538 results match your criteria dpcr

Presence of defective viral genes in H1N1 live attenuated influenza vaccine strains is not associated with reduced human cell fitness or vaccine effectiveness.

Vaccine 2021 Oct 15. Epub 2021 Oct 15.

Flu-BPD, Biopharmaceuticals R&D, AstraZeneca, Liverpool, UK.

In the 2013-2014 and 2015-2016 seasons, quadrivalent live attenuated influenza vaccine (LAIV) showed reduced pandemic 2009 H1N1 (A/H1N1pdm09) vaccine effectiveness (VE) in the U.S. Impaired fitness of A/H1N1pdm09 LAIV strains in primary human nasal epithelial cells (hNEC) was subsequently shown to be associated with reduced VE. Read More

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October 2021

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

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October 2021

A Secreted Chorismate Mutase from pv. Attenuates Virulence and Walnut Blight Symptoms.

Int J Mol Sci 2021 Sep 26;22(19). Epub 2021 Sep 26.

Department of Plant Sciences, University of California, Davis, CA 95616, USA.

Walnut blight is a significant above-ground disease of walnuts caused by pv. (Xaj). The secreted form of chorismate mutase (CM), a key enzyme of the shikimate pathway regulating plant immunity, is highly conserved between plant-associated beta and gamma proteobacteria including phytopathogens belonging to the Xanthomonadaceae family. Read More

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September 2021

Resistance to Tyrosine Kinase Inhibitors in Chronic Myeloid Leukemia-From Molecular Mechanisms to Clinical Relevance.

Cancers (Basel) 2021 Sep 26;13(19). Epub 2021 Sep 26.

Laboratory of Oncobiology and Hematology, University Clinic of Hematology, Faculty of Medicine (FMUC), University of Coimbra, 3000-548 Coimbra, Portugal.

Resistance to targeted therapies is a complex and multifactorial process that culminates in the selection of a cancer clone with the ability to evade treatment. Chronic myeloid leukemia (CML) was the first malignancy recognized to be associated with a genetic alteration, the t(9;22)(q34;q11). This translocation originates the fusion gene, encoding the cytoplasmic chimeric BCR-ABL1 protein that displays an abnormally high tyrosine kinase activity. Read More

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September 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

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September 2021

Development of a Molecular Assay for Detection and Quantification of the BRAF Variation in Residual Tissue From Thyroid Nodule Fine-Needle Aspiration Biopsy Specimens.

JAMA Netw Open 2021 Oct 1;4(10):e2127243. Epub 2021 Oct 1.

Alex and Simona Shnaider Research Laboratory in Molecular Oncology, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Mount Sinai Hospital, Toronto, Canada.

Importance: Thyroid cancer, predominantly papillary thyroid carcinoma (PTC), is common, but an estimated 30% of ultrasonography-guided fine-needle aspiration (FNA) biopsies of thyroid nodules are indeterminate. BRAF variation, associated with poor clinicopathological characteristics, is a useful molecular marker for diagnostics.

Objective: To develop a sensitive molecular assay for BRAF V600E detection in remaining tissue of thyroid FNA biopsies to identify patients with cancer carrying a BRAF variation. Read More

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October 2021

A Portable Digital Loop-Mediated Isothermal Amplification Platform Based on Microgel Array and Hand-Held Reader.

ACS Sens 2021 Oct 4. Epub 2021 Oct 4.

The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, China.

Digital polymerase chain reaction (dPCR) has found widespread applications in molecular diagnosis of various diseases owing to its sensitive single-molecule detection capability. However, the existing dPCR platforms rely on the auxiliary procedure to disperse DNA samples, which needs complicated operation, expensive apparatus, and consumables. Besides, the complex and costly dPCR readers also impede the applications of dPCR for point-of-care testing (POCT). Read More

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October 2021

Emerging methods for and novel insights gained by absolute quantification of mitochondrial DNA copy number and its clinical applications.

Pharmacol Ther 2021 Sep 27:107995. Epub 2021 Sep 27.

Biomedical Physiology & Kinesiology, Simon Fraser University, Burnaby, Canada; Centre for Cell Biology, Development, and Disease, Simon Fraser University, Burnaby, Canada. Electronic address:

The past thirty years have seen a surge in interest in pathophysiological roles of mitochondria, and the accurate quantification of mitochondrial DNA copy number (mCN) in cells and tissue samples is a fundamental aspect of assessing changes in mitochondrial health and biogenesis. Quantification of mCN between studies is surprisingly variable due to a combination of physiological variability and diverse protocols being used to measure this endpoint. The advent of novel methods to quantify nucleic acids like digital polymerase chain reaction (dPCR) and high throughput sequencing offer the ability to measure absolute values of mCN. Read More

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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

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September 2021

Early dynamics of circulating tumor DNA predict chemotherapy responses for patients with esophageal cancer.

Carcinogenesis 2021 Sep 24. Epub 2021 Sep 24.

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

We investigated whether early circulating tumor DNA (ctDNA) changes, measured using digital PCR (dPCR), can predict later chemotherapy responses in esophageal squamous cell cancer (ESCC). We compared the dynamics of ctDNA and tumor volumes during chemotherapy in 42 ESCC. The accuracy of predictions of later chemotherapy responses were evaluated by the ratio of the variant allele frequency (VAF) of ctDNA (post-/pre-ctDNA) and the total tumor volume (post-/pre-volume) before and after an initial chemotherapy cycle using a receiver-operating characteristic curve analysis. Read More

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September 2021

Congenital infection of SARS-CoV-2 with intrauterine foetal death: a clinicopathological study with molecular analysis.

Clin Infect Dis 2021 Sep 23. Epub 2021 Sep 23.

Department of Pathology and Neuropathology, La Timone Hospital, Aix Marseille, University, Marseille, France.

Observations of vertical transmission of SARS-CoV-2 infection from mother to foetus have recently been described in the literature. However, the consequences of such transmission, whether foetal or neonatal, are poorly understood. From a case of in utero foetal death at 24 +2 weeks of gestation that occurred seven days after the diagnosis of symptomatic SARS-CoV-2 infection in the mother, we isolated the incriminating virus by immunochemistry and molecular techniques in several foetal tissues, with a variant analysis of the SARS-CoV-2 genome. Read More

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September 2021

Duplex dPCR system for rapid identification of gram-negative pathogens in the blood of patients with bloodstream infection: A culture-independent approach.

J Microbiol Biotechnol 2021 Sep 11;31(1). Epub 2021 Sep 11.

Department of Microbiology, The Catholic University of Korea, College of Medicine, Seoul 06591, Republic of Korea.

Early and accurate detection of pathogens is important to improve clinical outcomes of bloodstream infections (BSI), especially in the case of drug-resistant pathogens. In this study, we aimed to develop a culture-independent digital PCR (dPCR) system for multiplex detection of major sepsis-causing gram-negative pathogens and antimicrobial resistance genes using plasma DNA from BSI patients. Our duplex dPCR system successfully detected nine targets (five bacteria-specific targets and four antimicrobial resistance genes) through five reactions within 3 hours. Read More

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September 2021

Diagnostic evaluation of qRT-PCR-based kit and dPCR-based kit for COVID-19.

Genes Genomics 2021 11 15;43(11):1277-1288. Epub 2021 Sep 15.

Department of Bio-Convergence Engineering, Dankook University, Jukjeon, 16890, Republic of Korea.

Background: Coronavirus disease of 2019 (COVID-19) is well known as a fatal disease, first discovered at Wuhan in China, ranging from mild to death, such as shortness of breath and fever. Early diagnosis of COVID-19 is a crucial point in preventing global prevalence.

Objective: We aimed to evaluate the diagnostic competency and efficiency with the Allplex™ 2019-nCoV Assay kit and the Dr. Read More

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November 2021

Increased Sensitivity of Detection of and DNA Fragments in Serum of Prostate Cancer Patients: Optimisation of Diagnostics Using OBBPA-ddPCR.

Cancers (Basel) 2021 Sep 4;13(17). Epub 2021 Sep 4.

Institute of Clinical Chemistry and Laboratory Medicine, Carl Gustav Carus University Hospital, Technische Universität Dresden, Fetscherstr. 74, D-01307 Dresden, Germany.

Identification of aberrant DNA methylation is a promising tool in prostate cancer (PCa) diagnosis and treatment. In this study, we evaluated a two-step method named optimised bias-based preamplification followed by digital PCR (OBBPA-dPCR). The method was used to identify promoter hypermethylation of 2 tumour suppressor genes and in the circulating cell-free DNA (cfDNA) from serum samples of PCa patients ( = 75), benign prostatic hyperplasia (BPH, = 58), and healthy individuals (controls, = 155). Read More

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September 2021

Digital PCR can augment the interpretation of RT-qPCR Cq values for SARS-CoV-2 diagnostics.

Methods 2021 Aug 26. Epub 2021 Aug 26.

LGC Genomics GmbH, Research and Development, TGS Haus 8, Ostendstraße 25, 12459 Berlin, Germany; Molecular Diagnostics Unit, Medical Technology Research Centre, Anglia Ruskin University, UK. Electronic address:

Coronavirus disease 2019 (COVID-19) is an infectious, acute respiratory disease caused mainly by person-to-person transmission of the coronavirus SARS-CoV-2. Its emergence has caused a world-wide acute health crisis, intensified by the challenge of reliably identifying individuals likely to transmit the disease. Diagnosis is hampered by the many unknowns surrounding this disease, including those relating to infectious viral burden. Read More

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Development of multiplex digital PCR assays for the detection of PIK3CA mutations in the plasma of metastatic breast cancer patients.

Sci Rep 2021 08 27;11(1):17316. Epub 2021 Aug 27.

Department of Medical Oncology, Centre Eugène Marquis, Unicancer, Rennes, France.

With the approval of new therapies targeting the PI3K pathway, the detection of PIK3CA mutations has become a key factor in treatment management for HR+/HER2- metastatic breast cancer (MBC). We developed multiplex digital PCR (dPCR) assays to detect and quantify PIK3CA mutations. A first screening assay allows the detection of 21 mutations, with a drop-off system targeting the 542-546 hotspot mutations combined with the simultaneous detection of N345K, C420R, H1047L and H1047R mutations. Read More

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Development of a Duck Genomic Reference Material by Digital PCR Platforms for the Detection of Meat Adulteration.

Foods 2021 Aug 15;10(8). Epub 2021 Aug 15.

Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China.

Low-cost meat, such as duck, is frequently used to adulterate more expensive foods like lamb or beef in many countries. However, the lack of DNA-based reference materials has limited the quality control and detection of adulterants. Here, we report the development and validation of duck genomic DNA certified reference materials (CRMs) through the detection of the duck () gene by digital PCR (dPCR) for the identification of duck meat in food products. Read More

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Diagnosis of Infection and Recent Advances.

Hang Yang Bing Hu

Diagnostics (Basel) 2021 Jul 21;11(8). Epub 2021 Jul 21.

Department of Gastroenterology, West China Hospital, Sichuan University, Chengdu 610041, China.

Background: () infects approximately 50% of the world population. Its infection is associated with gastropathies, extra-gastric digestive diseases, and diseases of other systems. There is a canonical process from acute-on-chronic inflammation, chronic atrophic gastritis (CAG), intestinal metaplasia (IM), dysplasia, and intraepithelial neoplasia, eventually to gastric cancer (GC). Read More

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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

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An alternative approach for bioanalytical assay optimization for wastewater-based epidemiology of SARS-CoV-2.

Sci Total Environ 2021 May 26;789:148043. Epub 2021 May 26.

Laboratory for Microbiology, Parasitology and Hygiene, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium.

Wastewater-based epidemiology of SARS-CoV-2 could play a role in monitoring the spread of the virus in the population and controlling possible outbreaks. However, sensitive sample preparation and detection methods are necessary to detect trace levels of SARS-CoV-2 RNA in influent wastewater (IWW). Unlike predecessors, method optimization of a SARS-CoV-2 RNA concentration and detection procedure was performed with IWW samples with high viral SARS-CoV-2 RNA loads. Read More

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Endpoint PCR coupled with capillary electrophoresis (celPCR) provides sensitive and quantitative measures of environmental DNA in singleplex and multiplex reactions.

PLoS One 2021 23;16(7):e0254356. Epub 2021 Jul 23.

Department of Zoology, University of Innsbruck, Innsbruck, Austria.

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). Read More

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The Environmental Microbiology Minimum Information (EMMI) Guidelines: qPCR and dPCR Quality and Reporting for Environmental Microbiology.

Environ Sci Technol 2021 08 21;55(15):10210-10223. Epub 2021 Jul 21.

Insitute for the Environment, University of North Carolina, Chapel Hill, North Carolina 27517, United States.

Real-time quantitative polymerase chain reaction (qPCR) and digital PCR (dPCR) methods have revolutionized environmental microbiology, yielding quantitative organism-specific data of nucleic acid targets in the environment. Such data are essential for characterizing interactions and processes of microbial communities, assessing microbial contaminants in the environment (water, air, fomites), and developing interventions (water treatment, surface disinfection, air purification) to curb infectious disease transmission. However, our review of recent qPCR and dPCR literature in our field of health-related environmental microbiology showed that many researchers are not reporting necessary and sufficient controls and methods, which would serve to strengthen their study results and conclusions. Read More

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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

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Absolute quantification of SARS-CoV-2 with Clarity Plus™ digital PCR.

Methods 2021 Jul 15. Epub 2021 Jul 15.

Singapore Institute of Technology, 10 Dover Dr, Singapore 138683, Singapore.

In recent years, the usage of digital polymerase chain reaction (dPCR) for various clinical applications has increased exponentially. In this study, a dPCR assay optimized on the Clarity Plus™ dPCR system was evaluated for the absolute quantification of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of the global coronavirus disease 2019 (COVID-19) outbreak. The assay demonstrated good inter- and intra- assay precision, accuracy, as well as excellent linearity across a range of over 6 orders of magnitude for target gene quantification. Read More

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High-sensitivity SARS-CoV-2 group testing by digital PCR among symptomatic patients in hospital settings.

J Clin Virol 2021 08 3;141:104895. Epub 2021 Jul 3.

CNRS- CREST, Ecole Polytechnique, Palaiseau, France and London School of Economics, London, United Kingdom.

Background: Worldwide demand for SARS-CoV-2 RT-PCR testing is still high as testing remains central to follow the disease spread and vaccine efficacy. Group testing has been proposed as a solution to expand testing capabilities but sensitivity concerns may limit its impact on the management of the pandemic. Digital PCR (RT-dPCR) has been shown to be highly sensitive and could help by providing larger testing capabilities without compromising sensitivity. Read More

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Pre-Degassed Microfluidic Chamber-Based Digital PCR Device for Meat Authentication Applications.

Micromachines (Basel) 2021 Jun 14;12(6). Epub 2021 Jun 14.

Department of Electronic and Information Engineering, Hebei University of Technology, Langfang 065000, China.

Droplet digital polymerase chain reaction (ddPCR) suffers from the need for specific equipment and skilled personnel; thus, we here present a chamber-based digital PCR microfluidic device that is compatible with fluorescence image read-out systems and removes bubbles by a pre-degassed microfluidic device that consists of a pilot channel and micro chamber arrays. Digitalized PCR reagents are introduced into micro chambers, and thermocycles are taken to perform a DNA amplification process. Then, fluorescence images of a micro chamber array are read out and analyzed to obtain the total number of positive chambers. Read More

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Digital PCR for accurate quantification of pathogens: Principles, applications, challenges and future prospects.

Int J Biol Macromol 2021 Aug 24;184:750-759. Epub 2021 Jun 24.

Guangdong Provincial Key Laboratory of Food Quality and Safety, College of Food Science, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory of Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, China. Electronic address:

Pathogens pose a severe threat to food safety and human health. The traditional methods for pathogen detection can't meet the growing diagnosis and control need. Digital PCR (dPCR) attracts a considerable attention for its ability to absolutely quantify pathogens with features of high selectivity, simplicity, accuracy and rapidity. Read More

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Oncological evaluation in the perioperative period using cfDNA with BRAF V600E mutation in patients with colorectal cancer.

Sci Rep 2021 06 24;11(1):13263. Epub 2021 Jun 24.

Department of Gastroenterological Surgery, Fukuoka University Faculty of Medicine, 7-45-1 Nanakuma, Jonan-ku, Fukuoka, 814-0180, Japan.

The detection of circulating cell-free DNA (cfDNA) by liquid biopsy is reported to provide prognostic information in colorectal cancer (CRC). Although the frequency of BRAF V600E mutation in CRC is less than 10%, it is associated with poor responses to conventional chemotherapy. We conducted a prospective study to investigate the relationship between the perioperative mutant allele frequency (MAF) of BRAF V600E and tumor recurrence, and to evaluate the possibility of early detection of recurrence. Read More

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Quantitation of Long Noncoding RNA Using Digital PCR.

Methods Mol Biol 2021 ;2348:113-121

Mayo Clinic, Jacksonville, FL, USA.

Long noncoding RNAs (lncRNAs) are implicated in many physiological or disease processes and alterations in their expression may contribute to the development of various diseases. Accurate quantitation of lncRNA can be useful in measuring changes in expression in different settings such as in the circulation where the measurement of lncRNA may be useful as a biomarker of disease. However, the low levels of lncRNA expression require the use of highly sensitive detection technologies for accurate quantitation. Read More

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September 2021

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

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October 2021