82 results match your criteria dpcr applied

Diagnostic performances of common nucleic acid tests for SARS-CoV-2 in hospitals and clinics: a systematic review and meta-analysis.

Lancet Microbe 2021 Oct 13. Epub 2021 Oct 13.

Department of Chemical Pathology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong Special Administrative Region, China.

Background: An optimised standard experimental setup across different hospitals is urgently needed to ensure consistency in nucleic acid test results for SARS-CoV-2 detection. A standard comparison across different nucleic acid tests and their optimal experimental setups is not present. We assessed the performance of three common nucleic acid tests, namely digital PCR (dPCR), quantitative PCR (qPCR), and loop-mediated isothermal amplification (LAMP), to detect SARS-CoV-2 in clinical settings. Read More

View Article and Full-Text PDF
October 2021

High-accuracy quantitative principle of a new compact digital PCR equipment: Lab On An Array.

Genomics Inform 2021 Sep 30;19(3):e34. Epub 2021 Sep 30.

Department of Bioconvergence Engineering, Dankook University, Yongin 16890, Korea.

Digital PCR (dPCR) is the third-generation PCR that enables real-time absolute quantification without reference materials. Recently, global diagnosis companies have developed new dPCR equipment. In line with the development, the Lab On An Array (LOAA) dPCR analyzer (Optolane) was launched last year. Read More

View Article and Full-Text PDF
September 2021

HPV Sequencing Facilitates Ultrasensitive Detection of HPV Circulating Tumor DNA.

Clin Cancer Res 2021 Sep 27. Epub 2021 Sep 27.

Department of Radiation Oncology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada.

Purpose: Human papillomavirus (HPV) DNA offers a convenient circulating tumor DNA (ctDNA) marker for HPV-associated malignancies, but current methods, such as digital PCR (dPCR), provide insufficient accuracy for clinical applications in patients with low disease burden. We asked whether a next-generation sequencing approach, HPV sequencing (HPV-seq), could provide quantitative and qualitative assessment of HPV ctDNA in low disease burden settings.

Experimental Design: We conducted preclinical technical validation studies on HPV-seq and applied it retrospectively to a prospective multicenter cohort of patients with locally advanced cervix cancer (NCT02388698) and a cohort of patients with oropharynx cancer. Read More

View Article and Full-Text PDF
September 2021

Measurement of Transgene Copy Number in Plants Using Droplet Digital PCR.

Bio Protoc 2021 Jul 5;11(13):e4075. Epub 2021 Jul 5.

Earlham Institute, Norwich Research Park, Colney lane, Norwich, UK.

Transgenic plants are produced both to investigate gene function and to confer desirable traits into crops. Transgene copy number is known to influence expression levels, and consequently, phenotypes. Similarly, knowledge of transgene zygosity is desirable for making quantitative assessments of phenotype and tracking the inheritance of transgenes in progeny generations. Read More

View Article and Full-Text PDF

Virtual Fluorescence Color Channels by Selective Photobleaching in Digital PCR Applied to the Quantification of Point Mutations.

Anal Chem 2021 08 19;93(30):10538-10545. Epub 2021 Jul 19.

Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany.

Multiplexing of analyses is essential to reduce sample and reagent consumption in applications with large target panels. In applications such as cancer diagnostics, the required degree of multiplexing often exceeds the number of available fluorescence channels in polymerase chain reaction (PCR) devices. The combination of photobleaching-sensitive and photobleaching-resistant fluorophores of the same color can boost the degree of multiplexing by a factor of 2 per channel. Read More

View Article and Full-Text PDF

Comparison of two digital PCR methods for EGFR DNA and SARS-CoV-2 RNA quantification.

Clin Chim Acta 2021 Oct 16;521:9-18. Epub 2021 Jun 16.

Biomolecular Measurement Team, Korea Research Institute of Standards and Science, Daejeon, Republic of Korea. Electronic address:

Background: The COVID-19 pandemic caused by the severe acute SARS-CoV-2 virus has undeniably highlighted the importance of reliable nucleic acid quantification. Digital PCR (dPCR) is capable of the absolute quantification of nucleic acids.

Method: By using the droplet dPCR (QX200) and the digital real-time PCR (LOAA), the copy numbers were compared via multiple assays for three distinct targerts; EGFR DNA, SARS-CoV-2 and HIV-1 RNA. Read More

View Article and Full-Text PDF
October 2021

Digital PCR for Genotype Quantification: A Case Study in a Pasta Production Chain.

Biology (Basel) 2021 May 9;10(5). Epub 2021 May 9.

Plant Breeding, Wageningen University Research, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands.

Digital polymerase chain reaction (dPCR) is a breakthrough technology based on the partitioning of the analytical sample and detection of individual end-point amplifications into the separate compartments. Among the numerous applications of this technology, its suitability in mutation detection is relevant and characterized by unprecedented levels of precision. The actual applicability of this analytical technique to quantify the presence of a specific plant genotype, in both raw materials and transformed products, by exploiting a point polymorphism has been evaluated. Read More

View Article and Full-Text PDF

Development of a 3':5' digital PCR assay to determine horse mRNA integrity.

Anal Biochem 2021 08 1;626:114217. Epub 2021 May 1.

Department of Morphology, Faculty of Veterinary Medicine, Ghent University, B-9820, Merelbeke, Belgium; Ghent University Digital PCR Consortium, Ghent University, B-9000, Ghent, Belgium. Electronic address:

Accurate tools to measure RNA integrity are essential to obtain reliable gene expression data. The reverse transcription quantitative PCR (RT-qPCR) based 3':5' assay permits a direct determination of messenger RNA (mRNA) integrity. However, the use of standard curves and the possible effect of PCR inhibitors make this method cumbersome and prone to variation, especially in small samples. Read More

View Article and Full-Text PDF

Digital PCR (dPCR) and qPCR mediated determination of transgene copy number in the forage legume white clover (Trifolium repens).

Mol Biol Rep 2021 Apr 16;48(4):3069-3077. Epub 2021 Apr 16.

School of Applied Systems Biology, La Trobe University, Melbourne, VIC, 3086, Australia.

Obtaining data on transgene copy number is an integral step in the generation of transgenic plants. Techniques such as Southern blot, segregation analysis, and quantitative PCR (qPCR) have routinely been used for this task, in a range of species. More recently, use of Digital PCR (dPCR) has become prevalent, with a measurement accuracy higher than qPCR reported. Read More

View Article and Full-Text PDF

[Clinical Application of Circulating Tumor DNA in Diffuse Large B-Cell Lymphoma--Review].

Zhongguo Shi Yan Xue Ye Xue Za Zhi 2021 Apr;29(2):638-642

Department of Hematology, The First Affiliated Hospital of Bengbu Medical College, Bengbu 233003, Anhui Province, China,E-mail: 4119469 @ qq.com.

Diffuse large B-cell lymphoma (DLBCL) as an aggressive lymphoma, there has not a good molecular marker to assess the therapeutic efficacy and prognosis of the disease. As compared with the traditional deteation method, it was found that the circulating tumor DNA (ctDNA) can be used as a non-invasive specific biomarker which can dynamically provide the information about the lymphoma. ctDNA in DLBCL can be obtained by dideoxy chain termination method combined with PCR, so as to detect genetic markers, targeted sequences of gene which is related to lymphoma; the digital PCR (dPCR) for lymphoma somatic mutations and the detection of abnormal methylation; ctDNA is closely related to the diagncsis, therapeutic efficiency and prognosis of DLBCL, thus ctDNA can be used for the early detection, mid-term and prognostic monitoring in DLBCL, which makes ctDNA have a broad clinical applied prospect. Read More

View Article and Full-Text PDF

The Antioxidant Effect of Curcumin and Rutin on Oxidative Stress Biomarkers in Experimentally Induced Periodontitis in Hyperglycemic Wistar Rats.

Molecules 2021 Mar 2;26(5). Epub 2021 Mar 2.

Dental Medicine Department, Faculty of Medicine and Pharmacy, University of Oradea, 410068 Oradea, Romania.

Background: There is a growing interest in the correlation between antioxidants and periodontal disease. In this study, we aimed to investigate the effect of oxidative stress and the impact of two antioxidants, curcumin and rutin, respectively, in the etiopathology of experimentally induced periodontitis in diabetic rats.

Methods: Fifty Wistar albino rats were randomly divided into five groups and were induced with diabetes mellitus and periodontitis: (1) (CONTROL)-control group, (2) (DPP)-experimentally induced diabetes mellitus and periodontitis, (3) (DPC)-experimentally induced diabetes mellitus and periodontitis treated with curcumin (C), (4) (DPR)-experimentally induced diabetes mellitus and periodontitis treated with rutin (R) and (5) (DPCR)-experimentally induced diabetes mellitus and periodontitis treated with C and R. Read More

View Article and Full-Text PDF

Identification of Reduced Host Transcriptomic Signatures for Tuberculosis Disease and Digital PCR-Based Validation and Quantification.

Front Immunol 2021 2;12:637164. Epub 2021 Mar 2.

Section of Paediatrics, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom.

Recently, host whole blood gene expression signatures have been identified for diagnosis of tuberculosis (TB). Absolute quantification of the concentrations of signature transcripts in blood have not been reported, but would facilitate diagnostic test development. To identify minimal transcript signatures, we applied a transcript selection procedure to microarray data from African adults comprising 536 patients with TB, other diseases (OD) and latent TB (LTBI), divided into training and test sets. Read More

View Article and Full-Text PDF
September 2021

Detection of tumor-derived extracellular vesicles in plasma from patients with solid cancer.

BMC Cancer 2021 Mar 24;21(1):315. Epub 2021 Mar 24.

Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus MC, Room Be400, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands.

Background: Extracellular vesicles (EVs) are actively secreted by cells into body fluids and contain nucleic acids of the cells they originate from. The goal of this study was to detect circulating tumor-derived EVs (ctEVs) by mutant mRNA transcripts (EV-RNA) in plasma of patients with solid cancers and compare the occurrence of ctEVs with circulating tumor DNA (ctDNA) in cell-free DNA (cfDNA).

Methods: For this purpose, blood from 20 patients and 15 healthy blood donors (HBDs) was collected in different preservation tubes (EDTA, BCT, CellSave) and processed into plasma within 24 h from venipuncture. Read More

View Article and Full-Text PDF

An assessment of the reproducibility of reverse transcription digital PCR quantification of HIV-1.

Methods 2021 Mar 12. Epub 2021 Mar 12.

National Measurement Laboratory, LGC, Queens Road, Teddington, Middlesex TW11 0LY, United Kingdom; School of Biosciences & Medicine, Faculty of Health & Medical Science, University of Surrey, Guildford GU2 7XH, United Kingdom. Electronic address:

Viral load monitoring in human immunodeficiency virus type 1 (HIV-1) infection is often performed using reverse transcription quantitative PCR (RT-qPCR) to observe response to treatment and identify the development of resistance. Traceability is achieved using a calibration hierarchy traceable to the International Unit (IU). IU values are determined using consensus agreement derived from estimations by different laboratories. Read More

View Article and Full-Text PDF

Specific and Sensitive Diagnosis of -ITD in Various Cancers by Digital PCR.

Front Oncol 2021 25;11:645512. Epub 2021 Feb 25.

APHM, CHU Timone, Service d'Anatomie Pathologique et de Neuropathologie, Marseille, France.

is an epigenetic regulator altered by various mechanisms including -internal tandem duplication (-ITD) in a wide range of cancers. Six different -ITD in the 3'-part of the coding sequence of exon 15 have been reported ranging from 89 to 114 bp in length. -ITD is a common genetic alteration found in clear cell sarcoma of the kidney and primitive myxoid mesenchymal tumor of infancy (PMMTI) and it characterizes a new type of central nervous system tumor: "CNS tumor with -ITD". Read More

View Article and Full-Text PDF
February 2021

Frequent post-operative monitoring of colorectal cancer using individualised ctDNA validated by multiregional molecular profiling.

Br J Cancer 2021 04 3;124(9):1556-1565. Epub 2021 Mar 3.

Division of Biomedical Research and Development, Iwate Medical University Institute for Biomedical Sciences, Iwate, Japan.

Background: Circulating tumour DNA (ctDNA) is known as a tumour-specific personalised biomarker, but the mutation-selection criteria from heterogeneous tumours remain a challenge.

Methods: We conducted multiregional sequencing of 42 specimens from 14 colorectal tumours of 12 patients, including two double-cancer cases, to identify mutational heterogeneity to develop personalised ctDNA assays using 175 plasma samples.

Results: "Founder" mutations, defined as a mutation that is present in all regions of the tumour in a binary manner (i. Read More

View Article and Full-Text PDF

Simultaneous absolute quantification and sequencing of fish environmental DNA in a mesocosm by quantitative sequencing technique.

Sci Rep 2021 Feb 23;11(1):4372. Epub 2021 Feb 23.

Graduate School of Human Development and Environment, Kobe University, Kobe, Japan.

The combination of high-throughput sequencing technology and environmental DNA (eDNA) analysis has the potential to be a powerful tool for comprehensive, non-invasive monitoring of species in the environment. To understand the correlation between the abundance of eDNA and that of species in natural environments, we have to obtain quantitative eDNA data, usually via individual assays for each species. The recently developed quantitative sequencing (qSeq) technique enables simultaneous phylogenetic identification and quantification of individual species by counting random tags added to the 5' end of the target sequence during the first DNA synthesis. Read More

View Article and Full-Text PDF
February 2021

Detection of SMN1 to SMN2 gene conversion events and partial SMN1 gene deletions using array digital PCR.

Neurogenetics 2021 03 7;22(1):53-64. Epub 2021 Jan 7.

Center for Applied Clinical Genomics, Nemours Biomedical Research, Nemours Alfred I. duPont Hospital for Children, Wilmington, DE, USA.

Proximal spinal muscular atrophy (SMA), a leading genetic cause of infant death worldwide, is an early-onset motor neuron disease characterized by loss of α-motor neurons and associated muscle atrophy. SMA is caused by deletion or other disabling mutations of survival motor neuron 1 (SMN1) but retention of one or more copies of the paralog SMN2. Within the SMA population, there is substantial variation in SMN2 copy number (CN); in general, those individuals with SMA who have a high SMN2 CN have a milder disease. Read More

View Article and Full-Text PDF

Compressed Air-Driven Continuous-Flow Thermocycled Digital PCR for HBV Diagnosis in Clinical-Level Serum Sample Based on Single Hot Plate.

Molecules 2020 Nov 30;25(23). Epub 2020 Nov 30.

State Key Laboratory of Applied Optics, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Changchun 130033, China.

We report a novel compressed air-driven continuous-flow digital PCR (dPCR) system based on a 3D microfluidic chip and self-developed software system to realize real-time monitoring. The system can ensure the steady transmission of droplets in long tubing without an external power source and generate stable droplets of suitable size for dPCR by two needles and a narrowed Teflon tube. The stable thermal cycle required by dPCR can be achieved by using only one constant temperature heater. Read More

View Article and Full-Text PDF
November 2020

Development and validation of a 4-color multiplexing spinal muscular atrophy (SMA) genotyping assay on a novel integrated digital PCR instrument.

Sci Rep 2020 11 16;10(1):19892. Epub 2020 Nov 16.

Combinati Inc., 2450 Embarcadero Way, Palo Alto, CA, 94303, USA.

Digital PCR (dPCR) technology has been proven to be highly sensitive and accurate in detecting copy number variations (CNV). However, a higher-order multiplexing dPCR assay for measuring SMN1 and SMN2 copy numbers in spinal muscular atrophy (SMA) samples has not been reported. Described here is a rapid multiplex SMA dPCR genotyping assay run on a fully integrated dPCR instrument with five optical channels. Read More

View Article and Full-Text PDF
November 2020

Three-dimensional digital PCR through light-sheet imaging of optically cleared emulsion.

Proc Natl Acad Sci U S A 2020 10 30;117(41):25628-25633. Epub 2020 Sep 30.

Department of Materials Science and Engineering, College of Engineering, Peking University, 100871 Beijing, China;

The realization of the vast potential of digital PCR (dPCR) to provide extremely accurate and sensitive measurements in the clinical setting has thus far been hindered by challenges such as assay robustness and high costs. Here we introduce a lossless and contamination-free dPCR technology, termed CLEAR-dPCR, which addresses these challenges by completing the dPCR sample preparation, PCR, and readout all in one tube. Optical clearing of the droplet dPCR emulsion was combined with emerging light-sheet fluorescence microscopy, to acquire a three-dimensional (3D) image of a half million droplets sealed in a tube in seconds. Read More

View Article and Full-Text PDF
October 2020

Introduction of Noninvasive Prenatal Testing for Blood Group and Platelet Antigens from Cell-Free Plasma DNA Using Digital PCR.

Transfus Med Hemother 2020 Jul 5;47(4):292-301. Epub 2019 Dec 5.

Institute of Transfusion Medicine and Immunology, Heidelberg University, Medical Faculty Mannheim, German Red Cross Blood Service Baden-Württemberg - Hessen, Mannheim, Germany.

Background: Noninvasive prenatal testing (NIPT) for fetal antigens is a common standard for targeted immune prophylaxis in RhD-mediated hemolytic disease of the fetus and newborn, and is most frequently done by quantitative PCR (qPCR). A similar approach is considered for other blood group and human platelet alloantigens (HPA). Because of a higher sensitivity compared to qPCR for rare molecule detection, we established and validated digital PCR (dPCR) assays for the detection of exons 3, 5 and 7, KEL1, HPA-1a, and HPA-5b from cell-free DNA (cfDNA) in plasma. Read More

View Article and Full-Text PDF

Moving from qPCR to Chip Digital PCR Assays for Tracking of some Species Causing Head Blight in Cereals.

Microorganisms 2020 Aug 27;8(9). Epub 2020 Aug 27.

Council for Agricultural Research and Economics, Research Centre for Genomics and Bioinformatics, I-29017 Fiorenzuola d'Arda PC, Italy.

Head Blight (FHB) is one of the major diseases affecting small-grain cereals, worldwide spread and responsible for severe yield and quality losses annually. Diagnostic tools, able to track species even in the early stages of infection, can contribute to mycotoxins' risk control. Among DNA-based technologies for detection, qPCR (single and multiplex assays) is currently the most applied method. Read More

View Article and Full-Text PDF

Utilization of Digital PCR in Quantity Verification of Plasmid Standards Used in Quantitative PCR.

Front Mol Biosci 2020 29;7:155. Epub 2020 Jul 29.

Department of Food and Feed Safety, Veterinary Research Institute, Brno, Czechia.

Quantitative PCR (qPCR) is a widely used method for nucleic acid quantification of various pathogenic microorganisms. For absolute quantification of microbial load by qPCR, it is essential to create a calibration curve from accurately quantified quantification standards, from which the number of pathogens in a sample is derived. Spectrophotometric measurement of absorbance is a routine method for estimating nucleic acid concentration, however, it may be affected by presence of other potentially contaminating nucleic acids or proteins and salts. Read More

View Article and Full-Text PDF

Accurate In-Vivo Quantification of CD19 CAR-T Cells after Treatment with Axicabtagene Ciloleucel (Axi-Cel) and Tisagenlecleucel (Tisa-Cel) Using Digital PCR.

Cancers (Basel) 2020 Jul 20;12(7). Epub 2020 Jul 20.

Department of Stem Cell Transplantation, University Medical Centre (UMC) Hamburg-Eppendorf, 20246 Hamburg, Germany.

Immunotherapy with CD19-specific chimeric antigen receptor (CAR-) T cells has shown excellent efficacy in relapsed/refractory B-cell cancers. The in vivo expansion and persistence of CAR-T cells after infusion are important response- and toxicity-determining variables, but diagnostic tools are largely missing. We showed previously for axi-cel that digital PCR (dPCR) is excellently suited to monitoring CAR-T cells in vivo. Read More

View Article and Full-Text PDF

A Chip Digital PCR Assay for Quantification of Common Wheat Contamination in Pasta Production Chain.

Foods 2020 Jul 10;9(7). Epub 2020 Jul 10.

Council for Agricultural Research and Economics, Research Centre for Genomics and Bioinformatics, Via San Protaso 302, I-29017 Fiorenzuola d'Arda PC, Italy.

Pasta, the Italian product par excellence, is made of pure durum wheat. The use of derived semolina is in fact mandatory for Italian pasta, in which species is considered a contamination that must not exceed the 3% maximum level. Over the last 50 years, various electrophoretic, chemical, and immuno-chemical methods have been proposed aimed to track the possible presence of common wheat in semolina and pasta. Read More

View Article and Full-Text PDF

Changing role of EMS -analyses of non-conveyed and conveyed patients in Finland.

Scand J Trauma Resusc Emerg Med 2020 May 29;28(1):45. Epub 2020 May 29.

Emergency Medical Services, Turku University Hospital and University of Turku, Turku, Finland.

Background: Emergency Medical Services (EMS) and Emergency Departments (ED) have seen increasing attendance rates in the last decades. Currently, EMS are increasingly assessing and treating patients without the need to convey patients to health care facility. The aim of this study was to describe and compare the patient case-mix between conveyed and non-conveyed patients and to analyze factors related to non-conveyance decision making. Read More

View Article and Full-Text PDF

Improving Quantitative Power in Digital PCR through Digital High-Resolution Melting.

J Clin Microbiol 2020 05 26;58(6). Epub 2020 May 26.

Department of Bioengineering, University of California, San Diego, La Jolla, California, USA

Applying digital PCR (dPCR) technology to challenging clinical and industrial detection tasks has become more prevalent because of its capability for absolute quantification and rare target detection. However, practices learned from quantitative PCR (qPCR) that promote assay robustness and wide-ranging utility are not readily applied in dPCR. These include internal amplification controls to account for false-negative reactions and amplicon high-resolution melt (HRM) analysis to distinguish true positives from false positives. Read More

View Article and Full-Text PDF

Fast, sensitive, and reliable detection of waterborne pathogens by digital PCR after coagulation and foam concentration.

J Biosci Bioeng 2020 Jul 5;130(1):76-81. Epub 2020 Mar 5.

Department of Civil and Environmental Engineering, Faculty of Engineering, University of Miyazaki, 1-1 Gakuen Kibanadai-Nishi, Miyazaki 889-2192, Japan. Electronic address:

The quantification of pathogens is important for assessing water safety and preventing disease outbreaks. Culture-independent approaches, such as quantitative PCR (qPCR) and digital PCR (dPCR), are useful techniques for quantifying pathogens in water samples. However, since pathogens are usually present at low concentrations in water, it is necessary to concentrate microbial cells before extracting their DNA. Read More

View Article and Full-Text PDF

PCR inhibition in qPCR, dPCR and MPS-mechanisms and solutions.

Anal Bioanal Chem 2020 Apr 12;412(9):2009-2023. Epub 2020 Feb 12.

Swedish National Forensic Centre, Swedish Police Authority, 581 94, Linköping, Sweden.

DNA analysis has seen an incredible development in terms of instrumentation, assays and applications over the last years. Massively parallel sequencing (MPS) and digital PCR are now broadly applied in research and diagnostics, and quantitative PCR is used for more and more practises. All these techniques are based on in vitro DNA polymerization and fluorescence measurements. Read More

View Article and Full-Text PDF