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Homogeneous and digital proximity ligation assays for the detection of Clostridium difficile toxins A and B
Conclusions PLA with either qPCR or dPCR readout have potential as new diagnostic applications for the detection of pathogens where nucleic acid based tests do not indicate viability or expression of toxins. Importantly, since it is not always necessary to use two different antibodies, the pool of potential antibodies useful for PLA diagnostic assays is usefully enhanced. (Source: Biomolecular Detection and Quantification)
Source: Biomolecular Detection and Quantification - August 31, 2016 Category: Molecular Biology Source Type: research

Validation of a digital PCR method for quantification of DNA copy number concentrations by using a certified reference material
Publication date: September 2016 Source:Biomolecular Detection and Quantification, Volume 9 Author(s): Liesbet Deprez, Philippe Corbisier, Anne-Marie Kortekaas, Stéphane Mazoua, Roxana Beaz Hidalgo, Stefanie Trapmann, Hendrik Emons Digital PCR has become the emerging technique for the sequence-specific detection and quantification of nucleic acids for various applications. During the past years, numerous reports on the development of new digital PCR methods have been published. Maturation of these developments into reliable analytical methods suitable for diagnostic or other routine testing purposes requires thei...
Source: Biomolecular Detection and Quantification - August 30, 2016 Category: Molecular Biology Source Type: research

Influence of primer & amp; probe chemistry and amplification target on reverse transcription digital PCR quantification of viral RNA
This study describes the impact of four experimental factors, namely primer and probe chemistry, PCR amplification target, duplexing, and template type, on the measurement results obtained by reverse transcription digital PCR (RT-dPCR) of viral RNA using influenza A virus as a model. Along conventional dual labelled probes (DLP), alternative primer and probe chemistries, including Zip Nucleic Acids (ZNAs), Locked Nucleic Acids (LNAs), and Scorpions®, were compared with two RNA template types: i) total genomic RNA extracted from cell cultured influenza A and ii) a synthetically prepared RNA transcript (In vitro transcribed...
Source: Biomolecular Detection and Quantification - August 27, 2016 Category: Molecular Biology Source Type: research

Science in the UK − whereto now?
Publication date: Available online 21 August 2016 Source:Biomolecular Detection and Quantification Author(s): Stephen Bustin (Source: Biomolecular Detection and Quantification)
Source: Biomolecular Detection and Quantification - August 20, 2016 Category: Molecular Biology Source Type: research

Methods for comparing multiple digital PCR experiments
Publication date: September 2016 Source:Biomolecular Detection and Quantification, Volume 9 Author(s): Michał Burdukiewicz, Stefan Rödiger, Piotr Sobczyk, Mario Menschikowski, Peter Schierack, Paweł Mackiewicz The estimated mean copy per partition (λ) is the essential information from a digital PCR (dPCR) experiment because λ can be used to calculate the target concentration in a sample. However, little information is available how to statistically compare dPCR runs of multiple runs or reduplicates. The comparison of λ values from several runs is a multiple comparison problem, which can be solved using the bi...
Source: Biomolecular Detection and Quantification - August 10, 2016 Category: Molecular Biology Source Type: research

Applicability of digital PCR to the investigation of pediatric-onset genetic disorders
Publication date: Available online 8 August 2016 Source:Biomolecular Detection and Quantification Author(s): Matthew E.R. Butchbach Early-onset rare diseases have a strong impact on child healthcare even though the incidence of each of these diseases is relatively low. In order to better manage the care of these children, it is imperative to quickly diagnose the molecular bases for these disorders as well as to develop technologies with prognostic potential. Digital PCR (dPCR) is well suited for this role by providing an absolute quantification of the target DNA within a sample. This review illustrates how dPCR can be u...
Source: Biomolecular Detection and Quantification - August 8, 2016 Category: Molecular Biology Source Type: research

Reliable measurement of multiplexed biomarker panel of RNA transcripts
Publication date: June 2016 Source:Biomolecular Detection and Quantification, Volume 8 Author(s): Robert Wielgosz (Source: Biomolecular Detection and Quantification)
Source: Biomolecular Detection and Quantification - August 5, 2016 Category: Molecular Biology Source Type: research

Flexible analysis of digital PCR experiments using generalized linear mixed models
Publication date: September 2016 Source:Biomolecular Detection and Quantification, Volume 9 Author(s): Matthijs Vynck, Jo Vandesompele, Nele Nijs, Björn Menten, Ariane De Ganck, Olivier Thas The use of digital PCR for quantification of nucleic acids is rapidly growing. A major drawback remains the lack of flexible data analysis tools. Published analysis approaches are either tailored to specific problem settings or fail to take into account sources of variability. We propose the generalized linear mixed models framework as a flexible tool for analyzing a wide range of experiments. We also introduce a metho...
Source: Biomolecular Detection and Quantification - July 25, 2016 Category: Molecular Biology Source Type: research

Aims & amp; Scope
Publication date: June 2015 Source:Biomolecular Detection and Quantification, Volume 4 (Source: Biomolecular Detection and Quantification)
Source: Biomolecular Detection and Quantification - June 17, 2016 Category: Molecular Biology Source Type: research

The potential of circulating extracellular small RNAs (smexRNA) in veterinary diagnostics —Identifying biomarker signatures by multivariate data analysis
Publication date: September 2015 Source:Biomolecular Detection and Quantification, Volume 5 Author(s): Spornraft Melanie, Kirchner Benedikt, Michael W. Pfaffl, Riedmaier Irmgard Worldwide growth and performance-enhancing substances are used in cattle husbandry to increase productivity. In certain countries however e.g., in the EU, these practices are forbidden to prevent the consumers from potential health risks of substance residues in food. To maximize economic profit, ‘black sheep‘ among farmers might circumvent the detection methods used in routine controls, which highlights the need for an innovative a...
Source: Biomolecular Detection and Quantification - June 17, 2016 Category: Molecular Biology Source Type: research

Differential amplicons ( ΔAmp)—a new molecular method to assess RNA integrity
Publication date: January 2016 Source:Biomolecular Detection and Quantification, Volume 6 Author(s): J. Björkman, D. Švec, E. Lott, M. Kubista, R. Sjöback Integrity of the mRNA in clinical samples has major impact on the quality of measured expression levels. This is independent of the measurement technique being next generation sequencing (NGS), Quantitative real-time PCR (qPCR) or microarray profiling. If mRNA is highly degraded or damaged, measured data will be very unreliable and the whole study is likely a waste of time and money. It is therefore common strategy to test the quality of RNA in samples b...
Source: Biomolecular Detection and Quantification - June 17, 2016 Category: Molecular Biology Source Type: research

Diagnostic RAS mutation analysis by polymerase chain reaction (PCR)
Publication date: June 2016 Source:Biomolecular Detection and Quantification, Volume 8 Author(s): Ian A. Cree RAS mutation analysis is an important companion diagnostic test. Treatment of colorectal cancer with anti-Epidermal Growth Factor Receptor (EGFR) therapy requires demonstration of RAS mutation status (both KRAS and NRAS), and it is good practice to include BRAF. In Non-Small Cell Lung Cancer (NSCLC) and melanoma, assessment of RAS mutation status can be helpful in triaging patient samples for more extensive testing. This mini-review will discuss the role of PCR methods in providing rapid diagnostic informati...
Source: Biomolecular Detection and Quantification - June 5, 2016 Category: Molecular Biology Source Type: research

An international comparability study on quantification of mRNA gene expression ratios: CCQM-P103.1
Publication date: June 2016 Source:Biomolecular Detection and Quantification, Volume 8 Author(s): Alison S. Devonshire, Rebecca Sanders, Alexandra S. Whale, Gavin J. Nixon, Simon Cowen, Stephen L.R. Ellison, Helen Parkes, P. Scott Pine, Marc Salit, Jennifer McDaniel, Sarah Munro, Steve Lund, Satoko Matsukura, Yuji Sekiguchi, Mamoru Kawaharasaki, José Mauro Granjeiro, Priscila Falagan-Lotsch, Antonio Marcos Saraiva, Paulo Couto, Inchul Yang, Hyerim Kwon, Sang-Ryoul Park, Tina Demšar, Jana Žel, Andrej Blejec, Mojca Milavec, Lianhua Dong, Ling Zhang, Zhiwei Sui,...
Source: Biomolecular Detection and Quantification - June 5, 2016 Category: Molecular Biology Source Type: research

Fundamentals of multiplexing with digital PCR
Publication date: Available online 27 May 2016 Source:Biomolecular Detection and Quantification Author(s): Alexandra S. Whale, Jim F. Huggett, Svilen Tzonev Over the past decade numerous publications have demonstrated how digital PCR (dPCR) enables precise and sensitive quantification of nucleic acids in a wide range of applications in both healthcare and environmental analysis. This has occurred in parallel with the advances in partitioning fluidics that enable a reaction to be subdivided into an increasing number of partitions. As the majority of dPCR systems are based on detection in two discrete optical chann...
Source: Biomolecular Detection and Quantification - May 27, 2016 Category: Molecular Biology Source Type: research

Designing and interpretation of digital assays: Concentration of target in the sample and in the source of sample
Publication date: Available online 17 May 2016 Source:Biomolecular Detection and Quantification Author(s): Pawel R. Debski, Piotr Garstecki We explain how to design classic digital assays, comprising identical partitions, in order to obtain the required precision of the estimate within a defined range of concentrations. The design, including the number and volume of partitions, depends significantly on whether the assay is to assess the concentration of the target analyte in the sample or in the source of the sample (e.g. a patient body) with a given precision. We also show how to translate the result referring to ...
Source: Biomolecular Detection and Quantification - May 17, 2016 Category: Molecular Biology Source Type: research