TW11 0LY, UK.
- Centre for Clinical Microbiology, Department of Infection, University College London, Royal Free Campus, London, UK.
- School of Biosciences & Medicine, Faculty of Health & Medical Sciences, University of Surrey, Guildford, UK.
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Zhao Y, Xia Q, Yin Y, Wang Z. Comparison of Droplet Digital PCR and Quantitative PCR Assays for Quantitative Detection of Xanthomonas citri Subsp. citri. PLoS One 2016; 11:e0159004. [PMID: 27427975 PMCID: PMC4948846 DOI: 10.1371/journal.pone.0159004] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 06/24/2016] [Indexed: 11/19/2022] Open
Abstract
Droplet digital polymerase chain reaction (ddPCR) is a novel molecular biology technique providing absolute quantification of target nucleic acids without the need for an external calibrator. Despite its emerging applications in medical diagnosis, there are few reports of its use for the detection of plant pathogens. This work was designed to assess the diagnosis potential of the ddPCR for absolute quantitative detection of Xanthomonas citri subsp. citri, a quarantine plant pathogenic bacterium that causes citrus bacterial canker in susceptible Citrus species. We transferred an established quantitative PCR (qPCR) assay for citrus bacterial canker diagnosis directly to the ddPCR format and compared the performance of the two methods. The qPCR assay has a broader dynamic range compared to the ddPCR assay and the ddPCR assay has a significantly higher degree of sensitivity compared to the qPCR assay. The influence of PCR inhibitors can be reduced considerably in the ddPCR assay because the collection of end-point fluorescent signals and the counting of binomial events (positive or negative droplets) are associated with a Poisson algorithm. The ddPCR assay also shows lower coefficient of variation compared to the qPCR assay especially in low target concentration. The linear association of the measurements by ddPCR and qPCR assays is strong (Pearson correlation = 0.8633; P<0.001). Receiver operating characteristic analysis indicates the ddPCR methodology is a more robust approach for diagnosis of citrus bacterial canker. In summary, the results demonstrated that the ddPCR assay has the potential for the quantitative detection of X. citri subsp. citri with high precision and accuracy as compared with the results from qPCR assay. Further studies are required to evaluate and validate the value of ddPCR technology in the diagnosis of plant disease and quarantine applications.
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Affiliation(s)
- Yun Zhao
- School of Life Science, Chongqing University, Chongqing, 400030, China
| | - Qingyan Xia
- School of Life Science, Chongqing University, Chongqing, 400030, China
| | - Youping Yin
- School of Life Science, Chongqing University, Chongqing, 400030, China
| | - Zhongkang Wang
- School of Life Science, Chongqing University, Chongqing, 400030, China
- * E-mail:
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30
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Ushio R, Yamamoto M, Nakashima K, Watanabe H, Nagai K, Shibata Y, Tashiro K, Tsukahara T, Nagakura H, Horita N, Sato T, Shinkai M, Kudo M, Ueda A, Kaneko T. Digital PCR assay detection of circulating Mycobacterium tuberculosis DNA in pulmonary tuberculosis patient plasma. Tuberculosis (Edinb) 2016; 99:47-53. [PMID: 27450004 DOI: 10.1016/j.tube.2016.04.004] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Revised: 04/02/2016] [Accepted: 04/10/2016] [Indexed: 11/19/2022]
Abstract
Nucleic acid amplification tests are a major diagnostic tool for pulmonary tuberculosis (PTB). Recently, digital PCR (dPCR) assay has improved sensitivity for the detection of small copy numbers of target molecules. The aim of this study is to explore the utility of dPCR for detecting Mycobacterium tuberculosis (MTB) DNA in PTB patient plasma. Total DNA was purified from plasma samples of newly diagnosed sputum smear-positive PTB patients. Copy numbers of MTB-specific genes in the samples were quantified with dPCR assays targeted for IS6110 or gyrB. A total of 33 PTB patients were enrolled. Significant differences between PTB patients and controls were observed in copy numbers of both targets: IS6110 mean ± SD, 144.8 ± 538.3 vs 0.44 ± 0.49 (copies/20 μL, p = 0.004; Mann-Whitney U test) and gyrB mean ± SD, 359.0 ± 2116 vs 0.07 ± 0.28 (copies/20 μL, p = 0.011; Mann-Whitney U test), respectively. This test had sensitivities of 65% or 29% and a specificity of 93% or 100% with the IS6110-targeted or gyrB-targeted assays, respectively. A dPCR assay successfully detected MTB DNA in PTB patient plasma. This minimally invasive and accurate method has potential to become an alternative diagnostic option.
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Affiliation(s)
- Ryota Ushio
- Department of Pulmonology, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Masaki Yamamoto
- Department of Pulmonology, Yokohama City University Graduate School of Medicine, Yokohama, Japan.
| | - Kentaro Nakashima
- Department of Pulmonology, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Hiroki Watanabe
- Department of Pulmonology, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Kenjiro Nagai
- Department of Pulmonology, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Yuji Shibata
- Department of Pulmonology, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Ken Tashiro
- Department of Pulmonology, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Toshinori Tsukahara
- Department of Pulmonology, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Hideyuki Nagakura
- Department of Pulmonology, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Nobuyuki Horita
- Department of Pulmonology, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Takashi Sato
- Department of Pulmonology, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Masaharu Shinkai
- Respiratory Disease Center, Yokohama City University Medical Center, Yokohama, Japan
| | - Makoto Kudo
- Respiratory Disease Center, Yokohama City University Medical Center, Yokohama, Japan
| | - Atsuhisa Ueda
- Department of Internal Medicine and Clinical Immunology, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Takeshi Kaneko
- Department of Pulmonology, Yokohama City University Graduate School of Medicine, Yokohama, Japan
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31
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Accurate quantification of supercoiled DNA by digital PCR. Sci Rep 2016; 6:24230. [PMID: 27063649 PMCID: PMC4827127 DOI: 10.1038/srep24230] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 03/15/2016] [Indexed: 11/19/2022] Open
Abstract
Digital PCR (dPCR) as an enumeration-based quantification method is capable of quantifying the DNA copy number without the help of standards. However, it can generate false results when the PCR conditions are not optimized. A recent international comparison (CCQM P154) showed that most laboratories significantly underestimated the concentration of supercoiled plasmid DNA by dPCR. Mostly, supercoiled DNAs are linearized before dPCR to avoid such underestimations. The present study was conducted to overcome this problem. In the bilateral comparison, the National Institute of Metrology, China (NIM) optimized and applied dPCR for supercoiled DNA determination, whereas Korea Research Institute of Standards and Science (KRISS) prepared the unknown samples and quantified them by flow cytometry. In this study, several factors like selection of the PCR master mix, the fluorescent label, and the position of the primers were evaluated for quantifying supercoiled DNA by dPCR. This work confirmed that a 16S PCR master mix avoided poor amplification of the supercoiled DNA, whereas HEX labels on dPCR probe resulted in robust amplification curves. Optimizing the dPCR assay based on these two observations resulted in accurate quantification of supercoiled DNA without preanalytical linearization. This result was validated in close agreement (101~113%) with the result from flow cytometry.
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32
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Optimization of digital droplet polymerase chain reaction for quantification of genetically modified organisms. BIOMOLECULAR DETECTION AND QUANTIFICATION 2016; 7:9-20. [PMID: 27077048 PMCID: PMC4827695 DOI: 10.1016/j.bdq.2015.12.003] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Revised: 12/14/2015] [Accepted: 12/14/2015] [Indexed: 11/24/2022]
Abstract
Experience matrix condenses ddPCR performance parameters in graphical presentation. Assay separation value based on absolute fluorescence signal distance and variation. Separation value and experience matrix simplify choice of best assay parameters. Influence of oligonucleotide concentration and annealing/extension temperature.
Digital PCR in droplets (ddPCR) is an emerging method for more and more applications in DNA (and RNA) analysis. Special requirements when establishing ddPCR for analysis of genetically modified organisms (GMO) in a laboratory include the choice between validated official qPCR methods and the optimization of these assays for a ddPCR format. Differentiation between droplets with positive reaction and negative droplets, that is setting of an appropriate threshold, can be crucial for a correct measurement. This holds true in particular when independent transgene and plant-specific reference gene copy numbers have to be combined to determine the content of GM material in a sample. Droplets which show fluorescent units ranging between those of explicit positive and negative droplets are called ‘rain’. Signals of such droplets can hinder analysis and the correct setting of a threshold. In this manuscript, a computer-based algorithm has been carefully designed to evaluate assay performance and facilitate objective criteria for assay optimization. Optimized assays in return minimize the impact of rain on ddPCR analysis. We developed an Excel based ‘experience matrix’ that reflects the assay parameters of GMO ddPCR tests performed in our laboratory. Parameters considered include singleplex/duplex ddPCR, assay volume, thermal cycler, probe manufacturer, oligonucleotide concentration, annealing/elongation temperature, and a droplet separation evaluation. We additionally propose an objective droplet separation value which is based on both absolute fluorescence signal distance of positive and negative droplet populations and the variation within these droplet populations. The proposed performance classification in the experience matrix can be used for a rating of different assays for the same GMO target, thus enabling employment of the best suited assay parameters. Main optimization parameters include annealing/extension temperature and oligonucleotide concentrations. The droplet separation value allows for easy and reproducible assay performance evaluation. The combination of separation value with the experience matrix simplifies the choice of adequate assay parameters for a given GMO event.
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Key Words
- ABI, LifeTechnologies (formerly AppliedBiosystems)
- Bio, DNA Technology/Biosearch Technologies
- Cat. No., catalogue number
- DNA, deoxyribonucleic acid
- Droplet digital PCR (ddPCR)
- EC, European Commission
- ERM, Certified European Reference Material
- EU, European Union
- EURL-GMFF, European Reference Laboratory for GM Food and Feed
- Experience matrix
- Food/feed analysis
- GM, genetically modified
- GMO, genetically modified organism
- Genetically modified organism (GMO)
- HEX,H, hexachlorfluorescein
- L, liter
- Lec, lectin gene of soy
- MIQE, minimal information for publication of quantitative digital PCR experiments
- MRPL, minimum required performance limit
- MS, Microsoft
- MWG, Eurofins-MWG
- MeanSignal, mean fluorescence signal value
- PCR, polymerase chain reaction
- Quantification
- SD, standard deviation (of fluorescence signals)
- TAMRA,T, tetramethylrhodamin
- TIB, TIB Molbiol
- Tech, technician
- VBA, visual basic for applications
- VIC,V, fluorescent dye (LifeTechnologies)
- cp/cp, (gene) copy per (gene) copy
- dPCR, digital PCR
- ddPCR, droplet digital PCR
- fluorescein, FAM,F
- gDNA, genomic DNA
- qPCR, (quantitative) real-time PCR
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33
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Assessment of the real-time PCR and different digital PCR platforms for DNA quantification. Anal Bioanal Chem 2015; 408:107-21. [PMID: 26521179 PMCID: PMC4706846 DOI: 10.1007/s00216-015-9107-2] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Revised: 10/02/2015] [Accepted: 10/08/2015] [Indexed: 12/31/2022]
Abstract
Digital PCR (dPCR) is beginning to supersede real-time PCR (qPCR) for quantification of nucleic acids in many different applications. Several analytical properties of the two most commonly used dPCR platforms, namely the QX100 system (Bio-Rad) and the 12.765 array of the Biomark system (Fluidigm), have already been evaluated and compared with those of qPCR. However, to the best of our knowledge, direct comparison between the three of these platforms using the same DNA material has not been done, and the 37 K array on the Biomark system has also not been evaluated in terms of linearity, analytical sensitivity and limit of quantification. Here, a first assessment of qPCR, the QX100 system and both arrays of the Biomark system was performed with plasmid and genomic DNA from human cytomegalovirus. With use of PCR components that alter the efficiency of qPCR, each dPCR platform demonstrated consistent copy-number estimations, which indicates the high resilience of dPCR. Two approaches, one considering the total reaction volume and the other considering the effective reaction size, were used to assess linearity, analytical sensitivity and variability. When the total reaction volume was considered, the best performance was observed with qPCR, followed by the QX100 system and the Biomark system. In contrast, when the effective reaction size was considered, all three platforms showed almost equal limits of detection and variability. Although dPCR might not always be more appropriate than qPCR for quantification of low copy numbers, dPCR is a suitable method for robust and reproducible quantification of viral DNA, and a promising technology for the higher-order reference measurement method.
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Comparison of four digital PCR platforms for accurate quantification of DNA copy number of a certified plasmid DNA reference material. Sci Rep 2015; 5:13174. [PMID: 26302947 PMCID: PMC4548226 DOI: 10.1038/srep13174] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 07/06/2015] [Indexed: 11/15/2022] Open
Abstract
Digital polymerase chain reaction (dPCR) is a unique approach to measurement of the absolute copy number of target DNA without using external standards. However, the comparability of different dPCR platforms with respect to measurement of DNA copy number must be addressed before dPCR can be classified fundamentally as an absolute quantification technique. The comparability of four dPCR platforms with respect to accuracy and measurement uncertainty was investigated by using a certified plasmid reference material. Plasmid conformation was found to have a significant effect on droplet-based dPCR (QX100 and RainDrop) not shared with chip-based QuantStudio 12k or BioMark. The relative uncertainty of partition volume was determined to be 0.7%, 0.8%, 2.3% and 2.9% for BioMark, QX100, QuantStudio 12k and RainDrop, respectively. The measurements of the certified pNIM-001 plasmid made using the four dPCR platforms were corrected for partition volume and closely consistent with the certified value within the expended uncertainty. This demonstrated that the four dPCR platforms are of comparable effectiveness in quantifying DNA copy number. These findings provide an independent assessment of this method of determining DNA copy number when using different dPCR platforms and underline important factors that should be taken into consideration in the design of dPCR experiments.
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35
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Shibayama S, Sakamaki H, Yamazaki T, Takatsu A. Metal free columns for determination of deoxynucleotide monophosphate by liquid chromatography/mass spectrometry and application to oligonucleotide. J Chromatogr A 2015; 1406:210-4. [PMID: 26141274 DOI: 10.1016/j.chroma.2015.06.033] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 06/10/2015] [Accepted: 06/14/2015] [Indexed: 02/06/2023]
Abstract
We have developed a highly sensitive method for the analysis of deoxynucleotide monophosphates (dNMPs), which involves the use of liquid chromatography/mass spectrometry (LC/MS) and a new metal-free column. The new column solves the problem that the phosphate group in dNMPs interacts with the metal portion of the device or column. After optimization of the analytical conditions, the limits of detection (LODs) of dNMPs were from 5.4ng/g to 6.3ng/g. Those values were 10 times lower than the LODs of previous methods. We applied the method to the determination of the base composition and the quantification of 20-mer oligonucleotide. Despite use of a very small sample amount of 14.5ng, we were able to determine the base composition, and the result was consistent with theoretical values. We were also able to quantify the mass fraction of oligonucleotide with 8.2% expanded uncertainty (k=2). By means of the developed method, we were able to analyze dNMPs with high sensitivity as well as determine the base composition and quantify the mass fraction of oligonucleotide despite use of a small amount of sample.
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Affiliation(s)
- Sachie Shibayama
- National Metrology Institute of Japan (NMIJ), National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono, Tsukuba, Ibaraki 305-8563, Japan.
| | - Hiroshi Sakamaki
- Chemicals Evaluation and Research Institute, 1600 Shimotakano, Sugito, Kitakatsushika, Saitama 345-0043, Japan
| | - Taichi Yamazaki
- National Metrology Institute of Japan (NMIJ), National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono, Tsukuba, Ibaraki 305-8563, Japan
| | - Akiko Takatsu
- National Metrology Institute of Japan (NMIJ), National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono, Tsukuba, Ibaraki 305-8563, Japan
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36
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Devonshire AS, Honeyborne I, Gutteridge A, Whale AS, Nixon G, Wilson P, Jones G, McHugh TD, Foy CA, Huggett JF. Highly Reproducible Absolute Quantification of Mycobacterium tuberculosis Complex by Digital PCR. Anal Chem 2015; 87:3706-13. [DOI: 10.1021/ac5041617] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Alison S. Devonshire
- Molecular
and Cell Biology Team, LGC, Teddington, Middlesex TW11 0LY, United Kingdom
| | - Isobella Honeyborne
- Centre
for Clinical Microbiology, Department of Infection, Royal Free Campus, University College London, London NW3 2PF, United Kingdom
| | - Alice Gutteridge
- Molecular
and Cell Biology Team, LGC, Teddington, Middlesex TW11 0LY, United Kingdom
| | - Alexandra S. Whale
- Molecular
and Cell Biology Team, LGC, Teddington, Middlesex TW11 0LY, United Kingdom
| | - Gavin Nixon
- Molecular
and Cell Biology Team, LGC, Teddington, Middlesex TW11 0LY, United Kingdom
| | - Philip Wilson
- Statistics
Team, LGC, Teddington, Middlesex TW11 0LY, United Kingdom
| | - Gerwyn Jones
- Molecular
and Cell Biology Team, LGC, Teddington, Middlesex TW11 0LY, United Kingdom
| | - Timothy D. McHugh
- Centre
for Clinical Microbiology, Department of Infection, Royal Free Campus, University College London, London NW3 2PF, United Kingdom
| | - Carole A. Foy
- Molecular
and Cell Biology Team, LGC, Teddington, Middlesex TW11 0LY, United Kingdom
| | - Jim F. Huggett
- Molecular
and Cell Biology Team, LGC, Teddington, Middlesex TW11 0LY, United Kingdom
- Centre
for Clinical Microbiology, Department of Infection, Royal Free Campus, University College London, London NW3 2PF, United Kingdom
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37
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DNA copy number concentration measured by digital and droplet digital quantitative PCR using certified reference materials. Anal Bioanal Chem 2015; 407:1831-40. [PMID: 25600685 PMCID: PMC4336415 DOI: 10.1007/s00216-015-8458-z] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Revised: 12/19/2014] [Accepted: 01/05/2015] [Indexed: 01/31/2023]
Abstract
The value assignment for properties of six certified reference materials (ERM-AD623a–f), each containing a plasmid DNA solution ranging from 1 million to 10 copies per μL, by using digital PCR (dPCR) with the BioMark™ HD System (Fluidigm) has been verified by applying droplet digital PCR (ddPCR) using the QX100 system (Bio-Rad). One of the critical factors in the measurement of copy number concentrations by digital PCR is the partition volume. Therefore, we determined the average droplet volume by optical microscopy, revealing an average droplet volume that is 8 % smaller than the droplet volume used as the defined parameter in the QuantaSoft software version 1.3.2.0 (Bio-Rad) to calculate the copy number concentration. This observation explains why copy number concentrations estimated with ddPCR and using an average droplet volume predefined in the QuantaSoft software were systematically lower than those measured by dPCR, creating a significant bias between the values obtained by these two techniques. The difference was not significant anymore when the measured droplet volume of 0.834 nL was used to estimate copy number concentrations. A new version of QuantaSoft software (version 1.6.6.0320), which has since been released with Bio-Rad’s new QX200 systems and QX100 upgrades, uses a droplet volume of 0.85 nL as a defined parameter to calculate copy number concentration. Monolayer of droplets generated by the droplet generator and observed under an optical microscope ![]()
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38
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Yang R, Paparini A, Monis P, Ryan U. Comparison of next-generation droplet digital PCR (ddPCR) with quantitative PCR (qPCR) for enumeration of Cryptosporidium oocysts in faecal samples. Int J Parasitol 2014; 44:1105-13. [PMID: 25229177 DOI: 10.1016/j.ijpara.2014.08.004] [Citation(s) in RCA: 123] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Revised: 08/20/2014] [Accepted: 08/21/2014] [Indexed: 02/08/2023]
Abstract
Clinical microbiology laboratories rely on quantitative PCR for its speed, sensitivity, specificity and ease-of-use. However, quantitative PCR quantitation requires the use of a standard curve or normalisation to reference genes. Droplet digital PCR provides absolute quantitation without the need for calibration curves. A comparison between droplet digital PCR and quantitative PCR-based analyses was conducted for the enteric parasite Cryptosporidium, which is an important cause of gastritis in both humans and animals. Two loci were analysed (18S rRNA and actin) using a range of Cryptosporidium DNA templates, including recombinant plasmids, purified haemocytometer-counted oocysts, commercial flow cytometry-counted oocysts and faecal DNA samples from sheep, cattle and humans. Each method was evaluated for linearity, precision, limit of detection and cost. Across the same range of detection, both methods showed a high degree of linearity and positive correlation for standards (R(2)⩾0.999) and faecal samples (R(2)⩾0.9750). The precision of droplet digital PCR, as measured by mean Relative Standard Deviation (RSD;%), was consistently better compared with quantitative PCR, particularly for the 18S rRNA locus, but was poorer as DNA concentration decreased. The quantitative detection of quantitative PCR was unaffected by DNA concentration, but droplet digital PCR quantitative PCR was less affected by the presence of inhibitors, compared with quantitative PCR. For most templates analysed including Cryptosporidium-positive faecal DNA, the template copy numbers, as determined by droplet digital PCR, were consistently lower than by quantitative PCR. However, the quantitations obtained by quantitative PCR are dependent on the accuracy of the standard curve and when the quantitative PCR data were corrected for pipetting and DNA losses (as determined by droplet digital PCR), then the sensitivity of both methods was comparable. A cost analysis based on 96 samples revealed that the overall cost (consumables and labour) of droplet digital PCR was two times higher than quantitative PCR. Using droplet digital PCR to precisely quantify standard dilutions used for high-throughput and cost-effective amplifications by quantitative PCR would be one way to combine the advantages of the two technologies.
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Affiliation(s)
- Rongchang Yang
- School of Veterinary and Life Sciences, Vector- and Water-Borne Pathogen Research Group, Murdoch University, Murdoch, Western Australia 6150, Australia
| | - Andrea Paparini
- School of Veterinary and Life Sciences, Vector- and Water-Borne Pathogen Research Group, Murdoch University, Murdoch, Western Australia 6150, Australia
| | - Paul Monis
- Australian Water Quality Centre, South Australian Water Corporation, 250 Victoria Square, Adelaide, SA 5000, Australia
| | - Una Ryan
- School of Veterinary and Life Sciences, Vector- and Water-Borne Pathogen Research Group, Murdoch University, Murdoch, Western Australia 6150, Australia.
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39
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Jahn M, Vorpahl C, Türkowsky D, Lindmeyer M, Bühler B, Harms H, Müller S. Accurate Determination of Plasmid Copy Number of Flow-Sorted Cells using Droplet Digital PCR. Anal Chem 2014; 86:5969-76. [DOI: 10.1021/ac501118v] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Michael Jahn
- Helmholtz-Centre
for Environmental Research − UFZ, Permoserstr. 15, 04318 Leipzig, Germany
| | - Carsten Vorpahl
- Helmholtz-Centre
for Environmental Research − UFZ, Permoserstr. 15, 04318 Leipzig, Germany
| | - Dominique Türkowsky
- Helmholtz-Centre
for Environmental Research − UFZ, Permoserstr. 15, 04318 Leipzig, Germany
| | - Martin Lindmeyer
- Laboratory
of Chemical Biotechnology, Department of Biochemical and Chemical
Engineering, TU Dortmund University, Emil-Figge-Str. 66, 44227 Dortmund, Germany
| | - Bruno Bühler
- Laboratory
of Chemical Biotechnology, Department of Biochemical and Chemical
Engineering, TU Dortmund University, Emil-Figge-Str. 66, 44227 Dortmund, Germany
| | - Hauke Harms
- Helmholtz-Centre
for Environmental Research − UFZ, Permoserstr. 15, 04318 Leipzig, Germany
| | - Susann Müller
- Helmholtz-Centre
for Environmental Research − UFZ, Permoserstr. 15, 04318 Leipzig, Germany
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