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Gene Quantification Newsletter
September & October 2017

is sponsored by

    Dear researcher,
dear Gene Quantification page reader,

Our newsletter informs about the latest news in gene expression profiling using qPCR and related methods, which are compiled and summarised on www.Gene-Quantification.info
The focus of this qPCR NEWS issue is:


Streaming portal  

Join the updated
eConferences streaming webportal
www.eConferences.de -- Amplify your knowledge in  qPCR, dPCR and NGS!
This streaming portal is dedicated to scientists from the community of qPCR, digital PCR, Next Generation Sequencing (NGS), MicroGenomics (MG) and Molecular Diagnostics (MDx). You’ll find here all the records of 350 presentations held at qPCR dPCR& NGS and MG Events in the past years qPCR 2010 in Vienna - qPCR dPCR & NGS 2017 in Freising-Weihenstephan.
We provide the presentations via movie streaming technology in high quality – high resolution and perfect sound quality in high speed – on any internet browser or mobile device.


The qPCR and dPCR MIQE guidelines – A success story!

The MIQE guidelines and the resulting scientific validity will be supported by more and more researchers, biological journals, academic and commercial institutions. Today we count around 6.300 citations for the MIQE guidelines applied in qPCR and 250 citations for the digital PCR (dPCR) MIQE guidelines (measured by Google Scholar). Hence the qPCR and dPCR MIQE guidelines are a worldwide full success story which will be driven forward by the scientific community.

The MIQE Guidelines - Minimum Information for Publication of Quantitative Real-Time PCR Experiments.
Stephen A. Bustin,  Vladimir Benes,  Jeremy A. Garson,  Jan Hellemans,  Jim Huggett, Mikael Kubista,  Reinhold Mueller,  Tania Nolan,  Michael W. Pfaffl,  Gregory L. Shipley, Jo Vandesompele,  and  Carl T. Wittwer
Clinical Chemistry 2009, 55(4): 611-622

BACKGROUND:  Currently, a lack of consensus exists on how best to perform and interpret quantitative real-time PCR (qPCR) experiments. The problem is exacerbated by a lack of sufficient experimental detail in many publications, which impedes a reader's ability to evaluate critically the quality of the results presented or to repeat the experiments.
CONTENT:  The Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) guidelines target the reliability of results to help ensure the integrity of the scientific literature, promote consistency between laboratories, and increase experimental transparency. MIQE is a set of guidelines that describe the minimum information necessary for evaluating qPCR experiments. Included is a checklist to accompany the initial submission of a manuscript to the publisher. By providing all relevant experimental conditions and assay characteristics, reviewers can assess the validity of the protocols used. Full disclosure of all reagents, sequences, and analysis methods is necessary to enable other investigators to reproduce results. MIQE details should be published either in abbreviated form or as an online supplement.
SUMMARY:  Following these guidelines will encourage better experimental practice, allowing more reliable and unequivocal interpretation of qPCR results.

Guidelines for Minimum Information for Publication of Quantitative Digital PCR Experiments.
Huggett JF, Foy CA, Benes V, Emslie K, Garson JA, Haynes R, Hellemans J, Kubista M, Mueller RD, Nolan T, Pfaffl MW, Shipley GL, Vandesompele J, Wittwer CT, Bustin SA.
Clin Chem 2013 59(6): 892-902

There is growing interest in digital PCR (dPCR) because technological progress makes it a practical and increasingly affordable technology. dPCR allows the precise quantification of nucleic acids, facilitating the measurement of small percentage differences and quantification of rare variants. dPCR may also be more reproducible and less susceptible to inhibition than quantitative real-time PCR (qPCR). Consequently, dPCR has the potential to have a substantial impact on research as well as diagnostic applications. However, as with qPCR, the ability to perform robust meaningful experiments requires careful design and adequate controls. To assist independent evaluation of experimental data, comprehensive disclosure of all relevant experimental details is required. To facilitate this process we present the Minimum Information for Publication of Quantitative Digital PCR Experiments guidelines. This report addresses known requirements for dPCR that have already been identified during this early stage of its development and commercial implementation. Adoption of these guidelines by the scientific community will help to standardize experimental protocols, maximize efficient utilization of resources, and enhance the impact of this promising new technology.


MIQE and qPCR QC talks presented ate the qPCR dPCR & NGS 2017 Event

... and much more MIQE and qPCR realted talks www.eConferences.de/MIQE-talks/



How to apply the MIQE guidelines - a visual, interactive and practical qPCR guide

2nd edition published 26th July 2016
Editors:  Afif M. Abdel Nour & Michael W. Pfaffl
ISBN 9783000488061
Free download via iTunes -- https://itunes.apple.com/book/miqe-qpcr/id993276375?mt=11

NEW -- NEW -- NEW  Download the new ePub version for any eBook reader

MIQE & qPCR Preface:  The qPCR and dPCR MIQE guidelines – A success story!
(Editorial for 2nd edition published 26. July 2016)

The MIQE guidelines and the resulting scientific validity will be supported by more and more researchers, biological journals, academic and commercial institutions. Today in July 2016 we count more than 4650 citations for the MIQE guideline applied in qPCR and around 160 citations for the digital PCR (dPCR) MIQE guideline (measured by Google Scholar). Hence the qPCR and dPCR MIQE guidelines are a worldwide full success story which will be driven forward by the scientific community, e.g. MIQE.Gene-Quantification.info

The present second edition of the MIQE & qPCR iBook should help to spread this MIQE idea even further in any laboratory worldwide and beyond in the scientists’ workflow and minds. It should clearly show how to apply the guidelines and serve as a handy, visual, interactive and practical guide. For now in the first year after publication of the first edition we could count more than 1200 downloads of the MIQE & qPCR iBook from more than 30 countries. Our goal for the second edition is to update the existing content by new chapters, and to improve this fancy interactive tool, interfacing scientific publications with educating pictures, videos and scientific talks. We implemented multiple new chapters, describing the significance of the reverse transcription reaction, why qPCR assay validation is so important for high sensitivity and good reproducibility, and one reviewing chapter about the necessity of performing quality control at all levels in the qPCR workflow. In summary we are proud to present a selection of international highly recognized authors from the academic field as well from industrial research presenting their latest applications. Described qPCR and dPCR methods and applications are linked to the MIQE context and show it on the basis of educational questionnaires or interactive ‘how to do’ instruction sheets. The at-hand MIQE & qPCR iBook should deliver the MIQE guidelines directly to the researcher and help to solve the daily problems in the molecular biology laboratory using quantitative PCR, digital PCR, single-cell qPCR, microRNA applications or any comparable techniques using PCR.

We hope you like our explanatory, interactive and educational iBook concept, showing the advantages of the MIQE guidelines in an easy and understandable way, and to guarantee the successful qPCR or dPCR application at the lab bench.

The editors
Afif M. Abdel Nour & Michael W. Pfaffl


New Chapters in 2nd edition:

   * Updated Editorial 2nd eds.
    * Reverse Transcription
    * qPCR Assay validation
    * Quality control in qPCR


GenEx 6.1

The most powerful tool for complex qPCR data analysis


GenEx offers advanced methods to analyze real-time qPCR data with simple mouse clicks

GenEx is the most popular software for qPCR data processing and analysis. Built in a modular fashion GenEx provides a multitude of functionalities for the qPCR community, ranging from basic data editing and management to advanced cutting-edge data analysis. GenEx 6.1 – the software compliant with MIQE and CLSI guidelines.

TATAA Biocenter, Europe´s leading provider of genomic services using quantitative real-time PCR (qPCR), and MultiD Analyses, Europe’s prime software developer for the analysis of multivariate data, release GenEx version 6 for accurate qPCR data analysi, compliant with current MIQE guideline and Clinical Laboratory Standards Institute (CLSI) guideline.


GenEx 6.1

international GenEx software presentations


Listen to GenEx presentations:

GenEx 6.1

Compliant with MIQE and CLSI guidelines


Basic data editing and management
Arguably the most important part of qPCR experiments is to pre-process the raw data into shape for subsequent statistical analyses. The pre-processing steps need to be performed consistently in correct order and with confidence. GenEx Standard’s streamlined and user-friendly interface ensures mistake-free data handling. Intuitive and powerful presentation tools allow professional illustrations of even the most complex experimental designs.

Advanced cutting-edge data analysis
When you need more advanced analyses GenEx Enterprise is the product for you. Powerful enough to demonstrate feasibility it often proves sufficient for most users demands. Current features include parametric and non-parametric statistical tests, Hierarchical Cluster Analysis (HCA), Heatmap, Principal Component Analysis (PCA, and Artificial Neural Networks. New features are continuously added to GenEx with close attention to customers’ needs.

New features
Sample handling and samples individual biology often contribute to confounding experimental variability. By using the new nested ANOVA feature in GenEx version 5 user will be able to evaluate variance contributions from each step in the experimental procedure. With a good knowledge of the variance contributions, an appropriate distribution of experimental replicates can be selected to minimize confounding variance and maximize the power of the experimental design! For experiments with complex features, such as for example multifactorial diseases, analytical relationships and classifications may not readily be available. The support vector machine feature in the new version of GenEx is so easy to use that it will make this advanced supervised classification method easily available to novice users, while providing access to advanced parameters for experts.

View our webpage and download a FREE GenEx 6.1 trial version => GenEx.gene-quantification.info



Best regards,

Michael W. Pfaffl
responsible Editor of the Gene Quantification Pages



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