Guest editor’s editorial: BDQ Special Issue — “Liquid Biopsy & Next Generation Biomarkers”: Published in conjunction with the 9th Gene Quantification Event in Freising Weihenstephan, Germany www.qPCR-dPCR-NGS-2019.net
Publication date: March 2019Source: Biomolecular Detection and Quantification, Volume 17Author(s): Michael W. Pfaffl (Source: Biomolecular Detection and Quantification)
Source: Biomolecular Detection and Quantification - April 20, 2019 Category: Molecular Biology Source Type: research

Editorial
Publication date: March 2019Source: Biomolecular Detection and Quantification, Volume 17Author(s): Michael W. Pfaffl (Source: Biomolecular Detection and Quantification)
Source: Biomolecular Detection and Quantification - March 23, 2019 Category: Molecular Biology Source Type: research

The emerging role of cell-free DNA as a molecular marker for cancer management
Publication date: March 2019Source: Biomolecular Detection and Quantification, Volume 17Author(s): Abel Jacobus Bronkhorst, Vida Ungerer, Stefan HoldenriederAbstractAn increasing number of studies demonstrate the potential use of cell-free DNA (cfDNA) as a surrogate marker for multiple indications in cancer, including diagnosis, prognosis, and monitoring. However, harnessing the full potential of cfDNA requires (i) the optimization and standardization of preanalytical steps, (ii) refinement of current analysis strategies, and, perhaps most importantly, (iii) significant improvements in our understanding of its origin, phys...
Source: Biomolecular Detection and Quantification - March 19, 2019 Category: Molecular Biology Source Type: research

Investigation of direct counting and sizing of DNA fragments in flow applying an improved data analysis and correction method
In this study, we analysed raw detector signals and the sizing performance for target identification and the effect of coincidence detection concerning concentration measurements. We present data of purified artificial DNA samples measured with the home-built setup. Main emphasis was to develop an improved data analysis method to gain insight into and carefully correct for coincident detection of DNA fragments and for estimation of the amount of fragment dimers. (Source: Biomolecular Detection and Quantification)
Source: Biomolecular Detection and Quantification - March 18, 2019 Category: Molecular Biology Source Type: research

The kinetic requirements of extreme qPCR
Publication date: March 2019Source: Biomolecular Detection and Quantification, Volume 17Author(s): Adam L. Millington, Jessica A. Houskeeper, John F. Quackenbush, James M. Trauba, Carl T. WittwerAbstractThe kinetic requirements of quantitative PCR were experimentally dissected into the stages of DNA denaturation, primer annealing, and polymerase extension. The temperature/time conditions for 2 stages were kept optimal, while the other was limited until the amplification efficiency decreased as measured by an increase in quantification cycle (Cq). Extension was studied in a commercial capillary LightCycler®. Usin...
Source: Biomolecular Detection and Quantification - March 15, 2019 Category: Molecular Biology Source Type: research

Next-generation sequencing of HIV-1 single genome amplicons
Publication date: March 2019Source: Biomolecular Detection and Quantification, Volume 17Author(s): Gustavo H. Kijak, Eric Sanders-Buell, Phuc Pham, Elizabeth A. Harbolick, Celina Oropeza, Anne Marie O’Sullivan, Meera Bose, Charmagne G. Beckett, Mark Milazzo, Merlin L. Robb, Sheila A. Peel, Paul T. Scott, Nelson L. Michael, Adam W. Armstrong, Jerome H. Kim, David M. Brett-Major, Sodsai TovanabutraAbstractThe analysis of HIV-1 sequences has helped understand the viral molecular epidemiology, monitor the development of antiretroviral drug resistance, and design candidate vaccines. The introduction of single genome ampli...
Source: Biomolecular Detection and Quantification - March 13, 2019 Category: Molecular Biology Source Type: research

Challenging the proposed causes of the PCR plateau phase
Publication date: March 2019Source: Biomolecular Detection and Quantification, Volume 17Author(s): Linda Jansson, Johannes HedmanAbstractDespite the wide-spread use of the polymerase chain reaction (PCR) in various life-science applications, the causes of arrested amplicon generation in late cycles have not been confidently identified. This so-called plateau phase has been attributed to depletion or thermal break-down of primers or nucleotides, thermal inactivation of the DNA polymerase, and product accumulation resulting in competition between primer annealing and product re-hybridization as well as blocking of DNA polyme...
Source: Biomolecular Detection and Quantification - March 5, 2019 Category: Molecular Biology Source Type: research

Corrigendum to “Incidence and detection of Beak and Feather disease virus in psittacine birds in the UAE” [Biomol. Detect. Quantif. 6 (January) (2016) 27–32]
Publication date: March 2019Source: Biomolecular Detection and Quantification, Volume 17Author(s): F. Hakimuddin, F. Abidi, O. Jafer, C. Li, U. Wernery, Ch. Hebel, K. Khazanehdari (Source: Biomolecular Detection and Quantification)
Source: Biomolecular Detection and Quantification - March 5, 2019 Category: Molecular Biology Source Type: research

Considerations and quality controls when analyzing cell-free tumor DNA
Publication date: March 2019Source: Biomolecular Detection and Quantification, Volume 17Author(s): Gustav Johansson, Daniel Andersson, Stefan Filges, Junrui Li, Andreas Muth, Tony E. Godfrey, Anders StåhlbergAbstractCirculating cell-free tumor DNA (ctDNA) is a promising biomarker in cancer. Ultrasensitive technologies enable detection of low (
Source: Biomolecular Detection and Quantification - February 14, 2019 Category: Molecular Biology Source Type: research

Shedding light: The importance of reverse transcription efficiency standards in data interpretation
Publication date: March 2019Source: Biomolecular Detection and Quantification, Volume 17Author(s): Jessica Schwaber, Stacey Andersen, Lars NielsenAbstractThe RNA-to-cDNA conversion step in transcriptomics experiments is widely recognised as inefficient and variable, casting doubt on the ability to do quantitative transcriptomics analyses. Multiple studies have focused on ways to optimise this process, resulting in contradictory recommendations. Here we explore the problem of reverse transcription efficiency using digital PCR and the RT method’s impact on subsequent data analysis. Using synthetic RNA standards, an exa...
Source: Biomolecular Detection and Quantification - February 13, 2019 Category: Molecular Biology Source Type: research

Development of event-specific qPCR detection methods for genetically modified alfalfa events J101, J163 and KK179
Publication date: March 2019Source: Biomolecular Detection and Quantification, Volume 17Author(s): Patrick Guertler, Lutz Grohmann, Heike Naumann, Melanie Pavlovic, Ulrich BuschAbstractGenetically modified alfalfa is authorized for cultivation in several countries since 2005. On the other hand, cultivation in or export to the European Union is not allowed and thus neither certified reference material nor official event-specific detection methods are available. Therefore, based on patent sequence information, event-specific real-time PCR detection methods targeting the junction sequence of the alfalfa genome and the transge...
Source: Biomolecular Detection and Quantification - February 13, 2019 Category: Molecular Biology Source Type: research

Essential role of polymerases for assay performance – Impact of polymerase replacement in a well-established assay
In this study, we compared ten different polymerases (or ready-to-use mastermixes) as possible (economic) alternatives to our gold standard Platinum Taq polymerase. We sought to determine the reproducibility of these assays under modified conditions, which are realistic because published assays are frequently used with substituted polymerases. Surprisingly, there was no amplification at all with some of the tested polymerases, even although the internal amplification control worked well. Since adaptation of the thermal profile and of MgCl2 concentration could restore amplification, simple replacement of the polymerase can ...
Source: Biomolecular Detection and Quantification - November 15, 2018 Category: Molecular Biology Source Type: research

Using ddPCR to assess the DNA yield of FFPE samples
ConclusionsSamples undergoing different pre-treatment conditions prior to extraction can impact the yield of amplifiable DNA. Our ddPCR assay can be used to assess for both DNA quantity and quality. (Source: Biomolecular Detection and Quantification)
Source: Biomolecular Detection and Quantification - November 7, 2018 Category: Molecular Biology Source Type: research

Algorithms for automated detection of hook effect-bearing amplification curves
In this study we present two approaches to automatically detect hook effect-like curvatures based on linear (hookreg) and nonlinear regression (hookregNL). As the hook effect is typical for qPCR data, both algorithms can be employed for the automated identification of regular structured qPCR curves. Therefore, our algorithms streamline quality control, but can also be used for assay optimization or machine learning. (Source: Biomolecular Detection and Quantification)
Source: Biomolecular Detection and Quantification - October 17, 2018 Category: Molecular Biology Source Type: research

Amplification of nonspecific products in quantitative polymerase chain reactions (qPCR)
Publication date: December 2017Source: Biomolecular Detection and Quantification, Volume 14Author(s): Adrián Ruiz-Villalba, Elizabeth van Pelt-Verkuil, Quinn D Gunst, Jan M Ruijter, Maurice JB van den HoffAbstractQuantitative PCR allows the precise measurement of DNA concentrations and is generally considered to be straightforward and trouble free. However, a survey with 93 validated assays for genes in the Wnt-pathway showed that the amplification of nonspecific products occurs frequently and is unrelated to Cq or PCR efficiency values. Titration experiments showed that the occurrence of low and high melting temper...
Source: Biomolecular Detection and Quantification - July 11, 2018 Category: Molecular Biology Source Type: research

Next-generation sequencing applications in clinical bacteriology
Publication date: December 2017Source: Biomolecular Detection and Quantification, Volume 14Author(s): Yair Motro, Jacob Moran-GiladAbstractWith the rapid advances in next generation sequencing (NGS) technologies, clinical and public health microbiology laboratories are increasingly adopting NGS technology in their workflows into their existing diagnostic cycles. In this bacteriology focused review, we review aspects and considerations for applying NGS in the clinical microbiology settings, and highlight the impact of such implementation on the analytical and post-analytical stages of diagnosis (Source: Biomolecular Detecti...
Source: Biomolecular Detection and Quantification - July 11, 2018 Category: Molecular Biology Source Type: research

qPCR primer design revisited
We present an overview of the main steps in the primer design workflow, with data that illustrate some of the unexpected variability that often occurs when theory is translated into practice. We also strongly urge researchers to report as much information about their assays as possible in their publications. (Source: Biomolecular Detection and Quantification)
Source: Biomolecular Detection and Quantification - July 11, 2018 Category: Molecular Biology Source Type: research

Small sample sizes in high-throughput miRNA screens: A common pitfall for the identification of miRNA biomarkers
Publication date: May 2018Source: Biomolecular Detection and Quantification, Volume 15Author(s): M.G.M. Kok, M.W.J. de Ronde, P.D. Moerland, J.M. Ruijter, E.E. Creemers, S.J. Pinto-SietsmaAbstractSince the discovery of microRNAs (miRNAs), circulating miRNAs have been proposed as biomarkers for disease. Consequently, many groups have tried to identify circulating miRNA biomarkers for various types of diseases including cardiovascular disease and cancer. However, the replicability of these experiments has been disappointingly low. In order to identify circulating miRNA candidate biomarkers, in general, first an unbiased high...
Source: Biomolecular Detection and Quantification - July 11, 2018 Category: Molecular Biology Source Type: research

An optimized targeted Next-Generation Sequencing approach for sensitive detection of single nucleotide variants
Publication date: May 2018Source: Biomolecular Detection and Quantification, Volume 15Author(s): S. Stasik, C. Schuster, C. Ortlepp, U. Platzbecker, M. Bornhäuser, J. Schetelig, G. Ehninger, G. Folprecht, C. ThiedeAbstractMonitoring of minimal residual disease (MRD) has become an important clinical aspect for early relapse detection during follow-up care after cancer treatment. Still, the sensitive detection of single base pair point mutations via Next-Generation Sequencing (NGS) is hampered mainly due to high substitution error rates. We evaluated the use of NGS for the detection of low-level variants on an Ion Torre...
Source: Biomolecular Detection and Quantification - July 11, 2018 Category: Molecular Biology Source Type: research

A PCR-based quantitative assay for the evaluation of mRNA integrity in rat samples
Publication date: May 2018Source: Biomolecular Detection and Quantification, Volume 15Author(s): Bhaja K. Padhi, Manjeet Singh, Marianela Rosales, Guillaume Pelletier, Sabit CakmakAbstractReverse Transcription quantitative real-time PCR (RT-qPCR) is applied to quantify gene transcript levels in a wide range of investigations. Proper assessment of RNA integrity is essential for reliable assessment of gene expression levels, as RNA molecules are acutely vulnerable to degradation. However, RNA quality control measures are still infrequently reported in rat toxicological studies, which impede proper evaluation of gene expressi...
Source: Biomolecular Detection and Quantification - July 11, 2018 Category: Molecular Biology Source Type: research

Effect of endogenous reference genes on digital PCR assessment of genetically engineered canola events
Publication date: May 2018Source: Biomolecular Detection and Quantification, Volume 15Author(s): Tigst Demeke, Monika EngAbstractDroplet digital PCR (ddPCR) has been used for absolute quantification of genetically engineered (GE) events. Absolute quantification of GE events by duplex ddPCR requires the use of appropriate primers and probes for target and reference gene sequences in order to accurately determine the amount of GE materials. Single copy reference genes are generally preferred for absolute quantification of GE events by ddPCR. Study has not been conducted on a comparison of reference genes for absolute quantif...
Source: Biomolecular Detection and Quantification - July 11, 2018 Category: Molecular Biology Source Type: research

Improving the standardization of mRNA measurement by RT-qPCR
Publication date: May 2018Source: Biomolecular Detection and Quantification, Volume 15Author(s): Rebecca Sanders, Stephen Bustin, Jim Huggett, Deborah MasonAbstractHuman health and safety depend on reliable measurements in medical diagnosis and on tests that support the selection and evaluation of therapeutic intervention and newly discovered molecular biomarkers must pass a rigorous evaluation process if they are to be of benefit to patients. Measurement standardization helps to maximize data quality and confidence and ultimately improves the reproducibility of published research. Failure to consider how a given experimen...
Source: Biomolecular Detection and Quantification - July 11, 2018 Category: Molecular Biology Source Type: research

Amplification of nonspecific products in quantitative polymerase chain reactions (qPCR)
Publication date: December 2017Source: Biomolecular Detection and Quantification, Volume 14Author(s): Adrián Ruiz-Villalba, Elizabeth van Pelt-Verkuil, Quinn D Gunst, Jan M Ruijter, Maurice JB van den HoffAbstractQuantitative PCR allows the precise measurement of DNA concentrations and is generally considered to be straightforward and trouble free. However, a survey with 93 validated assays for genes in the Wnt-pathway showed that the amplification of nonspecific products occurs frequently and is unrelated to Cq or PCR efficiency values. Titration experiments showed that the occurrence of low and high melting temper...
Source: Biomolecular Detection and Quantification - July 5, 2018 Category: Molecular Biology Source Type: research

Next-generation sequencing applications in clinical bacteriology
Publication date: December 2017Source: Biomolecular Detection and Quantification, Volume 14Author(s): Yair Motro, Jacob Moran-GiladAbstractWith the rapid advances in next generation sequencing (NGS) technologies, clinical and public health microbiology laboratories are increasingly adopting NGS technology in their workflows into their existing diagnostic cycles. In this bacteriology focused review, we review aspects and considerations for applying NGS in the clinical microbiology settings, and highlight the impact of such implementation on the analytical and post-analytical stages of diagnosis (Source: Biomolecular Detecti...
Source: Biomolecular Detection and Quantification - July 5, 2018 Category: Molecular Biology Source Type: research

qPCR primer design revisited
We present an overview of the main steps in the primer design workflow, with data that illustrate some of the unexpected variability that often occurs when theory is translated into practice. We also strongly urge researchers to report as much information about their assays as possible in their publications. (Source: Biomolecular Detection and Quantification)
Source: Biomolecular Detection and Quantification - July 5, 2018 Category: Molecular Biology Source Type: research

Small sample sizes in high-throughput miRNA screens: A common pitfall for the identification of miRNA biomarkers
Publication date: May 2018Source: Biomolecular Detection and Quantification, Volume 15Author(s): M.G.M. Kok, M.W.J. de Ronde, P.D. Moerland, J.M. Ruijter, E.E. Creemers, S.J. Pinto-SietsmaAbstractSince the discovery of microRNAs (miRNAs), circulating miRNAs have been proposed as biomarkers for disease. Consequently, many groups have tried to identify circulating miRNA biomarkers for various types of diseases including cardiovascular disease and cancer. However, the replicability of these experiments has been disappointingly low. In order to identify circulating miRNA candidate biomarkers, in general, first an unbiased high...
Source: Biomolecular Detection and Quantification - July 5, 2018 Category: Molecular Biology Source Type: research

An optimized targeted Next-Generation Sequencing approach for sensitive detection of single nucleotide variants
Publication date: May 2018Source: Biomolecular Detection and Quantification, Volume 15Author(s): S. Stasik, C. Schuster, C. Ortlepp, U. Platzbecker, M. Bornhäuser, J. Schetelig, G. Ehninger, G. Folprecht, C. ThiedeAbstractMonitoring of minimal residual disease (MRD) has become an important clinical aspect for early relapse detection during follow-up care after cancer treatment. Still, the sensitive detection of single base pair point mutations via Next-Generation Sequencing (NGS) is hampered mainly due to high substitution error rates. We evaluated the use of NGS for the detection of low-level variants on an Ion Torre...
Source: Biomolecular Detection and Quantification - July 5, 2018 Category: Molecular Biology Source Type: research

A PCR-based quantitative assay for the evaluation of mRNA integrity in rat samples
Publication date: May 2018Source: Biomolecular Detection and Quantification, Volume 15Author(s): Bhaja K. Padhi, Manjeet Singh, Marianela Rosales, Guillaume Pelletier, Sabit CakmakAbstractReverse Transcription quantitative real-time PCR (RT-qPCR) is applied to quantify gene transcript levels in a wide range of investigations. Proper assessment of RNA integrity is essential for reliable assessment of gene expression levels, as RNA molecules are acutely vulnerable to degradation. However, RNA quality control measures are still infrequently reported in rat toxicological studies, which impede proper evaluation of gene expressi...
Source: Biomolecular Detection and Quantification - July 5, 2018 Category: Molecular Biology Source Type: research

Effect of endogenous reference genes on digital PCR assessment of genetically engineered canola events
Publication date: May 2018Source: Biomolecular Detection and Quantification, Volume 15Author(s): Tigst Demeke, Monika EngAbstractDroplet digital PCR (ddPCR) has been used for absolute quantification of genetically engineered (GE) events. Absolute quantification of GE events by duplex ddPCR requires the use of appropriate primers and probes for target and reference gene sequences in order to accurately determine the amount of GE materials. Single copy reference genes are generally preferred for absolute quantification of GE events by ddPCR. Study has not been conducted on a comparison of reference genes for absolute quantif...
Source: Biomolecular Detection and Quantification - July 5, 2018 Category: Molecular Biology Source Type: research

Improving the standardization of mRNA measurement by RT-qPCR
Publication date: May 2018Source: Biomolecular Detection and Quantification, Volume 15Author(s): Rebecca Sanders, Stephen Bustin, Jim Huggett, Deborah MasonAbstractHuman health and safety depend on reliable measurements in medical diagnosis and on tests that support the selection and evaluation of therapeutic intervention and newly discovered molecular biomarkers must pass a rigorous evaluation process if they are to be of benefit to patients. Measurement standardization helps to maximize data quality and confidence and ultimately improves the reproducibility of published research. Failure to consider how a given experimen...
Source: Biomolecular Detection and Quantification - July 5, 2018 Category: Molecular Biology Source Type: research

Effect of endogenous reference genes on digital PCR assessment of genetically engineered canola events
Publication date: May 2018 Source:Biomolecular Detection and Quantification, Volume 15 Author(s): Tigst Demeke, Monika Eng Droplet digital PCR (ddPCR) has been used for absolute quantification of genetically engineered (GE) events. Absolute quantification of GE events by duplex ddPCR requires the use of appropriate primers and probes for target and reference gene sequences in order to accurately determine the amount of GE materials. Single copy reference genes are generally preferred for absolute quantification of GE events by ddPCR. Study has not been conducted on a comparison of reference genes for absolute quantificati...
Source: Biomolecular Detection and Quantification - April 10, 2018 Category: Molecular Biology Source Type: research

A PCR-based quantitative assay for the evaluation of mRNA integrity in rat samples
Publication date: May 2018 Source:Biomolecular Detection and Quantification, Volume 15 Author(s): Bhaja K. Padhi, Manjeet Singh, Marianela Rosales, Guillaume Pelletier, Sabit Cakmak Reverse Transcription quantitative real-time PCR (RT-qPCR) is applied to quantify gene transcript levels in a wide range of investigations. Proper assessment of RNA integrity is essential for reliable assessment of gene expression levels, as RNA molecules are acutely vulnerable to degradation. However, RNA quality control measures are still infrequently reported in rat toxicological studies, which impede proper evaluation of gene expression da...
Source: Biomolecular Detection and Quantification - March 17, 2018 Category: Molecular Biology Source Type: research

Improving the standardization of mRNA measurement by RT-qPCR
Publication date: May 2018 Source:Biomolecular Detection and Quantification, Volume 15 Author(s): Rebecca Sanders, Stephen Bustin, Jim Huggett, Deborah Mason Human health and safety depend on reliable measurements in medical diagnosis and on tests that support the selection and evaluation of therapeutic intervention and newly discovered molecular biomarkers must pass a rigorous evaluation process if they are to be of benefit to patients. Measurement standardization helps to maximize data quality and confidence and ultimately improves the reproducibility of published research. Failure to consider how a given experiment may...
Source: Biomolecular Detection and Quantification - March 16, 2018 Category: Molecular Biology Source Type: research

An optimized targeted Next-Generation Sequencing approach for sensitive detection of single nucleotide variants
Publication date: May 2018 Source:Biomolecular Detection and Quantification, Volume 15 Author(s): S. Stasik, C. Schuster, C. Ortlepp, U. Platzbecker, M. Bornhäuser, J. Schetelig, G. Ehninger, G. Folprecht, C. Thiede Monitoring of minimal residual disease (MRD) has become an important clinical aspect for early relapse detection during follow-up care after cancer treatment. Still, the sensitive detection of single base pair point mutations via Next-Generation Sequencing (NGS) is hampered mainly due to high substitution error rates. We evaluated the use of NGS for the detection of low-level variants on an Ion Torrent PG...
Source: Biomolecular Detection and Quantification - January 9, 2018 Category: Molecular Biology Source Type: research

Small sample sizes in high-throughput miRNA screens: A common pitfall for the identification of miRNA biomarkers
Publication date: May 2018 Source:Biomolecular Detection and Quantification, Volume 15 Author(s): M.G.M. Kok, M.W.J. de Ronde, P.D. Moerland, J.M. Ruijter, E.E. Creemers, S.J. Pinto-Sietsma Since the discovery of microRNAs (miRNAs), circulating miRNAs have been proposed as biomarkers for disease. Consequently, many groups have tried to identify circulating miRNA biomarkers for various types of diseases including cardiovascular disease and cancer. However, the replicability of these experiments has been disappointingly low. In order to identify circulating miRNA candidate biomarkers, in general, first an unbiased high-thro...
Source: Biomolecular Detection and Quantification - December 19, 2017 Category: Molecular Biology Source Type: research

qPCR primer design revisited
We present an overview of the main steps in the primer design workflow, with data that illustrate some of the unexpected variability that often occurs when theory is translated into practice. We also strongly urge researchers to report as much information about their assays as possible in their publications. (Source: Biomolecular Detection and Quantification)
Source: Biomolecular Detection and Quantification - November 23, 2017 Category: Molecular Biology Source Type: research

Amplification of nonspecific products in quantitative polymerase chain reactions (qPCR)
Publication date: December 2017 Source:Biomolecular Detection and Quantification, Volume 14 Author(s): Adrián Ruiz-Villalba, Elizabeth van Pelt-Verkuil, Quinn D Gunst, Jan M Ruijter, Maurice JB van den Hoff Quantitative PCR allows the precise measurement of DNA concentrations and is generally considered to be straightforward and trouble free. However, a survey with 93 validated assays for genes in the Wnt-pathway showed that the amplification of nonspecific products occurs frequently and is unrelated to Cq or PCR efficiency values. Titration experiments showed that the occurrence of low and high melting temperature...
Source: Biomolecular Detection and Quantification - November 1, 2017 Category: Molecular Biology Source Type: research

Next-generation sequencing applications in clinical bacteriology
Publication date: December 2017 Source:Biomolecular Detection and Quantification, Volume 14 Author(s): Yair Motro, Jacob Moran-Gilad With the rapid advances in next generation sequencing (NGS) technologies, clinical and public health microbiology laboratories are increasingly adopting NGS technology in their workflows into their existing diagnostic cycles. In this bacteriology focused review, we review aspects and considerations for applying NGS in the clinical microbiology settings, and highlight the impact of such implementation on the analytical and post-analytical stages of diagnosis (Source: Biomolecular Detection and Quantification)
Source: Biomolecular Detection and Quantification - October 23, 2017 Category: Molecular Biology Source Type: research

Evaluation of relative quantification of alternatively spliced transcripts using droplet digital PCR
Conclusions Our study recognizes the potential and validity of digital PCR but shows the value of a highly optimized qPCR for the relative quantification of isoforms. Cost efficiency and simplicity turned out to be better for RT-qPCR. (Source: Biomolecular Detection and Quantification)
Source: Biomolecular Detection and Quantification - September 21, 2017 Category: Molecular Biology Source Type: research

Quantification of mitochondrial DNA copy number in suspected cancer patients by a well optimized ddPCR method
Publication date: Available online 31 August 2017 Source:Biomolecular Detection and Quantification Author(s): Ashfaque A. Memon, Bengt Zöller, Anna Hedelius, Xiao Wang, Emelie Stenman, Jan Sundquist, Kristina Sundquist Changes in mitochondrial DNA (mtDNA) content is a useful clinical biomarker for various diseases, however results are controversial as several analytical factors can affect measurement of mtDNA. MtDNA is often quantified by taking ratio between a target mitochondrial gene and a reference nuclear gene (mtDNA/nDNA) using quantitative real time PCR often on two separate experiments. It measures relative l...
Source: Biomolecular Detection and Quantification - September 1, 2017 Category: Molecular Biology Source Type: research

*K-means and cluster models for cancer signatures
We present *K-means clustering algorithm and source code by expanding statistical clustering methods applied in https://ssrn.com/abstract=2802753 to quantitative finance. *K-means is statistically deterministic without specifying initial centers, etc. We apply *K-means to extracting cancer signatures from genome data without using nonnegative matrix factorization (NMF). *K-means’ computational cost is a fraction of NMF’s. Using 1389 published samples for 14 cancer types, we find that 3 cancers (liver cancer, lung cancer and renal cell carcinoma) stand out and do not have cluster-like structures. Two clusters ha...
Source: Biomolecular Detection and Quantification - August 2, 2017 Category: Molecular Biology Source Type: research

The Unyvero P55 ‘sample-in, answer-out’ pneumonia assay: A performance evaluation
Conclusions The Unyvero P55 is a rapid pathogen detection test for lower respiratory specimens, which identifies a larger number of pathogens than routine microbiology. The clinical significance of these additional organisms is yet to be determined. Further studies are required to determine the effect of the test in practise on antimicrobial prescribing and patient outcomes. (Source: Biomolecular Detection and Quantification)
Source: Biomolecular Detection and Quantification - June 29, 2017 Category: Molecular Biology Source Type: research

How to speed up the polymerase chain reaction
Publication date: Available online 20 June 2017 Source:Biomolecular Detection and Quantification Author(s): Stephen A. Bustin Reducing the time taken to run qPCR assays on today’s qPCR cyclers is rather straightforward and requires no specialised reagents or instruments. As the first article in a new series of short technical reports, I demonstrate that it is possible to reduce significantly both denaturation temperatures and cycling times, whilst retaining sensitivity and specificity of the original qPCR conditions. (Source: Biomolecular Detection and Quantification)
Source: Biomolecular Detection and Quantification - June 21, 2017 Category: Molecular Biology Source Type: research

The continuing problem of poor transparency of reporting and use of inappropriate methods for RT-qPCR
Publication date: Available online 23 May 2017 Source:Biomolecular Detection and Quantification Author(s): Stephen Bustin Attendance at this year’s European Calcified Tissue Society’s (ECTS) Congress reveals that the methods used to obtain qPCR results continue to be significantly flawed and that and their reporting remain inadequate. (Source: Biomolecular Detection and Quantification)
Source: Biomolecular Detection and Quantification - May 24, 2017 Category: Molecular Biology Source Type: research

Methods to determine limit of detection and limit of quantification in quantitative real-time PCR (qPCR)
Publication date: Available online 29 April 2017 Source:Biomolecular Detection and Quantification Author(s): Amin Forootan, Robert Sjöback, Jens Björkman, Björn Sjögreen, Lucas Linz, Mikael Kubista Quantitative Real-Time Polymerase Chain Reaction, better known as qPCR, is the most sensitive and specific technique we have for the detection of nucleic acids. Even though it has been around for more than 30 years and is preferred in research applications, it has yet to win broad acceptance in routine practice. This requires a means to unambiguously assess the performance of specific qPCR analyses. Here we ...
Source: Biomolecular Detection and Quantification - April 29, 2017 Category: Molecular Biology Source Type: research

Reproducibility of biomedical research – The importance of editorial vigilance
Publication date: Available online 21 February 2017 Source:Biomolecular Detection and Quantification Author(s): Stephen A. Bustin, Jim F. Huggett Many journal editors are a failing to implement their own authors’ instructions, resulting in the publication of many articles that do not meet basic standards of transparency, employ unsuitable data analysis methods and report overly optimistic conclusions. This problem is particularly acute where quantitative measurements are made and results in the publication of papers that lack scientific rigor and contributes to the concerns with regard to the reproducibility of biom...
Source: Biomolecular Detection and Quantification - February 21, 2017 Category: Molecular Biology Source Type: research

Molecular techniques for the personalised management of patients with chronic myeloid leukaemia
Publication date: Available online 14 February 2017 Source:Biomolecular Detection and Quantification Author(s): Mary Alikian, Robert Peter Gale, Jane F Apperley, Letizia Foroni Chronic myeloid leukemia (CML) is the paradigm for targeted cancer therapy. RT-qPCR is the gold standard for monitoring response to tyrosine kinase-inhibitor (TKI) therapy based on the reduction of blood or bone marrow BCR-ABL1. Some patients with CML and very low or undetectable levels of BCR-ABL1 transcripts can stop TKI-therapy without CML recurrence. However, about 60 percent of patients discontinuing TKI-therapy have rapid leukaemia recurrence...
Source: Biomolecular Detection and Quantification - February 15, 2017 Category: Molecular Biology Source Type: research

Digital PCR, a technique for the future
Publication date: December 2016 Source:Biomolecular Detection and Quantification, Volume 10 Author(s): -->Valerie Taly, Jim Huggett (Source: Biomolecular Detection and Quantification)
Source: Biomolecular Detection and Quantification - January 29, 2017 Category: Molecular Biology Source Type: research

Measuring E. coli and bacteriophage DNA in cell sonicates to evaluate the CAL1 reaction as a synthetic biology standard for qPCR
Publication date: Available online 29 December 2016 Source:Biomolecular Detection and Quantification Author(s): Alexander Templar, Desmond M. Schofield, Darren N. Nesbeth We measured the impact of the presence of total Escherichia coli (E. coli) cellular material on the performance of the Linear Regression of Efficiency (LRE) method of absolute quantitative PCR (LRE qPCR), which features the putatively universal CAL1 calibration reaction, which we propose as a synthetic biology standard. We firstly used a qPCR reaction in which a sequence present in the lone genomic BirA locus is amplified. Amplification efficiency for th...
Source: Biomolecular Detection and Quantification - December 30, 2016 Category: Molecular Biology Source Type: research

Inhibition of fat cell differentiation in 3T3-L1 pre-adipocytes by all-trans retinoic acid: Integrative analysis of transcriptomic and phenotypic data
In conclusion, the experimental workflow and the integrative microRNA–mRNA data analysis shown in this study represent a possibility for illustrating interactions in highly orchestrated biological processes. Further the applied global microRNA–mRNA interaction network may also be used for the pre-selection of potential new biomarkers with regard to obesity or for the identification of new pharmaceutical targets. (Source: Biomolecular Detection and Quantification)
Source: Biomolecular Detection and Quantification - November 22, 2016 Category: Molecular Biology Source Type: research