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Shahrajabian MH, Sun W. The Significance and Importance of dPCR, qPCR, and SYBR Green PCR Kit in the Detection of Numerous Diseases. Curr Pharm Des 2024; 30:169-179. [PMID: 38243947 DOI: 10.2174/0113816128276560231218090436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 10/27/2023] [Accepted: 11/07/2023] [Indexed: 01/22/2024]
Abstract
Digital PCR (dPCR) is the latest technique that has become commercially accessible for various types of research. This method uses Taq polymerase in a standard polymerase chain reaction (PCR) to amplify a target DNA fragment from a complex sample, like quantitative PCR (qPCR) and droplet digital PCR (dd- PCR). ddPCR may facilitate microRNA (miRNA) measurement, particularly in liquid biopsy, because it has been proven to be more effective and sensitive, and in this method, ddPCR can provide an unprecedented chance for deoxyribonucleic acid (DNA) methylation research because of its capability to increase sensitivity and precision over conventional PCR-based methods. qPCR has also been found to be a valuable standard technique to measure both copy DNA (cDNA) and genomic DNA (gDNA) levels, although the finding data can be significantly variable and non-reproducible without relevant validation and verification of both primers and samples. The SYBR green quantitative real-time PCR (qPCR) method has been reported as an appropriate technique for quantitative detection and species discrimination, and has been applied profitably in different experiments to determine, quantify, and discriminate species. Although both TaqMan qRT-PCR and SYBR green qRT-PCR are sensitive and rapid, the SYBR green qRT-PCR assay is easy and the TaqMan qRT-PCR assay is specific but expensive due to the probe required. This review aimed to introduce dPCR, qPCR, SYBR green PCR kit, and digital PCR, compare them, and also introduce their advantages in the detection of different diseases.
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Affiliation(s)
- Mohamad Hesam Shahrajabian
- National Key Laboratory of Agricultural Microbiology, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100086, China
| | - Wenli Sun
- National Key Laboratory of Agricultural Microbiology, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100086, China
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2
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Russo S, Cortimiglia C, Filippi A, Palladini G, Garbarino C, Massella E, Ricchi M. Validation of digital PCR assay for the quantification of Mycobacterium avium subsp. paratuberculosis in bovine faeces according to the ISO 20395:2019. J Microbiol Methods 2023; 213:106825. [PMID: 37739126 DOI: 10.1016/j.mimet.2023.106825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 09/18/2023] [Accepted: 09/19/2023] [Indexed: 09/24/2023]
Abstract
Paratuberculosis is an enteric disease caused by Mycobacterium avium subs. Paratuberculosis (MAP). Quantifying the load of MAP in faeces samples offers the advantage of determining the stage of infection and planning control measures. Currently, detection of MAP in faecal specimens relies on cultural assays and quantitative PCR (qPCR), but both methods have limitations such as prolonged isolation times for cultural assay and the absence of nucleic acid standards for qPCR. Digital PCR (dPCR) represents an advancement over qPCR as it allows direct quantification of nucleic acid in a sample without the need for a standard curve. The present paper reports about the validation process, following ISO 20395:2019 guidelines, of a F57 digital PCR assay for quantifying MAP cells in faecal samples. Based on our validation, the Limit Of Detection (LOD) corresponds to 7.85 104 MAP cells/g, and the Limit Of Quantification (LOQ) to 7.85 105 MAP cells, with an efficiency of recovery at LOQ estimated about 4.5%. To assess precision, we evaluated the same faecal sample extracted by two different operators at different times. The standard deviation under repeatability conditions (S Repeatability) and intersession variability conditions (S Intermediate) were calculated, resulting in values of 0.43 and 0.26, respectively. Trueness was determined at LOQ and a value ten times higher, yielding percentages of 3.35% and 5.16%, respectively. Linearity showed a R2 value of 0.998, indicating strong linear correlation. Measurement uncertainty was 26% in absolute value and 3% on a logarithmic base 10 scale. Overall, the assay exhibits good specificity and robustness. Our validation underlines the good performance of the quantification method and allow the laboratory to provide quantitative results of MAP/cells on faecal samples.
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Affiliation(s)
- Simone Russo
- National Reference Centre and WOAH Reference Laboratory for Paratuberculosis, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna "Bruno Ubertini", Piacenza, Italy..
| | - Claudia Cortimiglia
- Dipartimento di Scienze e Tecnologie Alimentari per una Filiera Agro-Alimentare Sostenibile (DISTAS), Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Anita Filippi
- National Reference Centre and WOAH Reference Laboratory for Paratuberculosis, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna "Bruno Ubertini", Piacenza, Italy
| | - Giorgia Palladini
- National Reference Centre and WOAH Reference Laboratory for Paratuberculosis, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna "Bruno Ubertini", Piacenza, Italy..
| | - Chiara Garbarino
- National Reference Centre and WOAH Reference Laboratory for Paratuberculosis, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna "Bruno Ubertini", Piacenza, Italy..
| | - Elisa Massella
- National Reference Centre and WOAH Reference Laboratory for Paratuberculosis, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna "Bruno Ubertini", Piacenza, Italy..
| | - Matteo Ricchi
- National Reference Centre and WOAH Reference Laboratory for Paratuberculosis, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna "Bruno Ubertini", Piacenza, Italy..
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3
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Nuraeni U, Malau J, Astuti RT, Dewantoro A, Apriori D, Lusiana ED, Prasetya B. Droplet digital PCR versus real-time PCR for in-house validation of porcine detection and quantification protocol: An artificial recombinant plasmid approach. PLoS One 2023; 18:e0287712. [PMID: 37450440 PMCID: PMC10348585 DOI: 10.1371/journal.pone.0287712] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 06/09/2023] [Indexed: 07/18/2023] Open
Abstract
Authenticity and traceability are essential for modern food and medicine inspection, and reliable techniques are important for the trade of halal foods, which reach more than 20 percent of the world market. A sensitive and accurate porcine detection method is required to develop a conformity assessment system that includes laboratory testing for porcine-free certification. This study proposes a procedure that could be incorporated into the development of a standardized control and protocol for real-time PCR (qPCR) methods and their traceability using droplet digital PCR (ddPCR). The design used a recombinant pUC57 plasmid as an amplification target to carry the 97 bp fragment of the porcine ATCB gene. The absolute quantification and linearity assessment showed high precision with R2 values of 0.9971 and 0.9998 for qPCR and ddPCR, respectively. In general, both methods showed comparable results in terms of linearity and detection limit. However, both limit of detection assessments showed high sensitivity, although ddPCR showed a slightly higher sensitivity than that of qPCR, especially at low DNA concentrations. Multiple-sample and inter-participatory testing evaluations revealed a high sensitivity, broad applicability, and robustness of the qPCR method. Therefore, we conclude that based on a recombinant plasmid analysis with a low quantity (less than five copy number), the digital PCR method produced more reliable results. These results could provide scientific information for regulatory authorities, especially those in Indonesia, to consider the development and formulation of a well-established qPCR protocol for porcine detection using expected DNA concentrations.
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Affiliation(s)
- Umi Nuraeni
- Laboratory of National Measurement Standards of Biology, The National Standard Agency of Indonesia (BSN), South Tangerang, Banten, Indonesia
| | - Jekmal Malau
- Department of Pharmacy, Faculty of Health Science, Universitas Singaperbangsa Karawang, West Java, Indonesia
| | - Retno Tri Astuti
- Department of Fisheries Product Technology, Faculty of Fisheries and Marine Science, Universitas Brawijaya, East Java, Indonesia
| | - Auraga Dewantoro
- Research Center for Genetic Engineering, The National Research and Innovation Agency of Indonesia (BRIN), Bogor, Indonesia
| | - Dini Apriori
- Laboratory of National Measurement Standards of Biology, The National Standard Agency of Indonesia (BSN), South Tangerang, Banten, Indonesia
| | - Evellin Dewi Lusiana
- Department of Aquatic Resource Management, Faculty of Fisheries and Marine Science, Universitas Brawijaya, East Java, Indonesia
| | - Bambang Prasetya
- Research Center for Testing Technology and Standards, The National Research and Innovation Agency of Indonesia (BRIN), South Tangerang, Indonesia
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4
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Flütsch S, Wiestner F, Butticaz L, Moor D, Stölting KN. Vibrio-Sequins - dPCR-traceable DNA standards for quantitative genomics of Vibrio spp. BMC Genomics 2023; 24:375. [PMID: 37403035 DOI: 10.1186/s12864-023-09429-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 06/05/2023] [Indexed: 07/06/2023] Open
Abstract
BACKGROUND Vibrio spp. are a diverse group of ecologically important marine bacteria responsible for several foodborne outbreaks of gastroenteritis around the world. Their detection and characterization are moving away from conventional culture-based methods towards next generation sequencing (NGS)-based approaches. However, genomic methods are relative in nature and suffer from technical biases arising from library preparation and sequencing. Here, we introduce a quantitative NGS-based method that enables the quantitation of Vibrio spp. at the limit of quantification (LOQ) through artificial DNA standards and their absolute quantification via digital PCR (dPCR). RESULTS We developed six DNA standards, called Vibrio-Sequins, together with optimized TaqMan assays for their quantification in individually sequenced DNA libraries via dPCR. To enable Vibrio-Sequin quantification, we validated three duplex dPCR methods to quantify the six targets. LOQs were ranging from 20 to 120 cp/µl for the six standards, whereas the limit of detection (LOD) was ~ 10 cp/µl for all six assays. Subsequently, a quantitative genomics approach was applied to quantify Vibrio-DNA in a pooled DNA mixture derived from several Vibrio species in a proof-of-concept study, demonstrating the increased power of our quantitative genomic pipeline through the coupling of NGS and dPCR. CONCLUSIONS We significantly advance existing quantitative (meta)genomic methods by ensuring metrological traceability of NGS-based DNA quantification. Our method represents a useful tool for future metagenomic studies aiming at quantifying microbial DNA in an absolute manner. The inclusion of dPCR into sequencing-based methods supports the development of statistical approaches for the estimation of measurement uncertainties (MU) for NGS, which is still in its infancy.
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Affiliation(s)
- Sabrina Flütsch
- Swiss Federal Institute of Metrology METAS, Lindenweg 50, Bern-Wabern, 3003, Switzerland.
- Swiss Federal Institute of Metrology METAS, Campus Liebefeld, Schwarzenburgstrasse 165, Bern-Köniz, 3097, Switzerland.
| | - Fabian Wiestner
- Swiss Federal Institute of Metrology METAS, Lindenweg 50, Bern-Wabern, 3003, Switzerland
- Swiss Federal Institute of Metrology METAS, Campus Liebefeld, Schwarzenburgstrasse 165, Bern-Köniz, 3097, Switzerland
| | - Lisa Butticaz
- Federal Food Safety and Veterinary Office FSVO, Schwarzenburgstrasse 165, Bern-Köniz, 3003, Switzerland
- Swiss Federal Institute of Metrology METAS, Campus Liebefeld, Schwarzenburgstrasse 165, Bern-Köniz, 3097, Switzerland
| | - Dominik Moor
- Federal Food Safety and Veterinary Office FSVO, Schwarzenburgstrasse 165, Bern-Köniz, 3003, Switzerland
- Swiss Federal Institute of Metrology METAS, Campus Liebefeld, Schwarzenburgstrasse 165, Bern-Köniz, 3097, Switzerland
| | - Kai N Stölting
- Swiss Federal Institute of Metrology METAS, Lindenweg 50, Bern-Wabern, 3003, Switzerland.
- Swiss Federal Institute of Metrology METAS, Campus Liebefeld, Schwarzenburgstrasse 165, Bern-Köniz, 3097, Switzerland.
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Aravind Kumar N, Vishnuraj MR, Vaithiyanathan S, Srinivas C, Chauhan A, Barbuddhe SB. Droplet Digital PCR Assay with Linear Regression Models for Quantification of Buffalo-Derived Materials in Different Food Matrices. FOOD ANAL METHOD 2023. [DOI: 10.1007/s12161-022-02441-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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Development and validation of methods that enable high-quality droplet digital PCR and hematological profiling data from microvolume blood samples. Bioanalysis 2022; 14:1197-1211. [PMID: 36331037 DOI: 10.4155/bio-2022-0162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Aim: Mouse models have been crucial to preclinical studies in the increasingly relevant fields of cell and gene therapy. However, only small quantities of mouse blood can be collected without producing adverse physiological effects that compromise data integrity. Results: To address this limitation, two combined methods were developed to create detailed droplet digital PCR (ddPCR) and hematological profiles using only ∼20 μl of mouse blood. The validation of these methods, which can serve as a foundation for a standardized regulatory pipeline for ddPCR, is discussed. Even when using small amounts of input, this ddPCR protocol is accurate, precise, selective, specific, stable and robust. Conclusion: These techniques enable more frequent sample collection for higher-resolution pharmacokinetic data that meets or exceeds quality standards.
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Strati A, Zavridou M, Paraskevis D, Magiorkinis G, Sapounas S, Lagiou P, Thomaidis NS, Lianidou ES. Development and Analytical Validation of a One-Step Five-Plex RT-ddPCR Assay for the Quantification of SARS-CoV-2 Transcripts in Clinical Samples. Anal Chem 2022; 94:12314-12322. [PMID: 35960711 PMCID: PMC9397566 DOI: 10.1021/acs.analchem.2c00868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 08/01/2022] [Indexed: 11/28/2022]
Abstract
Highly sensitive methodologies for SARS-CoV-2 detection are essential for the control of COVID-19 pandemic. We developed and analytically validated a highly sensitive and specific five-plex one-step RT-ddPCR assay for SARS-CoV-2. We first designed in-silico novel primers and probes for the simultaneous absolute quantification of three different regions of the nucleoprotein (N) gene of SARS-CoV-2 (N1, N2, N3), a synthetic RNA as an external control (RNA-EC), and Beta-2-Microglobulin (B2M) as an endogenous RNA internal control (RNA-IC). The developed assay was analytically validated using synthetic DNA and RNA calibrator standards and then was applied to 100 clinical specimens previously analyzed with a commercially available CE-IVD RT-qPCR assay. The analytical validation of the developed assay resulted in very good performance characteristics in terms of analytical sensitivity, linearity, analytical specificity, and reproducibility and recovery rates even at very low viral concentrations. The simultaneous absolute quantification of the RNA-EC and RNA-IC provides the necessary metrics for quality control assessment. Direct comparison of the developed one-step five-plex RT-ddPCR assay with a CE-IVD RT-qPCR kit revealed a very high concordance and a higher sensitivity [concordance: 99/100 (99.0%, Spearman's correlation coefficient: -0.850, p < 0.001)]. The developed assay is highly sensitive, specific, and reproducible and has a broad linear dynamic range, providing absolute quantification of SARS-COV-2 transcripts. The inclusion of two RNA quality controls, an external and an internal, is highly important for standardization of SARS-COV-2 molecular testing in clinical and wastewater samples.
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Affiliation(s)
- Areti Strati
- Lab of Analytical Chemistry, Department of Chemistry,
National and Kapodistrian University of Athens, 15771 Athens,
Greece
| | - Martha Zavridou
- Lab of Analytical Chemistry, Department of Chemistry,
National and Kapodistrian University of Athens, 15771 Athens,
Greece
| | - Dimitrios Paraskevis
- Department of Hygiene, Epidemiology and Medical
Statistics, Medical School, National and Kapodistrian University of
Athens, 11527 Athens, Greece
| | - Gkikas Magiorkinis
- Department of Hygiene, Epidemiology and Medical
Statistics, Medical School, National and Kapodistrian University of
Athens, 11527 Athens, Greece
| | | | - Pagona Lagiou
- Department of Hygiene, Epidemiology and Medical
Statistics, Medical School, National and Kapodistrian University of
Athens, 11527 Athens, Greece
| | - Nikolaos S. Thomaidis
- Lab of Analytical Chemistry, Department of Chemistry,
National and Kapodistrian University of Athens, 15771 Athens,
Greece
| | - Evi S. Lianidou
- Lab of Analytical Chemistry, Department of Chemistry,
National and Kapodistrian University of Athens, 15771 Athens,
Greece
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Tanvetthayanont P, Yata T, Boonnil J, Temisak S, Ponglowhapan S. Validation of droplet digital PCR for cytokeratin 19 mRNA detection in canine peripheral blood and mammary gland. Sci Rep 2022; 12:13623. [PMID: 35948591 PMCID: PMC9365843 DOI: 10.1038/s41598-022-17493-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 07/26/2022] [Indexed: 11/09/2022] Open
Abstract
In humans, peripheral blood cytokeratin 19 (CK19) mRNA-positive circulating tumor cells (CTCs) was utilized to identify early-stage breast cancer patients with micrometastatic disease who are at risk for disease progression and monitor treatment response in patients with advanced disease. To our knowledge, there has been little research regarding CK19 in canine mammary tumors (CMTs) using molecular methods. A droplet digital PCR (ddPCR) is proposed as a precise and sensitive quantification of nucleic acid targets. Hence, this study aimed to validate a newly designed assay for CK19 detection in canine blood and mammary tissue, along with the reference gene HPRT, by ddPCR. All primers and probes showed a precise match with the exon region of target genes. The assay exhibited PCR efficacy of 90.4% and 91.0% for CK19 and HPRT amplifications with linearity, respectively. The annealing temperature (Ta) for duplex ddPCR was 55 °C, providing the highest concentrations of both genes tested by the synthetic plasmid DNA. The limit of detection (LOD) of CK19 and HPRT were 2.16 ± 1.27 and 2.44 ± 1.31 copies/µL, respectively. Finally, the ddPCR assay was validated with canine peripheral blood, non-neoplastic mammary tissues and spiked samples. Our findings provide a new platform for CK19 studies in CMT diagnosis through blood and mammary tissues.
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Affiliation(s)
- Potsawat Tanvetthayanont
- Department of Obstetrics Gynaecology and Reproduction, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Teerapong Yata
- Unit of Biochemistry, Department of Physiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Jiranun Boonnil
- National Institute of Metrology (NIMT), Pathumthani, 12120, Thailand
| | - Sasithon Temisak
- National Institute of Metrology (NIMT), Pathumthani, 12120, Thailand.
| | - Suppawiwat Ponglowhapan
- Department of Obstetrics Gynaecology and Reproduction, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand.
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Dobre EG, Constantin C, Neagu M. Skin Cancer Research Goes Digital: Looking for Biomarkers within the Droplets. J Pers Med 2022; 12:jpm12071136. [PMID: 35887633 PMCID: PMC9323323 DOI: 10.3390/jpm12071136] [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: 06/02/2022] [Revised: 07/12/2022] [Accepted: 07/12/2022] [Indexed: 12/24/2022] Open
Abstract
Skin cancer, which includes the most frequent malignant non-melanoma carcinomas (basal cell carcinoma, BCC, and squamous cell carcinoma, SCC), along with the difficult to treat cutaneous melanoma (CM), pose important worldwide issues for the health care system. Despite the improved anti-cancer armamentarium and the latest scientific achievements, many skin cancer patients fail to respond to therapies, due to the remarkable heterogeneity of cutaneous tumors, calling for even more sophisticated biomarker discovery and patient monitoring approaches. Droplet digital polymerase chain reaction (ddPCR), a robust method for detecting and quantifying low-abundance nucleic acids, has recently emerged as a powerful technology for skin cancer analysis in tissue and liquid biopsies (LBs). The ddPCR method, being capable of analyzing various biological samples, has proved to be efficient in studying variations in gene sequences, including copy number variations (CNVs) and point mutations, DNA methylation, circulatory miRNome, and transcriptome dynamics. Moreover, ddPCR can be designed as a dynamic platform for individualized cancer detection and monitoring therapy efficacy. Here, we present the latest scientific studies applying ddPCR in dermato-oncology, highlighting the potential of this technology for skin cancer biomarker discovery and validation in the context of personalized medicine. The benefits and challenges associated with ddPCR implementation in the clinical setting, mainly when analyzing LBs, are also discussed.
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Affiliation(s)
- Elena-Georgiana Dobre
- Faculty of Biology, University of Bucharest, Splaiul Independentei 91–95, 050095 Bucharest, Romania;
- Correspondence:
| | - Carolina Constantin
- Immunology Department, “Victor Babes” National Institute of Pathology, 050096 Bucharest, Romania;
- Pathology Department, Colentina Clinical Hospital, 020125 Bucharest, Romania
| | - Monica Neagu
- Faculty of Biology, University of Bucharest, Splaiul Independentei 91–95, 050095 Bucharest, Romania;
- Immunology Department, “Victor Babes” National Institute of Pathology, 050096 Bucharest, Romania;
- Pathology Department, Colentina Clinical Hospital, 020125 Bucharest, Romania
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Generation of TRIM28 Knockout K562 Cells by CRISPR/Cas9 Genome Editing and Characterization of TRIM28-Regulated Gene Expression in Cell Proliferation and Hemoglobin Beta Subunits. Int J Mol Sci 2022; 23:ijms23126839. [PMID: 35743282 PMCID: PMC9224613 DOI: 10.3390/ijms23126839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 06/14/2022] [Accepted: 06/16/2022] [Indexed: 12/10/2022] Open
Abstract
TRIM28 is a scaffold protein that interacts with DNA-binding proteins and recruits corepressor complexes to cause gene silencing. TRIM28 contributes to physiological functions such as cell growth and differentiation. In the chronic myeloid leukemia cell line K562, we edited TRIM28 using CRISPR/Cas9 technology, and the complete and partial knockout (KO) cell clones were obtained and confirmed using quantitative droplet digital PCR (ddPCR) technology. The amplicon sequencing demonstrated no off-target effects in our gene editing experiments. The TRIM28 KO cells grew slowly and appeared red, seeming to have a tendency towards erythroid differentiation. To understand how TRIM28 controls K562 cell proliferation and differentiation, transcriptome profiling analysis was performed in wild-type and KO cells to identify TRIM28-regulated genes. Some of the RNAs that encode the proteins regulating the cell cycle were increased (such as p21) or decreased (such as cyclin D2) in TRIM28 KO cell clones; a tumor marker, the MAGE (melanoma antigen) family, which is involved in cell proliferation was reduced. Moreover, we found that knockout of TRIM28 can induce miR-874 expression to downregulate MAGEC2 mRNA via post-transcriptional regulation. The embryonic epsilon-globin gene was significantly increased in TRIM28 KO cell clones through the downregulation of transcription repressor SOX6. Taken together, we provide evidence to demonstrate the regulatory network of TRIM28-mediated cell growth and erythroid differentiation in K562 leukemia cells.
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11
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Dide-Agossou C, Rossmassler K, Reid J, Purohit J, Savic RM, Nahid P, Phillips PP, Moore CM, Walter ND. MOVER approximated CV: A tool for quantifying precision in ratiometric droplet digital PCR assays. J Pharm Biomed Anal 2022; 212:114664. [PMID: 35192991 PMCID: PMC8923918 DOI: 10.1016/j.jpba.2022.114664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 02/08/2022] [Accepted: 02/13/2022] [Indexed: 10/19/2022]
Abstract
Droplet digital PCR is a particularly valuable tool for ratiometric assays because it provides simultaneous absolute quantification of two target sequences in a single assay. This manuscript addresses a challenge in establishing a new ratiometric droplet digital PCR assay for use in sputum, the rRNA synthesis ratio. In principle, the methods established to evaluate precision and determine the limit of quantification for a single measurand cannot be applied to a ratiometric assay. The precision of a ratio depends on precision in both the numerator and denominator. Here, we evaluated the MOVER approximated coefficient of variation as indicator of assay precision that does not require technical replicates. We estimated the MOVER approximated coefficient of variation in dilution series and routine assays and evaluated its agreement with the traditional coefficient of variation. We found that the MOVER approximated coefficient of variation was able to recapitulate the traditional coefficient of variation without the requirement for replicate assays. We also demonstrated that the MOVER approximated coefficient of variation threshold can be used to define the limit of quantification of the rRNA synthesis Ratio. In conclusion, the MOVER approximated coefficient of variation may be useful not only for the rRNA synthesis ratio but for other assays that measure ratios via droplet digital PCR.
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12
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Corbisier P, Buttinger G, Savini C, Sacco MG, Gatto F, Emons H. Expression of GM content in mass fraction from digital PCR data. Food Control 2022; 133:108626. [PMID: 35241875 PMCID: PMC8756621 DOI: 10.1016/j.foodcont.2021.108626] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 10/15/2021] [Accepted: 10/16/2021] [Indexed: 11/17/2022]
Abstract
Nowadays the quantification of the content of genetically modified (GM) constituents in food or feed products is performed by using either quantitative real-time PCR (qPCR) or digital PCR (dPCR). The latter is increasingly used. Therefore, experimental protocols for the quantification of 52 GM events authorised in the EU have been converted into a digital format and minimum performance characteristics for dPCR methods are detailed. Because of the need to harmonise the transformation of PCR results between two different measurement scales, 50 conversion factors for Certified Reference Materials (CFCRM) have been experimentally determined by three and sometimes four independent expert laboratories. The uncertainty of each CFCRM has been estimated to express dPCR results in mass fraction with a consistent uncertainty contribution. In 38 out of 58 cases, the validated qPCR methods (for 52 event-specific and 6 taxon-specific measurements) could easily be transferred into dPCR methods by using the same oligo sequences, final oligo concentration or annealing temperatures for the dPCR procedure. Laboratories have nevertheless used different strategies to improve the resolution or to reduce the so-called rain in their dPCR outcome. Those modifications were needed for PCR procedures that could not be converted without changes into a digital format. Therefore, exclusion/quality criteria such as the maximum rate of partitions with intermediate fluorescence “rain”, the minimum resolution and repeatability are suggested for dPCR methods. The CFCRM determined in this study were generally in agreement with the declared zygosity of the GM parental donor for hemizygous maize events. In a limited number of GM events the CFCRM values were significantly different when measured with different maize-specific (ZmAdh1 or hmgA) genes. Digital PCR protocols for the quantification of 52 GM events Minimum performance criteria for digital PCR results Conversion factors to express GM content determined by digital PCR in mass fraction Harmonised measurement system for official GMO controls in the EU
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Affiliation(s)
- Philippe Corbisier
- European Commission, Joint Research Centre JRC, Retieseweg 111, 2440, Geel, Belgium
| | - Gerhard Buttinger
- European Commission, Joint Research Centre JRC, Retieseweg 111, 2440, Geel, Belgium
| | - Cristian Savini
- European Commission, Joint Research Centre JRC, Via Enrico Fermi 2749, 21027, Ispra, VA, Italy
| | - Maria Grazia Sacco
- European Commission, Joint Research Centre JRC, Via Enrico Fermi 2749, 21027, Ispra, VA, Italy
| | - Francesco Gatto
- European Commission, Joint Research Centre JRC, Via Enrico Fermi 2749, 21027, Ispra, VA, Italy
| | - Hendrik Emons
- European Commission, Joint Research Centre JRC, Retieseweg 111, 2440, Geel, Belgium
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Meta-analysis of variable-temperature PCR technique performance for diagnosising Schistosoma japonicum infections in humans in endemic areas. PLoS Negl Trop Dis 2022; 16:e0010136. [PMID: 35030167 PMCID: PMC8794272 DOI: 10.1371/journal.pntd.0010136] [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: 07/13/2021] [Revised: 01/27/2022] [Accepted: 01/03/2022] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND As China is moving onto schistosomiasis elimination/eradication, diagnostic methods with both high sensitivity and specificity for Schistosoma japonicum infections in humans are urgently needed. Microscopic identification of eggs in stool is proven to have poor sensitivity in low endemic regions, and antibody tests are unable to distinguish between current and previous infections. Polymerase chain reaction (PCR) technologies for the detection of parasite DNA have been theoretically assumed to show high diagnostic sensitivity and specificity. However, the reported performance of PCR for detecting S. japonicum infection varied greatly among studies. Therefore, we performed a meta-analysis to evaluate the overall diagnostic performance of variable-temperature PCR technologies, based on stool or blood, for detecting S. japonicum infections in humans from endemic areas. METHODS We searched literatures in eight electronic databases, published up to 20 January 2021. The heterogeneity and publication bias of included studies were assessed statistically. The risk of bias and applicability of each eligible study were assessed using the Quality Assessment of Diagnostic Accuracy Studies 2 tool (QUADAS-2). The bivariate mixed-effects model was applied to obtain the summary estimates of diagnostic performance. The hierarchical summary receiver operating characteristic (HSROC) curve was applied to visually display the results. Subgroup analyses and multivariate regression were performed to explore the source of heterogeneity. This research was performed following the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) guidelines and was registered prospectively in PROSPERO (CRD42021233165). RESULTS A total of 2791 papers were retrieved. After assessing for duplications and eligilibity a total of thirteen publications were retained for inclusion. These included eligible data from 4268 participants across sixteen studies. High heterogeneity existed among studies, but no publication bias was found. The pooled analyses of PCR data from all included studies resulted in a sensitivity of 0.91 (95% CI: 0.83 to 0.96), specificity of 0.85 (95% CI: 0.65 to 0.94), positive likelihood ratio of 5.90 (95% CI: 2.40 to 14.60), negative likelihood ratio of 0.10 (95% CI: 0.05 to 0.20) and a diagnostics odds ratio of 58 (95% CI: 19 to 179). Case-control studies showed significantly better performances for PCR diagnostics than cross-sectional studies. This was further evidenced by multivariate analyses. The four types of PCR approaches identified (conventional PCR, qPCR, Droplet digital PCR and nested PCR) differed significantly, with nested PCRs showing the best performance. CONCLUSIONS Variable-temperature PCR has a satisfactory performance for diagnosing S. japonicum infections in humans in endemic areas. More high quality studies on S. japonicum diagnostic techniques, especially in low endemic areas and for the detection of dual-sex and single-sex infections are required. These will likely need to optimise a nested PCR alongside a highly sensitive gene target. They will contribute to successfully monitoring endemic areas as they move towards the WHO 2030 targets, as well as ultimately helping areas to achieve these goals.
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Development and evaluation of a molecular based protocol for detection and quantification of Cryptosporidium spp. In wastewater. Exp Parasitol 2022; 234:108216. [DOI: 10.1016/j.exppara.2022.108216] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 01/13/2022] [Accepted: 01/21/2022] [Indexed: 12/19/2022]
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15
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Temisak S, Thangsunan P, Boonnil J, Yenchum W, Hongthong K, Oss Boll H, Yata T, Rios‐Solis L, Morris P. Accurate determination of meat mass fractions using DNA measurements for quantifying meat adulteration by digital PCR. Int J Food Sci Technol 2021. [DOI: 10.1111/ijfs.15375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Sasithon Temisak
- Bioanalysis Group, Chemical Metrology and Biometry Department National Institute of Metrology (NIMT) Pathum Thani Thailand
| | - Pattanapong Thangsunan
- Bioanalysis Group, Chemical Metrology and Biometry Department National Institute of Metrology (NIMT) Pathum Thani Thailand
| | - Jiranun Boonnil
- Bioanalysis Group, Chemical Metrology and Biometry Department National Institute of Metrology (NIMT) Pathum Thani Thailand
| | - Watiporn Yenchum
- Bioanalysis Group, Chemical Metrology and Biometry Department National Institute of Metrology (NIMT) Pathum Thani Thailand
| | - Kanjana Hongthong
- Bioanalysis Group, Chemical Metrology and Biometry Department National Institute of Metrology (NIMT) Pathum Thani Thailand
| | - Heloísa Oss Boll
- Department of Genetics and Morphology Institute of Biological Sciences University of Brasília Brasília Federal District Brazil
- Institute for Bioengineering School of Engineering University of Edinburgh Kings Buildings Edinburgh UK
- Centre for Synthetic and Systems Biology (SynthSys) University of Edinburgh Kings Buildings Edinburgh UK
| | - Teerapong Yata
- Faculty of Veterinary Science Chulalongkorn University Bangkok Thailand
| | - Leonardo Rios‐Solis
- Institute for Bioengineering School of Engineering University of Edinburgh Kings Buildings Edinburgh UK
- Centre for Synthetic and Systems Biology (SynthSys) University of Edinburgh Kings Buildings Edinburgh UK
| | - Phattaraporn Morris
- Bioanalysis Group, Chemical Metrology and Biometry Department National Institute of Metrology (NIMT) Pathum Thani Thailand
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O'Malley K, McNamara P, McDonald W. Antibiotic resistance genes in an urban stream before and after a state fair. JOURNAL OF WATER AND HEALTH 2021; 19:885-894. [PMID: 34874897 DOI: 10.2166/wh.2021.151] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The global spread of antibiotic resistance genes (ARGs) concomitant with a decrease in antibiotic effectiveness is a major public health issue. While research has demonstrated the impact of various urban sources, such as wastewater treatment plant (WWTP) effluent, stormwater runoff, and industrial discharge on ARG abundance in receiving waters, the impact of short-term gatherings such as state fairs is not comprehensively understood. The objective of this research was to explore the impact of a 2-week Wisconsin State Fair gathering - over 1.1 million visitors and 7,100 farm animals - on the abundance of the ARG blaTEM, the integrase of the class 1 integron (intI1), a marker for horizontal gene transfer, and the 16S rRNA gene, a marker for total biomass, in an urban stream receiving runoff from the state fair. Stream samples downstream of the state fair were taken before and after the event and quantified via a droplet digital polymerase chain reaction. The absolute abundance of all genes was significantly higher (p<0.05) following the event. This research showcases the prevalence and persistence of ARG contamination in an urban stream before and after a state fair gathering, suggesting that short-term events can be a significant source of ARGs into the environment.
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Affiliation(s)
- Kassidy O'Malley
- Department of Civil, Construction, and Environmental Engineering, Marquette University, Milwaukee, WI 53233, USA E-mail:
| | - Patrick McNamara
- Department of Civil, Construction, and Environmental Engineering, Marquette University, Milwaukee, WI 53233, USA E-mail:
| | - Walter McDonald
- Department of Civil, Construction, and Environmental Engineering, Marquette University, Milwaukee, WI 53233, USA E-mail:
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17
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Yakimowski SB, Teitel Z, Caruso CM. Defence by duplication: The relation between phenotypic glyphosate resistance and EPSPS gene copy number variation in Amaranthus palmeri. Mol Ecol 2021; 30:5328-5342. [PMID: 34662479 DOI: 10.1111/mec.16231] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 08/17/2021] [Accepted: 09/08/2021] [Indexed: 12/12/2022]
Abstract
Gene copy number variation (CNV) has been increasingly associated with organismal responses to environmental stress, but we know little about the quantitative relation between CNV and phenotypic variation. In this study we quantify the relation between variation in EPSPS (5-enolpyruvylshikimate-3-phosphate synthase) copy number using digital drop PCR and variation in phenotypic glyphosate resistance in 22 populations of Amaranthus palmeri (Palmer Amaranth), a range-expanding agricultural weed. Overall, we detected a significant positive relation between population mean copy number and resistance. The majority of populations exhibited high glyphosate resistance yet maintained low-resistance individuals, resulting in bimodality in many populations. We also investigated threshold models for the relation between copy number and resistance, and found evidence for a threshold of ~15 EPSPS copies: there was a steep increase in resistance below the threshold, followed by a much shallower increase. Across 924 individuals, as copy number increased the range of variation in resistance decreased, yielding an increasing frequency of high phenotypic resistance individuals. Among populations we detected a decline in variation (s.d.) as mean phenotypic resistance increased from moderate to high, consistent with the prediction that as phenotypic resistance increases in populations, stabilizing selection decreases variation in the trait. Our study demonstrates that populations of A. palmeri can harbour wide variation in EPSPS copy number and phenotypic glyphosate resistance, reflecting the history of, and template for future, resistance evolution.
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Affiliation(s)
| | - Zachary Teitel
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
| | - Christina M Caruso
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
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18
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Jerič Kokelj B, Štalekar M, Vencken S, Dobnik D, Kogovšek P, Stanonik M, Arnol M, Ravnikar M. Feasibility of Droplet Digital PCR Analysis of Plasma Cell-Free DNA From Kidney Transplant Patients. Front Med (Lausanne) 2021; 8:748668. [PMID: 34692738 PMCID: PMC8531215 DOI: 10.3389/fmed.2021.748668] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 09/13/2021] [Indexed: 12/03/2022] Open
Abstract
Increasing research demonstrates the potential of donor-derived cell-free DNA (dd-cfDNA) as a biomarker for monitoring the health of various solid organ transplants. Several methods have been proposed for cfDNA analysis, including real-time PCR, digital PCR, and next generation sequencing-based approaches. We sought to revise the droplet digital PCR (ddPCR)-based approach to quantify relative dd-cfDNA in plasma from kidney transplant (KTx) patients using a novel pilot set of assays targeting single nucleotide polymorphisms that have a very high potential to distinguish cfDNA from two individuals. The assays are capable of accurate quantification of down to 0.1% minor allele content when analyzing 165 ng of human DNA. We found no significant differences in the yield of extracted cfDNA using the three different commercial kits tested. More cfDNA was extracted from the plasma of KTx patients than from healthy volunteers, especially early after transplantation. The median level of donor-derived minor alleles in KTx samples was 0.35%. We found that ddPCR using the evaluated assays within specific range is suitable for analysis of KTx patients' plasma but recommend prior genotyping of donor DNA and performing reliable preamplification of cfDNA.
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Affiliation(s)
- Barbara Jerič Kokelj
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Maja Štalekar
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | | | - David Dobnik
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Polona Kogovšek
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | | | - Miha Arnol
- Department of Nephrology, University Medical Centre Ljubljana, Ljubljana, Slovenia.,Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Maja Ravnikar
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
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19
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Competitiveness of Quantitative Polymerase Chain Reaction (qPCR) and Droplet Digital Polymerase Chain Reaction (ddPCR) Technologies, with a Particular Focus on Detection of Antibiotic Resistance Genes (ARGs). Appl Microbiol 2021. [DOI: 10.3390/applmicrobiol1030028] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
With fast-growing polymerase chain reaction (PCR) technologies and various application methods, the technique has benefited science and medical fields. While having strengths and limitations on each technology, there are not many studies comparing the efficiency and specificity of PCR technologies. The objective of this review is to summarize a large amount of scattered information on PCR technologies focused on the two majorly used technologies: qPCR (quantitative polymerase chain reaction) and ddPCR (droplet-digital polymerase chain reaction). Here we analyze and compare the two methods for (1) efficiency, (2) range of detection and limitations under different disciplines and gene targets, (3) optimization, and (4) status on antibiotic resistance genes (ARGs) analysis. It has been identified that the range of detection and quantification limit varies depending on the PCR method and the type of sample. Careful optimization of target gene analysis is essential for building robust analysis for both qPCR and ddPCR. In our era where mutation of genes may lead to a pandemic of viral infectious disease or antibiotic resistance-induced health threats, this study hopes to set guidelines for meticulous detection, quantification, and analysis to help future prevention and protection of global health, the economy, and ecosystems.
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20
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Sahu R, Vishnuraj MR, Srinivas C, Dadimi B, Megha GK, Pollumahanti N, Malik SS, Vaithiyanathan S, Rawool DB, Barbuddhe SB. Development and comparative evaluation of droplet digital PCR and quantitative PCR for the detection and quantification of Chlamydia psittaci. J Microbiol Methods 2021; 190:106318. [PMID: 34592374 DOI: 10.1016/j.mimet.2021.106318] [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: 07/06/2021] [Revised: 08/28/2021] [Accepted: 08/29/2021] [Indexed: 10/20/2022]
Abstract
Chlamydia psittaci is a zoonotic pathogen mainly transmitted by psittacine birds and poultry. The low shedding rate of the pathogen in the apparently healthy birds and human clinical cases may result in false-negative results. In the present study, a droplet digital PCR (ddPCR) assay was developed and compared with optimized quantitative PCR (qPCR) for the detection of C. psittaci from the clinical samples. The ddPCR assay was found to be comparatively more sensitive than the qPCR, wherein the limit of detection (LOD) of ddPCR was upto 2.4 copies of the DNA template, whereas, the qPCR could detect upto 38 copies of the DNA template in the reaction mixture. Overall, the developed ddPCR assay was found to be robust, specific, and could reliably quantify up to 17.8 copies of the DNA template. Finally, the applicability of the developed ddPCR assay was tested by screening the field samples (n = 124), comprising lung tissues from dead poultry and feral birds; pooled faecal samples from the free-living birds, commercial and backyard poultry farms; pharyngeal and cloacal swabs collected from the duck farms. Of these, a total of seven samples were found to be positive by the ddPCR, whereas, three samples could be detected as positive using the qPCR. The developed ddPCR could serve as a reliable screening tool, particularly in those clinical samples wherein the shedding of C. psittaci is substantially very low.
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Affiliation(s)
- Radhakrishna Sahu
- ICAR-National Research Centre on Meat, Chengicherla, Hyderabad 500092, India; Department of Veterinary Public Health, ICAR- Indian Veterinary Research Institute, Izatnagar 243122, India
| | - M R Vishnuraj
- ICAR-National Research Centre on Meat, Chengicherla, Hyderabad 500092, India
| | - Ch Srinivas
- ICAR-National Research Centre on Meat, Chengicherla, Hyderabad 500092, India
| | - Bhargavi Dadimi
- Department of Veterinary Public Health, ICAR- Indian Veterinary Research Institute, Izatnagar 243122, India
| | - G K Megha
- Department of Veterinary Public Health, ICAR- Indian Veterinary Research Institute, Izatnagar 243122, India
| | | | - Satyaveer S Malik
- Department of Veterinary Public Health, ICAR- Indian Veterinary Research Institute, Izatnagar 243122, India
| | - S Vaithiyanathan
- ICAR-National Research Centre on Meat, Chengicherla, Hyderabad 500092, India
| | - Deepak B Rawool
- ICAR-National Research Centre on Meat, Chengicherla, Hyderabad 500092, India
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21
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Ampaporn K, Phasuk Y, Duangjinda M. Droplet digital polymerase chain reaction assay for identifying and quantifying pork products. Anim Sci J 2021; 92:e13595. [PMID: 34318546 DOI: 10.1111/asj.13595] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 06/21/2021] [Indexed: 11/29/2022]
Abstract
Halal products are growing in consumer markets worldwide, and pork meat is classified as non-halal. Manufacturers of processed foods and products must ensure that their products follow Islamic dietary law because pork is prohibited for Muslims. Droplet digital polymerase chain reaction (PCR) (ddPCR) is a novel method for identifying pig species and quantifying pork products. This experiment aimed to investigate pork species and establish the proportion of pork in meat products using the mitochondrial cytochrome b gene (CYTB). The study found that the correlation coefficient between the meat weight and DNA concentration of pork was 0.997, and the correlation coefficient between the DNA concentration and the target DNA copy number of pork was 0.998. The accuracy of the ddPCR assay was verified using a sample of a known proportion of pork, and it was revealed that this method is highly precise in quantifying pork products. Nine products contained an undeclared meat proportion (90%). The limit of detection for pork was 0.0001 ng. The analysis indicated that the ddPCR assay has high accuracy and sensitivity for quantifying pork products. Therefore, the predictive model can be used in routine laboratories for quality assurance of halal food products.
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Affiliation(s)
- Kessara Ampaporn
- Department of Animal Science, Faculty of Agriculture, Khon Kaen University, Khon Kaen, Thailand
| | - Yupin Phasuk
- Department of Animal Science, Faculty of Agriculture, Khon Kaen University, Khon Kaen, Thailand
| | - Monchai Duangjinda
- Department of Animal Science, Faculty of Agriculture, Khon Kaen University, Khon Kaen, Thailand.,Network Center for Animal Breeding and Omics Research, Faculty of Agriculture, Khon Kaen University, Khon Kaen, Thailand
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22
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Thalinger B, Pütz Y, Traugott M. Endpoint PCR coupled with capillary electrophoresis (celPCR) provides sensitive and quantitative measures of environmental DNA in singleplex and multiplex reactions. PLoS One 2021; 16:e0254356. [PMID: 34297715 PMCID: PMC8301609 DOI: 10.1371/journal.pone.0254356] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 06/24/2021] [Indexed: 11/18/2022] Open
Abstract
The use of sensitive methods is key for the detection of target taxa from trace amounts of environmental DNA (eDNA) in a sample. In this context, digital PCR (dPCR) enables direct quantification and is commonly perceived as more sensitive than endpoint PCR. However, endpoint PCR coupled with capillary electrophoresis (celPCR) potentially embodies a viable alternative as it quantitatively measures signal strength after PCR in Relative Fluorescence Units (RFU). Provided comparable levels of sensitivity are reached, celPCR permits the development of cost-efficient multiplex reactions, enabling the simultaneous detection of several target taxa. Here, we compared the sensitivity of singleplex and multiplex celPCR to dPCR for species-specific primer pairs amplifying mitochondrial DNA (COI) of fish species occurring in European freshwaters by analyzing dilution series of tissue extracts as well as field-collected water samples. Both singleplex and multiplex celPCR and dPCR displayed comparable sensitivity with reliable positive amplifications starting at two to 10 target DNA copies per μl extract. celPCR was suitable for quantifying target DNA and direct inference of copy numbers from RFU was possible after accounting for primer effects in linear mixed-effects models and calibration via dPCR. Furthermore, multiplex celPCR and dPCR were successfully used for the detection and quantification of fish-eDNA in field-collected water samples, confirming the results of the dilution series experiment and exemplifying the high sensitivity of the two approaches. The possibility of detection and quantification via multiplex celPCR is appealing for the cost-efficient screening of high sample numbers. The present results confirm the sensitivity of this approach thus enabling its application for future eDNA-based monitoring efforts.
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Affiliation(s)
- Bettina Thalinger
- Department of Zoology, University of Innsbruck, Innsbruck, Austria
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
- Department of Integrative Biology, College of Biological Science, University of Guelph, Guelph, Ontario, Canada
| | - Yannick Pütz
- Department of Zoology, University of Innsbruck, Innsbruck, Austria
| | - Michael Traugott
- Department of Zoology, University of Innsbruck, Innsbruck, Austria
- Sinsoma GmbH, Lannes 6, Völs, Austria
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23
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Assessing sensitivity and reproducibility of RT-ddPCR and RT-qPCR for the quantification of SARS-CoV-2 in wastewater. J Virol Methods 2021; 297:114230. [PMID: 34252511 PMCID: PMC8267102 DOI: 10.1016/j.jviromet.2021.114230] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 07/02/2021] [Accepted: 07/03/2021] [Indexed: 12/29/2022]
Abstract
Throughout the COVID-19 global pandemic there has been significant interest and investment in using Wastewater-Based Epidemiology (WBE) for surveillance of viral pathogen presence and infections at the community level. There has been a push for widescale implementation of standardized protocols to quantify viral loads in a range of wastewater systems. To address concerns regarding sensitivity, limits of quantification, and large-scale reproducibility, a comparison of two similar workflows using RT-qPCR and RT-ddPCR was conducted. Sixty raw wastewater influent samples were acquired from nine distinct wastewater treatment plants (WWTP’s) served by the Hampton Roads Sanitation District (HRSD, Virginia Beach, Virginia) over a 6-month period beginning March 9th, 2020. Common reagents, controls, master mixes and nucleic acid extracts were shared between two individual processing groups based out of HRSD and the UNC Chapel Hill Institute of Marine Sciences (IMS, Morehead City, North Carolina). Samples were analyzed in parallel using One-Step RT-qPCR and One-Step RT-ddPCR with Nucleocapsid Protein 2 (N2) specific primers and probe. Influent SARS-CoV-2 N2 concentrations steadily increased over time spanning a range from non-detectable to 2.13E + 05 copies/L. Systematic dilution of the extracts indicated that inhibitory components in the wastewater matrices did not significantly impede the detection of a positive N2 signal for either workflow. The RT-ddPCR workflow had a greater analytical sensitivity with a lower Limit of Detection (LOD) at 0.066 copies/μl of template compared to RT-qPCR with a calculated LOD of 12.0 copies/μL of template. Interlaboratory comparisons using non-parametric correlation analysis demonstrated that there was a strong, significant, positive correlation between split extracts when employing RT-ddPCR for analysis with a ρ value of 0.86.
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Identification and semi-quantification of Atlantic salmon in processed and mixed seafood products using Droplet Digital PCR (ddPCR). Food Chem Toxicol 2021; 154:112329. [PMID: 34116106 DOI: 10.1016/j.fct.2021.112329] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 05/12/2021] [Accepted: 06/05/2021] [Indexed: 11/24/2022]
Abstract
Fishery products are often subject to substitution fraud, which is hard to trace due to a lack of morphologic traits when processed, gutted, or decapitated. Traditional molecular methods (DNA barcoding) fail to identify products containing multiple species and cannot estimate original weight percentages. As a proof of concept, an Atlantic salmon (Salmo salar) specific ddPCR assay was designed to authenticate mixed food products. The method proved to be specific and able to accurately quantify S. salar when using DNA extracts, even in the presence of DNA from closely related salmon species. The ddPCR estimates correlated well with the percentage of S. salar in artificially assembled tissue mixtures. The effect of common salmon processing techniques (freezing, smoking, poaching with a "Bellevue" recipe and marinating with a 'Gravad lax' recipe) on the ddPCR output was investigated and freezing and marinating appeared to lower the copies detected by the ddPCR. Finally, the assay was applied to 46 retail products containing Atlantic or Pacific salmon, and no indications of substitution fraud were detected. The method allows for a semi-quantitative evaluation of the S. salar content in processed food products and can rapidly screen Atlantic salmon products and flag potentially tampered samples for further investigation.
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Hwang SH, Kim JH, Park J, Park KS. Fluorescence nucleobase analogue-based strategy with high signal-to-noise ratio for ultrasensitive detection of food poisoning bacteria. Analyst 2021; 145:6307-6312. [PMID: 32706347 DOI: 10.1039/d0an01026j] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
We developed a simple and ultrasensitive strategy for the identification of foodborne pathogens utilizing a fluorescent nucleobase analogue [2-aminopurine (2-AP)]-containing split G-quadruplex that binds blocker DNA. Compared to a previous strategy that did not use blocker DNA, this strategy showed a significant increase in the signal-to-noise ratio-by approximately 300%-owing to the displacement of the blocker DNA by the target DNA that induces the formation of an active G-quadruplex structure, thereby leading to a substantial increase in the 2-AP fluorescence signal. The proposed strategy was rationally combined with polymerase chain reaction, which resulted in the successful determination of genomic DNA (within the range of 10-106 copies) derived from the food poisoning bacterium Escherichia coli, with a limit of detection of 5.2 copies and high selectivity. In addition, the practical applicability of this method was demonstrated by analyzing E. coli-spiked lettuce samples.
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Affiliation(s)
- Sung Hyun Hwang
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul 05029, Republic of Korea.
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Application of One-Step Reverse Transcription Droplet Digital PCR for Dengue Virus Detection and Quantification in Clinical Specimens. Diagnostics (Basel) 2021; 11:diagnostics11040639. [PMID: 33916081 PMCID: PMC8066273 DOI: 10.3390/diagnostics11040639] [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: 03/04/2021] [Revised: 03/26/2021] [Accepted: 03/26/2021] [Indexed: 12/24/2022] Open
Abstract
Detection and quantification of viruses in laboratory and clinical samples are standard assays in dengue virus (DENV) studies. The quantitative reverse transcription polymerase chain reaction (qRT-PCR) is considered to be the standard for DENV detection and quantification due to its high sensitivity. However, qRT-PCR offers only quantification relative to a standard curve and consists of several "in-house" components resulting in interlaboratory variations. We developed and optimized a protocol for applying one-step RT-droplet digital PCR (RT-ddPCR) for DENV detection and quantification. The lower limit of detection (LLOD95) and the lower limit of quantification (LLOQ) for RT-ddPCR were estimated to be 1.851 log10-copies/reaction and 2.337 log10-copies/reaction, respectively. The sensitivity of RT-ddPCR was found to be superior to qRT-PCR (94.87% vs. 90.38%, p = 0.039) while no false positives were detected. Quantification of DENV in clinical samples was independently performed in three laboratories showing interlaboratory variations with biases <0.5 log10-copies/mL. The RT-ddPCR protocol presented here could help harmonize DENV quantification results and improve findings in the field such as identifying a DENV titer threshold correlating with disease severity.
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Validation of a One-Step Reverse Transcription-Droplet Digital PCR (RT-ddPCR) Approach to Detect and Quantify SARS-CoV-2 RNA in Nasopharyngeal Swabs. DISEASE MARKERS 2021; 2021:8890221. [PMID: 33747257 PMCID: PMC7934789 DOI: 10.1155/2021/8890221] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 01/15/2021] [Accepted: 02/23/2021] [Indexed: 12/13/2022]
Abstract
Background Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has rapidly spread worldwide from the beginning of 2020. Quantitative reverse transcription-PCR (RT-qPCR) is, to this day, the preferred methodology for viral RNA detection, even if not without problems. To overcome some of the limitations still existing for the detection and quantification of nucleic acids in various applications, the use of one-step reverse transcription-droplet digital PCR (RT-ddPCR) has been established. The purpose of this study was, then, to evaluate the efficacy of ddPCR for the detection of SARS-CoV-2 RNA in nasopharyngeal swabs, optimizing the detection of low-viral load-burdened samples. Methods The RT-ddPCR workflow was validated for sensitivity, specificity, linearity, reproducibility, and precision using samples from 90 COVID-19-infected patients referred to the Department of Laboratory Medicine of the University Hospital of Udine (Italy). Results The present study shows that RT-ddPCR allows the detection of as low as 10.3 copies of a SARS-COV-2 E-gene per sample with a higher level of accuracy and precision, especially at low concentration. Conclusion During the postpeak phase of the SARS-CoV-2 pandemic, it is essential to rely on a highly robust molecular biology method to identify infected subjects, whether they have symptoms or not, in order to prepare appropriate containment measures.
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Srisutham S, Suwannasin K, Sugaram R, Dondorp AM, Imwong M. Measurement of gene amplifications related to drug resistance in Plasmodium falciparum using droplet digital PCR. Malar J 2021; 20:120. [PMID: 33639924 PMCID: PMC7916280 DOI: 10.1186/s12936-021-03659-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 02/19/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Copy number variations (CNVs) of the Plasmodium falciparum multidrug resistance 1 (pfmdr1), P. falciparum plasmepsin2 (pfplasmepsin2) and P. falciparum GTP cyclohydrolase 1 (pfgch1) genes are associated with anti-malarial drug resistance in P. falciparum malaria. Droplet digital PCR (ddPCR) assays have been developed for accurate assessment of CNVs in several human genes. The aim of the present study was to develop and validate ddPCR assays for detection of the CNVs of P. falciparum genes associated with resistance to anti-malarial drugs. METHODS A multiplex ddPCR assay was developed to detect the CNVs in the pfmdr1 and pfplasmepsin2 genes, while a duplex ddPCR assay was developed to detect CNV in the pfgch1 gene. The gene copy number (GCN) quantification limit, as well as the accuracy and precision of the ddPCR assays were determined and compared to conventional quantitative PCR (qPCR). In order to reduce the cost of testing, a multiplex ddPCR assay of two target genes, pfmdr1 and pfplasmepsin2, was validated. In addition, the CNVs of genes of field samples collected from Thailand from 2015 to 2019 (n = 84) were assessed by ddPCR and results were compared to qPCR as the reference assay. RESULTS There were no significant differences between the GCN results obtained from uniplex and multiplex ddPCR assays for detection of CNVs in the pfmdr1 and pfplasmepsin2 genes (p = 0.363 and 0.330, respectively). Based on the obtained gene copy number quantification limit, the accuracy and percent relative standard deviation (%RSD) value of the multiplex ddPCR assay were 95% and 5%, respectively, for detection of the CNV of the pfmdr1 gene, and 91% and 5% for detection of the CNV of the pfplasmepsin2 gene. There was no significant difference in gene copy numbers assessed by uniplex or duplex ddPCR assays regarding CNV in the pfgch1 gene (p = 0.276). The accuracy and %RSD value of the duplex ddPCR assay were 95% and 4%, respectively, regarding pfgch1 GCN. In the P. falciparum field samples, pfmdr1 and pfplasmepsin2 GCNs were amplified in 15% and 27% of samples from Ubon Ratchathani, Thailand, while pfgch1 GCN was amplified in 50% of samples from Yala, Thailand. There was 100% agreement between the GCN results obtained from the ddPCR and qPCR assays (κ = 1.00). The results suggested that multiplex ddPCR assay is the optional assay for the accurate detection of gene copy number without requiring calibration standards, while the cost and required time are reduced. Based on the results of this study, criteria for GCN detection by ddPCR analysis were generated. CONCLUSIONS The developed ddPCR assays are simple, accurate, precise and cost-effective tools for detection of the CNVs in the pfmdr1, pfplasmepsin2 and pfgch1 genes of P. falciparum. The ddPCR assay is a useful additional tool for the surveillance of anti-malarial drug resistance.
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Affiliation(s)
- Suttipat Srisutham
- Department of Clinical Microscopy, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Kanokon Suwannasin
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Rungniran Sugaram
- Division of Vector Borne Diseases, Department of Disease Control, Ministry of Public Health, Nonthaburi, Thailand
| | - Arjen M Dondorp
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Mallika Imwong
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.
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Nawkarkar P, Chugh S, Sharma S, Jain M, Kajla S, Kumar S. Characterization of the Chloroplast Genome Facilitated the Transformation of Parachlorella kessleri-I, A Potential Marine Alga for Biofuel Production. Curr Genomics 2021; 21:610-623. [PMID: 33414682 PMCID: PMC7770631 DOI: 10.2174/1389202921999201102164754] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 07/28/2020] [Accepted: 08/27/2020] [Indexed: 11/22/2022] Open
Abstract
Introduction The microalga Parachlorella kessleri-I produces high biomass and lipid content that could be suitable for producing economically viable biofuel at a commercial scale. Sequencing the complete chloroplast genome is crucial for the construction of a species-specific chloroplast transformation vector. Methods In this study, the complete chloroplast genome sequence (cpDNA) of P. kessleri-I was assembled; annotated and genetic transformation of the chloroplast was optimized. For the chloroplast transformation, we have tested two antibiotic resistance makers, aminoglycoside adenine transferase (aadA) gene and Sh-ble gene conferring resistance to spectinomycin and zeocin, respectively. Transgene integration and homoplasty determination were confirmed using PCR, Southern blot and Droplet Digital PCR. Results The chloroplast genome (109,642 bp) exhibited a quadripartite structure with two reverse repeat regions (IRA and IRB), a long single copy (LSC), and a small single copy (SSC) region. The genome encodes 116 genes, with 80 protein-coding genes, 32 tRNAs and 4 rRNAs. The cpDNA provided essential information like codons, UTRs and flank sequences for homologous recombination to make a species-specific vector that facilitated the transformation of P. kessleri-I chloroplast. The transgenic algal colonies were retrieved on a TAP medium containing 400 mg. L-1 spectinomycin, but no transgenic was recovered on the zeocin-supplemented medium. PCR and Southern blot analysis ascertained the transgene integration into the chloroplast genome, via homologous recombination. The chloroplast genome copy number in wildtype and transgenic P. kessleri-I was determined using Droplet Digital PCR. Conclusion The optimization of stable chloroplast transformation in marine alga P. kessleri-I should open a gateway for directly engineering the strain for carbon concentration mechanisms to fix more CO2, improving the photosynthetic efficiency and reducing the overall biofuels production cost.
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Affiliation(s)
- Prachi Nawkarkar
- 1 International Centre for Genetic Engineering and Biotechnology, New Delhi110067, India; 2School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi110067, India; 3Tata Steel Limited, Research &
Development, P O Burmamines, Jamshedpur831007, India
| | - Sagrika Chugh
- 1 International Centre for Genetic Engineering and Biotechnology, New Delhi110067, India; 2School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi110067, India; 3Tata Steel Limited, Research &
Development, P O Burmamines, Jamshedpur831007, India
| | - Surbhi Sharma
- 1 International Centre for Genetic Engineering and Biotechnology, New Delhi110067, India; 2School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi110067, India; 3Tata Steel Limited, Research &
Development, P O Burmamines, Jamshedpur831007, India
| | - Mukesh Jain
- 1 International Centre for Genetic Engineering and Biotechnology, New Delhi110067, India; 2School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi110067, India; 3Tata Steel Limited, Research &
Development, P O Burmamines, Jamshedpur831007, India
| | - Sachin Kajla
- 1 International Centre for Genetic Engineering and Biotechnology, New Delhi110067, India; 2School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi110067, India; 3Tata Steel Limited, Research &
Development, P O Burmamines, Jamshedpur831007, India
| | - Shashi Kumar
- 1 International Centre for Genetic Engineering and Biotechnology, New Delhi110067, India; 2School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi110067, India; 3Tata Steel Limited, Research &
Development, P O Burmamines, Jamshedpur831007, India
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García-Alegría AM, Anduro-Corona I, Pérez-Martínez CJ, Guadalupe Corella-Madueño MA, Rascón-Durán ML, Astiazaran-Garcia H. Quantification of DNA through the NanoDrop Spectrophotometer: Methodological Validation Using Standard Reference Material and Sprague Dawley Rat and Human DNA. Int J Anal Chem 2020; 2020:8896738. [PMID: 33312204 PMCID: PMC7719535 DOI: 10.1155/2020/8896738] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Revised: 11/03/2020] [Accepted: 11/16/2020] [Indexed: 02/07/2023] Open
Abstract
This study aimed to validate an analytical method to determine DNA concentration using standard reference material (NIST SRM 2372) and Sprague Dawley rat and human DNA. Microvolumes were used to analyse DNA samples. Linearity showed correlation coefficients higher than R ≥ 0.9950, and the precision value was ≤2% CV. Trueness based on bias and the percentage of recovery showed bias values lower than Z-test with a 95% confidence level and a recovery percentage within the range (% Rec = 100% ± 5%), and the stability of the samples was 60 days (2-4°C).
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Affiliation(s)
| | - Iván Anduro-Corona
- Centro de Investigación en Alimentación y Desarrollo, A.C. (CIAD AC), Coordinación de Nutrición, Hermosillo, Sonora CP 83304, Mexico
| | | | | | - María Lucila Rascón-Durán
- Universidad de Sonora, Departamento de Ciencias Químico Biológicas, Hermosillo, Sonora CP 83000, Mexico
| | - Humberto Astiazaran-Garcia
- Universidad de Sonora, Departamento de Ciencias Químico Biológicas, Hermosillo, Sonora CP 83000, Mexico
- Centro de Investigación en Alimentación y Desarrollo, A.C. (CIAD AC), Coordinación de Nutrición, Hermosillo, Sonora CP 83304, Mexico
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Sena-Torralba A, Pallás-Tamarit Y, Morais S, Maquieira Á. Recent advances and challenges in food-borne allergen detection. Trends Analyt Chem 2020. [DOI: 10.1016/j.trac.2020.116050] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Villamil C, Calderon MN, Arias MM, Leguizamon JE. Validation of Droplet Digital Polymerase Chain Reaction for Salmonella spp. Quantification. Front Microbiol 2020; 11:1512. [PMID: 32733415 PMCID: PMC7358645 DOI: 10.3389/fmicb.2020.01512] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 06/10/2020] [Indexed: 01/08/2023] Open
Abstract
Salmonellosis is a foodborne disease caused by Salmonella spp. Although cell culture is the gold standard for its identification, validated molecular methods are becoming an alternative, because of their rapidity, selectivity, and specificity. A simplex and duplex droplet digital polymerase chain reaction (ddPCR)-based method for the identification and quantification of Salmonella using ttr, invA, hilA, spaQ, and siiA gene sequences was validated. The method has high specificity, working interval between 8 and 8,000 cp/μL in ddPCR reaction, a limit of detection of 0.5 copies/μL, and precision ranging between 5 and 10% measured as a repeatability standard deviation. The relative standard measurement uncertainty was between 2 and 12%. This tool will improve food safety in national consumption products and will increase the competitiveness in agricultural product trade.
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Affiliation(s)
- Carolina Villamil
- Departamento de Química, Universidad Nacional de Colombia, Bogota, Colombia
| | | | - Maria Mercedes Arias
- Grupo de Metrología en Bioanálisis, Instituto Nacional de Metrología, Bogota, Colombia
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Santeramo I, Bagnati M, Harvey EJ, Hassan E, Surmacz-Cordle B, Marshall D, Di Cerbo V. Vector Copy Distribution at a Single-Cell Level Enhances Analytical Characterization of Gene-Modified Cell Therapies. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2020; 17:944-956. [PMID: 32420408 PMCID: PMC7217927 DOI: 10.1016/j.omtm.2020.04.016] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 04/22/2020] [Indexed: 12/28/2022]
Abstract
The ability to deliver transgenes into the human genome using viral vectors is a major enabler of the gene-modified cell therapy field. However, the control of viral transduction is difficult and can lead to product heterogeneity, impacting efficacy and safety, as well as increasing the risk of batch failure during manufacturing. To address this, we generated a novel analytical method to measure vector copy distribution at the single-cell level in a gene-modified, lentiviral-based immunotherapy model. As the limited amount of genomic DNA in a single cell hinders reliable quantification, we implemented a preamplification strategy on selected lentiviral and human gene targets in isolated live single cells, followed by quantification of amplified material by droplet digital PCR. Using a bespoke probability framework based on Bayesian statistics, we show that we can estimate vector copy number (VCN) integers with maximum likelihood scores. Notably, single-cell data are consistent with population analysis and also provide an overall measurement of transduction efficiency by discriminating transduced (VCN ≥ 1) from nontransduced (VCN = 0) cells. The ability to characterize cell-to-cell variability provides a powerful high-resolution approach for product characterization, which could ultimately allow improved control over product quality and safety.
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Affiliation(s)
- Ilaria Santeramo
- Cell and Gene Therapy Catapult, 12th Floor Tower Wing, Guy's Hospital, Great Maze Pond, London SE1 9RT, United Kingdom
| | - Marta Bagnati
- Cell and Gene Therapy Catapult, 12th Floor Tower Wing, Guy's Hospital, Great Maze Pond, London SE1 9RT, United Kingdom
| | - Emily Jane Harvey
- Cell and Gene Therapy Catapult, 12th Floor Tower Wing, Guy's Hospital, Great Maze Pond, London SE1 9RT, United Kingdom
| | - Enas Hassan
- Cell and Gene Therapy Catapult, 12th Floor Tower Wing, Guy's Hospital, Great Maze Pond, London SE1 9RT, United Kingdom
| | - Beata Surmacz-Cordle
- Cell and Gene Therapy Catapult, 12th Floor Tower Wing, Guy's Hospital, Great Maze Pond, London SE1 9RT, United Kingdom
| | - Damian Marshall
- Cell and Gene Therapy Catapult, 12th Floor Tower Wing, Guy's Hospital, Great Maze Pond, London SE1 9RT, United Kingdom
| | - Vincenzo Di Cerbo
- Cell and Gene Therapy Catapult, 12th Floor Tower Wing, Guy's Hospital, Great Maze Pond, London SE1 9RT, United Kingdom
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Dang ATH, Tran VU, Tran TT, Thi Pham HA, Le DT, Nguyen L, Nguyen NV, Thi Nguyen TH, Nguyen CV, Le HT, Thi Nguyen ML, Le VT, Nguyen PH, Vo BT, Thi Dao HT, Nguyen LT, Van Nguyen TC, Bui QTN, Nguyen LH, Nguyen NH, Thi Nguyen QT, Le TX, Do TTT, Dinh KT, Do HN, Phan MD, Nguyen HN, Tran LS, Giang H. Actionable Mutation Profiles of Non-Small Cell Lung Cancer patients from Vietnamese population. Sci Rep 2020; 10:2707. [PMID: 32066856 PMCID: PMC7026432 DOI: 10.1038/s41598-020-59744-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 01/09/2020] [Indexed: 12/24/2022] Open
Abstract
Comprehensive profiling of actionable mutations in non-small cell lung cancer (NSCLC) is vital to guide targeted therapy, thereby improving the survival rate of patients. Despite the high incidence and mortality rate of NSCLC in Vietnam, the actionable mutation profiles of Vietnamese patients have not been thoroughly examined. Here, we employed massively parallel sequencing to identify alterations in major driver genes (EGFR, KRAS, NRAS, BRAF, ALK and ROS1) in 350 Vietnamese NSCLC patients. We showed that the Vietnamese NSCLC patients exhibited mutations most frequently in EGFR (35.4%) and KRAS (22.6%), followed by ALK (6.6%), ROS1 (3.1%), BRAF (2.3%) and NRAS (0.6%). Interestingly, the cohort of Vietnamese patients with advanced adenocarcinoma had higher prevalence of EGFR mutations than the Caucasian MSK-IMPACT cohort. Compared to the East Asian cohort, it had lower EGFR but higher KRAS mutation prevalence. We found that KRAS mutations were more commonly detected in male patients while EGFR mutations was more frequently found in female. Moreover, younger patients (<61 years) had higher genetic rearrangements in ALK or ROS1. In conclusions, our study revealed mutation profiles of 6 driver genes in the largest cohort of NSCLC patients in Vietnam to date, highlighting significant differences in mutation prevalence to other cohorts.
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Affiliation(s)
- Anh-Thu Huynh Dang
- University of Medicine and Pharmacy at Ho Chi Minh city, Ho Chi Minh city, Vietnam
| | | | | | | | | | - Lam Nguyen
- Pham Ngoc Thach Hospital, Ho Chi Minh city, Vietnam
| | | | | | | | - Ha Thu Le
- Ha Noi Oncology hospital, Ha Noi, Vietnam
| | | | | | - Phuc Huu Nguyen
- University of Medicine and Pharmacy at Ho Chi Minh city, Ho Chi Minh city, Vietnam
| | | | | | | | | | | | | | | | | | - Truong Xuan Le
- University of Medicine and Pharmacy at Ho Chi Minh city, Ho Chi Minh city, Vietnam
| | - Thanh-Thuy Thi Do
- University of Medicine and Pharmacy at Ho Chi Minh city, Ho Chi Minh city, Vietnam
| | | | | | - Minh-Duy Phan
- Gene Solutions, Ho Chi Minh city, Vietnam
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Australia
| | - Hoai-Nghia Nguyen
- University of Medicine and Pharmacy at Ho Chi Minh city, Ho Chi Minh city, Vietnam.
| | - Le Son Tran
- Gene Solutions, Ho Chi Minh city, Vietnam.
- Institute of Molecular and Cellular Biology, Astar, Singapore.
| | - Hoa Giang
- Gene Solutions, Ho Chi Minh city, Vietnam.
- Medical Genetics Institute, Ho Chi Minh City, Vietnam.
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Nguyen HT, Tran DH, Ngo QD, Pham HAT, Tran TT, Tran VU, Pham TVN, Le TK, Le NAT, Nguyen NM, Vo BT, Nguyen LT, Nguyen TCV, Bui QTN, Nguyen HN, Luong BA, Le LGH, Do DM, Do TTT, Hoang AV, Dinh KT, Phan MD, Tran LS, Giang H, Nguyen HN. Evaluation of a Liquid Biopsy Protocol using Ultra-Deep Massive Parallel Sequencing for Detecting and Quantifying Circulation Tumor DNA in Colorectal Cancer Patients. Cancer Invest 2020; 38:85-93. [DOI: 10.1080/07357907.2020.1713350] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
| | - Duc Huy Tran
- University Medical Center, Ho Chi Minh City, Vietnam
| | - Quoc Dat Ngo
- University of Medicine and Pharmacy, Ho Chi Minh City, Vietnam
| | - Hong-Anh Thi Pham
- Gene Solutions, Ho Chi Minh City, Vietnam
- Medical Genetics Institute, Ho Chi Minh City, Vietnam
| | - Thanh-Truong Tran
- Gene Solutions, Ho Chi Minh City, Vietnam
- Medical Genetics Institute, Ho Chi Minh City, Vietnam
| | - Vu-Uyen Tran
- Gene Solutions, Ho Chi Minh City, Vietnam
- Medical Genetics Institute, Ho Chi Minh City, Vietnam
| | | | - Trung Kien Le
- University Medical Center, Ho Chi Minh City, Vietnam
| | | | - Ngoc Mai Nguyen
- Gene Solutions, Ho Chi Minh City, Vietnam
- Medical Genetics Institute, Ho Chi Minh City, Vietnam
| | - Binh Thanh Vo
- Gene Solutions, Ho Chi Minh City, Vietnam
- Medical Genetics Institute, Ho Chi Minh City, Vietnam
| | - Luan Thanh Nguyen
- Gene Solutions, Ho Chi Minh City, Vietnam
- Medical Genetics Institute, Ho Chi Minh City, Vietnam
| | - Thien-Chi Van Nguyen
- Gene Solutions, Ho Chi Minh City, Vietnam
- Medical Genetics Institute, Ho Chi Minh City, Vietnam
| | - Quynh Tram Nguyen Bui
- Gene Solutions, Ho Chi Minh City, Vietnam
- Medical Genetics Institute, Ho Chi Minh City, Vietnam
| | - Huu-Nguyen Nguyen
- Gene Solutions, Ho Chi Minh City, Vietnam
- Medical Genetics Institute, Ho Chi Minh City, Vietnam
| | - Bac An Luong
- University of Medicine and Pharmacy, Ho Chi Minh City, Vietnam
| | | | - Duc Minh Do
- University of Medicine and Pharmacy, Ho Chi Minh City, Vietnam
| | - Thanh-Thuy Thi Do
- University of Medicine and Pharmacy, Ho Chi Minh City, Vietnam
- Medical Genetics Institute, Ho Chi Minh City, Vietnam
| | - Anh Vu Hoang
- University of Medicine and Pharmacy, Ho Chi Minh City, Vietnam
| | | | - Minh-Duy Phan
- Gene Solutions, Ho Chi Minh City, Vietnam
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Australia
| | | | - Hoa Giang
- Gene Solutions, Ho Chi Minh City, Vietnam
- Medical Genetics Institute, Ho Chi Minh City, Vietnam
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Tran LS, Pham HAT, Tran VU, Tran TT, Dang ATH, Le DT, Nguyen SL, Nguyen NV, Nguyen TV, Vo BT, Dao HTT, Nguyen NH, Tran TH, Nguyen CV, Pham PC, Dang-Mai AT, Dinh-Nguyen TK, Phan VH, Do TTT, Truong Dinh K, Do HN, Phan MD, Giang H, Nguyen HN. Ultra-deep massively parallel sequencing with unique molecular identifier tagging achieves comparable performance to droplet digital PCR for detection and quantification of circulating tumor DNA from lung cancer patients. PLoS One 2019; 14:e0226193. [PMID: 31841547 PMCID: PMC6913927 DOI: 10.1371/journal.pone.0226193] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 11/21/2019] [Indexed: 12/24/2022] Open
Abstract
The identification and quantification of actionable mutations are of critical importance for effective genotype-directed therapies, prognosis and drug response monitoring in patients with non-small-cell lung cancer (NSCLC). Although tumor tissue biopsy remains the gold standard for diagnosis of NSCLC, the analysis of circulating tumor DNA (ctDNA) in plasma, known as liquid biopsy, has recently emerged as an alternative and noninvasive approach for exploring tumor genetic constitution. In this study, we developed a protocol for liquid biopsy using ultra-deep massively parallel sequencing (MPS) with unique molecular identifier tagging and evaluated its performance for the identification and quantification of tumor-derived mutations from plasma of patients with advanced NSCLC. Paired plasma and tumor tissue samples were used to evaluate mutation profiles detected by ultra-deep MPS, which showed 87.5% concordance. Cross-platform comparison with droplet digital PCR demonstrated comparable detection performance (91.4% concordance, Cohen’s kappa coefficient of 0.85 with 95% CI = 0.72–0.97) and great reliability in quantification of mutation allele frequency (Intraclass correlation coefficient of 0.96 with 95% CI = 0.90–0.98). Our results highlight the potential application of liquid biopsy using ultra-deep MPS as a routine assay in clinical practice for both detection and quantification of actionable mutation landscape in NSCLC patients.
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Affiliation(s)
- Le Son Tran
- Gene Solutions, Ho Chi Minh, Vietnam
- Medical Genetics Institute, Ho Chi Minh City, Vietnam
- * E-mail: (LST); (HG); (HNN)
| | - Hong-Anh Thi Pham
- Gene Solutions, Ho Chi Minh, Vietnam
- Graduate program of Genetics, Ho Chi Minh city University of Science, Ho Chi Minh city, Vietnam
| | - Vu-Uyen Tran
- Gene Solutions, Ho Chi Minh, Vietnam
- Graduate program of Genetics, Ho Chi Minh city University of Science, Ho Chi Minh city, Vietnam
| | - Thanh-Truong Tran
- Gene Solutions, Ho Chi Minh, Vietnam
- Graduate program of Genetics, Ho Chi Minh city University of Science, Ho Chi Minh city, Vietnam
| | | | | | | | | | | | - Binh Thanh Vo
- Gene Solutions, Ho Chi Minh, Vietnam
- Graduate program of Genetics, Ho Chi Minh city University of Science, Ho Chi Minh city, Vietnam
| | - Hong-Thuy Thi Dao
- Gene Solutions, Ho Chi Minh, Vietnam
- Graduate program of Genetics, Ho Chi Minh city University of Science, Ho Chi Minh city, Vietnam
| | | | - Tam Huu Tran
- Center for Standardization and QC in Medical Lab of Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | | | | | | | | | - Van Hieu Phan
- Center for Forensic Science, Ho Chi Minh City, Vietnam
| | | | | | | | - Minh-Duy Phan
- Gene Solutions, Ho Chi Minh, Vietnam
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Australia
| | - Hoa Giang
- Gene Solutions, Ho Chi Minh, Vietnam
- Medical Genetics Institute, Ho Chi Minh City, Vietnam
- * E-mail: (LST); (HG); (HNN)
| | - Hoai-Nghia Nguyen
- University of Medicine and Pharmacy, Ho Chi Minh city, Vietnam
- * E-mail: (LST); (HG); (HNN)
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Baume M, Cariou A, Leveau A, Fessy N, Pastori F, Jarraud S, Pierre S. Quantification of Legionella DNA certified reference material by digital droplet PCR. J Microbiol Methods 2018; 157:50-53. [PMID: 30578889 DOI: 10.1016/j.mimet.2018.12.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 12/18/2018] [Accepted: 12/18/2018] [Indexed: 11/25/2022]
Abstract
A value was assigned in 2009 to the Legionella DNA Certified Reference Material, and the stability study conducted using quantitative PCR found a low level of degradation. Herein, the Digital Droplet PCR method for Legionella DNA was qualified and used to provide absolute quantification of the CRM.
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Affiliation(s)
- Maud Baume
- Hospices Civils de Lyon, Centre National de Référence des Légionelles, Lyon, France.
| | - Astrid Cariou
- Bio-Rad, Food Science Division, Marnes-la-Coquette, France
| | | | - Noémie Fessy
- Hospices Civils de Lyon, Centre National de Référence des Légionelles, Lyon, France
| | | | - Sophie Jarraud
- Hospices Civils de Lyon, Centre National de Référence des Légionelles, Lyon, France
| | - Sophie Pierre
- Bio-Rad, Food Science Division, Marnes-la-Coquette, France
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Milosevic D, Mills JR, Campion MB, Vidal-Folch N, Voss JS, Halling KC, Highsmith WE, Liu MC, Kipp BR, Grebe SKG. Applying Standard Clinical Chemistry Assay Validation to Droplet Digital PCR Quantitative Liquid Biopsy Testing. Clin Chem 2018; 64:1732-1742. [DOI: 10.1373/clinchem.2018.291278] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 08/23/2018] [Indexed: 11/06/2022]
Abstract
Abstract
BACKGROUND
Droplet digital PCR (ddPCR) is an emerging technology for quantitative cell-free DNA oncology applications. However, assay performance criteria must be established in a standardized manner to harness this potential. We reasoned that standard protocols used in clinical chemistry assay validation should be able to fill this need.
METHODS
We validated KRAS, EGFR, and BRAF quantitative ddPCR assays based on the Clinical Laboratory Improvement Act regulations for laboratory-developed tests in clinical chemistry and the matching Clinical and Laboratory Standards Institute guidelines. This included evaluation of limit of the blank (LOB), limit of detection (LOD), limit of quantification (LOQ), intraassay and interassay imprecision, analytical range, dilution linearity, accuracy (including comparison with orthogonal platforms), reference range study, interference, and stability studies.
RESULTS
For the ddPCR assays, the LOB was 4 mutant copies, LODs were 12 to 22 copies, and LOQs were 35 to 64 copies. The upper limit of the dynamic range was 30000 copies, and dilutions were linear down to the LOQs with good accuracy of spike recovery of Horizon reference material. Method comparisons with next-generation sequencing and an alternative ddPCR platform showed complete qualitative agreement and quantitative concordance, with slopes of 0.73 to 0.97 and R2s of 0.83 to 0.99. No substantial interferences were discovered. Wild-type copy numbers in plasma ranged from 462 to 6169/mL in healthy individuals.
CONCLUSIONS
Standard clinical chemistry assay validation protocols can be applied to quantitative ddPCR assays. This should facilitate comparison of the performance of different assays and allow establishment of minimal significant change thresholds in monitoring applications.
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Affiliation(s)
- Dragana Milosevic
- Department of Laboratory Medicine and Pathology, Division of Clinical Biochemistry and Immunology, Mayo Clinic, Rochester, MN
| | - John R Mills
- Department of Laboratory Medicine and Pathology, Division of Clinical Biochemistry and Immunology, Mayo Clinic, Rochester, MN
| | - Michael B Campion
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics and Genomics, Mayo Clinic, Rochester, MN
| | - Noemi Vidal-Folch
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics and Genomics, Mayo Clinic, Rochester, MN
| | - Jesse S Voss
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics and Genomics, Mayo Clinic, Rochester, MN
| | - Kevin C Halling
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics and Genomics, Mayo Clinic, Rochester, MN
| | - W Edward Highsmith
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics and Genomics, Mayo Clinic, Rochester, MN
| | - Minetta C Liu
- Department of Laboratory Meidicne and Pathology, Division of Anatomic Pathology, Mayo Clinic, Rochester, MN
- Department of Oncology, Division of Medical Oncology Mayo Clinic, Rochester, MN
| | - Benjamin R Kipp
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics and Genomics, Mayo Clinic, Rochester, MN
| | - Stefan K G Grebe
- Department of Laboratory Medicine and Pathology, Division of Clinical Biochemistry and Immunology, Mayo Clinic, Rochester, MN
- Department of Medicine, Division of Endocrinology, Mayo Clinic, Rochester, MN
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Quantification of the allergen soy (Glycine max) in food using digital droplet PCR (ddPCR). Eur Food Res Technol 2018. [DOI: 10.1007/s00217-018-3182-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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40
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Jacchia S, Kagkli DM, Lievens A, Angers-Loustau A, Savini C, Emons H, Mazzara M. Identification of single target taxon-specific reference assays for the most commonly genetically transformed crops using digital droplet PCR. Food Control 2018; 93:191-200. [PMID: 30393444 PMCID: PMC6058085 DOI: 10.1016/j.foodcont.2018.06.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 06/01/2018] [Accepted: 06/07/2018] [Indexed: 11/24/2022]
Abstract
Knowledge of the number of DNA sequences targeted by the taxon-specific reference assays is essential for correct GM quantification and is key to the harmonisation of measurement results. In the present study droplet digital PCR (ddPCR) was used to determine the number of DNA target copies of taxon-specific assays validated for real-time PCR for the four main genetically modified (GM) crops. The transferability of experimental conditions from real-time PCR to ddPCR was also explored, as well as the effect of DNA digestion. The results of this study indicate that for each crop at least one taxon-specific assay can be identified as having a single DNA target. A short list of taxon-specific reference assays is proposed as best candidates for the relative quantification of GM events for soybean, maize, cotton and oilseed rape. The investigated assays could be in most cases transferred to ddPCR without further optimisation. The use of DNA digestion did not improve ddPCR characteristics such as rain and resolution at the conditions tested.
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Affiliation(s)
- Sara Jacchia
- European Commission, Joint Research Centre (JRC), via E. Fermi 2749, 21027 Ispra, Italy
| | - Dafni-Maria Kagkli
- European Commission, Joint Research Centre (JRC), via E. Fermi 2749, 21027 Ispra, Italy
| | - Antoon Lievens
- European Commission, Joint Research Centre (JRC), Retieseweg 111, 2440 Geel, Belgium
| | | | - Christian Savini
- European Commission, Joint Research Centre (JRC), via E. Fermi 2749, 21027 Ispra, Italy
| | - Hendrik Emons
- European Commission, Joint Research Centre (JRC), Retieseweg 111, 2440 Geel, Belgium
| | - Marco Mazzara
- European Commission, Joint Research Centre (JRC), via E. Fermi 2749, 21027 Ispra, Italy
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41
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Mehle N, Dobnik D, Ravnikar M, Pompe Novak M. Validated reverse transcription droplet digital PCR serves as a higher order method for absolute quantification of Potato virus Y strains. Anal Bioanal Chem 2018; 410:3815-3825. [DOI: 10.1007/s00216-018-1053-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 03/20/2018] [Accepted: 03/29/2018] [Indexed: 01/14/2023]
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42
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Evaluating droplet digital PCR for the quantification of human genomic DNA: converting copies per nanoliter to nanograms nuclear DNA per microliter. Anal Bioanal Chem 2018; 410:2879-2887. [PMID: 29556737 DOI: 10.1007/s00216-018-0982-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Revised: 02/05/2018] [Accepted: 02/22/2018] [Indexed: 12/19/2022]
Abstract
The highly multiplexed polymerase chain reaction (PCR) assays used for forensic human identification perform best when used with an accurately determined quantity of input DNA. To help ensure the reliable performance of these assays, we are developing a certified reference material (CRM) for calibrating human genomic DNA working standards. To enable sharing information over time and place, CRMs must provide accurate and stable values that are metrologically traceable to a common reference. We have shown that droplet digital PCR (ddPCR) limiting dilution end-point measurements of the concentration of DNA copies per volume of sample can be traceably linked to the International System of Units (SI). Unlike values assigned using conventional relationships between ultraviolet absorbance and DNA mass concentration, entity-based ddPCR measurements are expected to be stable over time. However, the forensic community expects DNA quantity to be stated in terms of mass concentration rather than entity concentration. The transformation can be accomplished given SI-traceable values and uncertainties for the number of nucleotide bases per human haploid genome equivalent (HHGE) and the average molar mass of a nucleotide monomer in the DNA polymer. This report presents the considerations required to establish the metrological traceability of ddPCR-based mass concentration estimates of human nuclear DNA. Graphical abstract The roots of metrological traceability for human nuclear DNA mass concentration results. Values for the factors in blue must be established experimentally. Values for the factors in red have been established from authoritative source materials. HHGE stands for "haploid human genome equivalent"; there are two HHGE per diploid human genome.
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43
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Pinheiro LB, O'Brien H, Druce J, Do H, Kay P, Daniels M, You J, Burke D, Griffiths K, Emslie KR. Interlaboratory Reproducibility of Droplet Digital Polymerase Chain Reaction Using a New DNA Reference Material Format. Anal Chem 2017; 89:11243-11251. [PMID: 28968098 DOI: 10.1021/acs.analchem.6b05032] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Use of droplet digital PCR technology (ddPCR) is expanding rapidly in the diversity of applications and number of users around the world. Access to relatively simple and affordable commercial ddPCR technology has attracted wide interest in use of this technology as a molecular diagnostic tool. For ddPCR to effectively transition to a molecular diagnostic setting requires processes for method validation and verification and demonstration of reproducible instrument performance. In this study, we describe the development and characterization of a DNA reference material (NMI NA008 High GC reference material) comprising a challenging methylated GC-rich DNA template under a novel 96-well microplate format. A scalable process using high precision acoustic dispensing technology was validated to produce the DNA reference material with a certified reference value expressed in amount of DNA molecules per well. An interlaboratory study, conducted using blinded NA008 High GC reference material to assess reproducibility among seven independent laboratories demonstrated less than 4.5% reproducibility relative standard deviation. With the exclusion of one laboratory, laboratories had appropriate technical competency, fully functional instrumentation, and suitable reagents to perform accurate ddPCR based DNA quantification measurements at the time of the study. The study results confirmed that NA008 High GC reference material is fit for the purpose of being used for quality control of ddPCR systems, consumables, instrumentation, and workflow.
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Affiliation(s)
- Leonardo B Pinheiro
- National Measurement Institute (NMI) , Lindfield, Sydney, New South Wales 2070, Australia
| | - Helen O'Brien
- Research and Development, Australian Red Cross Blood Service , Kelvin Grove, Queensland 4059, Australia
| | - Julian Druce
- Victorian Infectious Diseases Reference Laboratory , Melbourne, Victoria 3000, Australia
| | - Hongdo Do
- Olivia Newton-John Cancer Research Institute , Translation Genomics and Epigenomics Laboratory, Heidelberg, Victoria 3084, Australia
| | - Pippa Kay
- Agri-Bio Molecular Genetics, Biosciences Research Division, Bundoora, Victoria 3083, Australia
| | - Marissa Daniels
- The Prince Charles Hospital University of Queensland , Thoracic Research Centre, Chermside, Queensland 4032, Australia
| | - Jingjing You
- Save Sight Institute, Sydney Eye Hospital, Sydney Medical School, University of Sydney , Sydney, New South Wales 2000, Australia
| | - Daniel Burke
- National Measurement Institute (NMI) , Lindfield, Sydney, New South Wales 2070, Australia
| | - Kate Griffiths
- National Measurement Institute (NMI) , Lindfield, Sydney, New South Wales 2070, Australia
| | - Kerry R Emslie
- National Measurement Institute (NMI) , Lindfield, Sydney, New South Wales 2070, Australia
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Wong YK, Tsang HF, Xue VW, Chan CM, Au TC, Cho WC, Chan LW, Wong SC. Applications of digital PCR in precision medicine. EXPERT REVIEW OF PRECISION MEDICINE AND DRUG DEVELOPMENT 2017. [DOI: 10.1080/23808993.2017.1347482] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Y. K. Wong
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - H. F. Tsang
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - V. W. Xue
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - C. M. Chan
- Department of Clinical Oncology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China
| | - T. C. Au
- Department of Clinical Oncology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China
| | - W. C. Cho
- Department of Clinical Oncology, Queen Elizabeth Hospital, Hong Kong Special Administrative Region, China
| | - L. W. Chan
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - S. C. Wong
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
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45
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Kline MC, Duewer DL. Evaluating Droplet Digital Polymerase Chain Reaction for the Quantification of Human Genomic DNA: Lifting the Traceability Fog. Anal Chem 2017; 89:4648-4654. [PMID: 28347134 DOI: 10.1021/acs.analchem.7b00240] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Digital polymerase chain reaction (dPCR) end point platforms directly estimate the number of DNA target copies per reaction partition, λ, where the partitions are fixed-location chambers (cdPCR) or aqueous droplets floating in oil (ddPCR). For use in the certification of target concentration in primary calibrant certified reference materials (CRMs), both λ and the partition volume, V, must be metrologically traceable to some accessible reference system, ideally, the International System of Units (SI). The fixed spatial distribution of cdPCR chambers enables real-time monitoring of PCR amplification. Analysis of the resulting reaction curves enables validation of the critical dPCR assumptions that are essential for establishing the SI traceability of λ. We know of no direct method for validating these assumptions for ddPCR platforms. The manufacturers of the cdPCR and ddPCR systems available to us do not provide traceable partition volume specifications. Our colleagues at the National Institute of Standards and Technology (NIST) have developed a reliable method for determining ddPCR droplet volume and have demonstrated that different ddPCR reagents yield droplets of somewhat different size. Thus, neither dPCR platform by itself provides metrologically traceable estimates of target concentration. We show here that evaluating split samples with both cdPCR and ddPCR platforms can transfer the λ traceability characteristics of a cdPCR assay to its ddPCR analogue, establishing fully traceable ddPCR estimates of CRM target concentration.
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Affiliation(s)
- Margaret C Kline
- Materials Measurement Laboratory , National Institute of Standards and Technology , Gaithersburg, Maryland 20899, United States
| | - David L Duewer
- Materials Measurement Laboratory , National Institute of Standards and Technology , Gaithersburg, Maryland 20899, United States
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