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Gene Quantification Newsletter
November 2016

is sponsored by

     
     

Streamlined and automated NGS workflow 

   
  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 280 presentations held at qPCR & NGS and MG Events in the past years – qPCR 2010 in Vienna  to qPCR & NGS 2015 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!
MIQE.Gene-Quantification.info

The MIQE guidelines and the resulting scientific validity will be supported by more and more researchers, biological journals, academic and commercial institutions. Today late November 2016 we count 5000 citations for the MIQE guideline applied in qPCR and 185 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.

 


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.

 
 

Download MIQE:

MIQE Guidelines - English (original)

MIQE Guidelines for digital PCR - English (original)

MIQE Guidelines - Chinese translation

MIQE Guidelines - Japanese translation

MIQE Guidelines - Arabian translation


 

The Top 5  Most Cited Articles on Molecular Diagnostics
Clinical Chemistry's January 2015 issue is dedicated to Molecular Diagnostics. Drs. Rossa W.K. Chiu, Frank R. Cockerill, Y.M. Dennis Lo, and Carl T. Wittwer will highlight recent advances in molecular diagnostics that focus on clinical applications that use molecular diagnostics to reach novel conclusions about disease and therapy and on new technologies that improve test turnaround time, high-volume needs, comprehensive analysis, or ease of use.
In view of this exciting Molecular Diagnostics Special Issue in January, find here the mostly highly cited Clinical Chemistry articles focused on molecular diagnostics since 2009.
Stephen A. Bustin et al. -- The MIQE Guidelines: Minimum Information for Publication of Quantitative Real-Time PCR Experiments. Volume 55 Issue 4: April 2009

 
 

MIQE Talks and Seminars

A selection of MIQE talks and seminars, held at various qPCR symposia worldwide www.eConferences.de/MIQE-talks/

 
 

Download for free!
MIQE & qPCR iBook


Talk @ qPCR & NGS 2015 Event

MIQE & qPCR iBook – a digital publication:
How making the MIQE guidelines easier to follow.

MIQE & qPCR iBook
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

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 PCR 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 / 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

 

 

“Stay in touch while on the bench” MIQE qPCR

More and more people have an mobile device. From now on, those mobile devices can be used to increase quality of qPCR experimant or publication, by providing a ‘MIQE APP’. This new application could be used by scientists to check whether their experiment or the used literature fulfills the MIQE requirement or not. The ‘MIQE Guidelines’ checklist provides 85 parameters that qPCR studies should be required or recommended to meet before being considered for publication.
This checklist is based on the original published MIQE checklist and we hope it will increase future publication quality and reliability. But there are much more wider seen goals of the ‘MIQE guidelines’, all in all the goals might be summarized; to increase reliability of results to help to insure the integrity of scientific work, with major focus on biological relevance. The MIQE applet will provide an interactive and portable follow up of these parameters for any qPCR research application. The applet will be free for download and upon installed connected to our MIQE databank, collecting all the information.

Download MIQE qPCR APP for Android

 

Join
8th Gene Quantification Event
in April 2017

qPCR dPCR & NGS 2017

qPCR dPCR & NGS 2017
8th international Gene Quantification Event
Symposium & Industrial Exhibition & Application Workshops

Main topics:   Liquid Biopsy, Integrative Big Data Analysis, Biomarker Signature … and beyond
3 - 7 April 2017, in Freising-Weihenstephan,
School of Life Sciences, Technical University of Munich, Weihenstephan, Germany
www.qPCR-dPCR-NGS-2017.net

Scientific Event Announcement => Announcement.qPCR-dPCR-NGS-2017.net

Confirmed speakers and their topics => Talks.qPCR-dPCR-NGS-2017.net 

Event Promotion Trailer => www.eConferences.de/qPCR-dPCR-NGS-2017/

Scientific Symposium Sessions:

  • Liquid Biopsy & Circulating Nucleic Acids
  • Advanced Molecular Diagnostics
  • Integrative Big Data Analysis
  • Biomarker Signatures
  • Digital PCR
  • Non-coding RNAs -- microRNA, isomiRs, small RNAs, long non-coding RNAs
  • MicroGenomics & Single-Cells Diagnostics
  • Next Generation Sequencing (NGS)
  • Molecular Diagnostics in Life Science
  • MIQE & QM & Standardisation Strategies in Molecular Diagnostics

Register & Submit your scientific contribution (talk or poster abstracts) => Registration.qPCR-dPCR-NGS-2017.net

 

GenEx 6.1

The most powerful tool for complex qPCR data analysis

Compliant with MIQE and CLSI guidelines

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

Download a FREE GenEx 6.1 trial version => GenEx.Gene-Quantification.info
GenEx is a 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

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.

Download a free GenEx 6.1 trail version => GenEx.gene-quantification.info
 

 

Best regards,

Michael W. Pfaffl
responsible Editor of the Gene Quantification Pages

 

   

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