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Gene Quantification Newsletter
November 2014
is sponsored by

     
     

Streamlined and automated NGS workflow


 
  Dear researcher,
dear Gene Quantification page reader,

Our newsletter informs about the latest news in quantitative real-time PCR (qPCR and RT-qPCR), which are compiled and summarised on the www.Gene-Quantification.info
The focus of this newsletter issue is:
   


 

streaming portal

Join the new eConferences streaming webportal -- www.eConferences.de -- Amplify your knowledge!
This portal is dedicated to scientists from the community of qPCR, digital-PCR, NGS and Molecular Diagnostics. You’ll find here all the records from around 200 presentations held at qPCR & NGS Events in the past years. 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, including Android or iOS.

 

 

MIQE and hot papers in the field of QC

Reliable Gene Expression Analysis by Reverse Transcription-Quantitative PCR: Reporting and Minimizing the Uncertainty in Data Accuracy.
Remans T, Keunen E, Bex GJ, Smeets K, Vangronsveld J, Cuypers A.
Plant Cell. 2014 Oct 31

Variability of the Reverse Transcription Step: Practical Implications.
Bustin SA, Dhillon HS, Kirvell S, Greenwood C, Parker M, Shipley GL, Nolan T.
Clin Chem. 2014 Oct 31

Minimum Information Necessary for Quantitative Real- Time PCR Experiments
Gemma Johnson, Afi f Abdel Nour, Tania Nolan, Jim Huggett, and Stephen Bustin
Roberto Biassoni and Alessandro Raso (eds.), Quantitative Real-Time PCR: Methods and Protocols, Methods in Molecular Biology,
vol. 1160, Springer Science+Business Media New York 2014

Five Years MIQE Guidelines: The Case of the Arabian Countries
Afif M. Abdel Nour, Esam Azhar, Ghazi Damanhouri, Stephen A. Bustin
PLoS ONE 9(2) (2014): e88266.

Toward Enhanced MIQE Compliance: Reference Residual Normalization of qPCR Gene Expression Data
Richard C. Edmunds, Jenifer K. McIntyre, J. Adam Luckenbach, David H. Baldwin, and John P. Incardona
JOURNAL OF BIOMOLECULAR TECHNIQUES, VOLUME 25 (2) 2014

Considerations for accurate gene expression measurement by reverse transcription quantitative PCR when analysing clinical samples
Sanders R, Mason DJ, Foy CA, Huggett JF
Anal Bioanal Chem. 2014 May 25

Evaluation of quantitative miRNA expression platforms in the microRNA quality control (miRQC) study
Mestdagh P et al
Nat Methods. 2014 Jun 29

An evidence based strategy for normalization of quantitative PCR data from miRNA expression analysis in forensically relevant body fluids.
Sauer E, Madea B, Courts C.
Forensic Sci Int Genet. 2014 11: 174-181

An evidence based strategy for normalization of quantitative PCR data from miRNA expression analysis in forensic organ tissue identification.
Sauer E, Babion I, Madea B, Courts C.
Forensic Sci Int Genet. 2014 13: 217-223

... more MIQE related papers MIQE.gene-quantification.info

 
A nice review about qPCR data analysis tools

A survey of tools for the analysis of quantitative PCR (qPCR) data.
Stephan Pabinger, Stefan Rödiger, Albert Kriegner, Klemens Vierlinger, Andreas Weinhäusel
Biomolecular Detection and Quantification 1 (2014) 23–33

Real-time quantitative polymerase-chain-reaction (qPCR) is a standard technique in most laboratories used for various applications in basic research. Analysis of qPCR data is a crucial part of the entire experiment, which has led to the development of a plethora of methods. The released tools either cover specific parts of the workflow or provide complete analysis solutions. Here, we surveyed 27 open-access software packages and tools for the analysis of qPCR data. The survey includes 8 Microsoft Windows, 5 web-based, 9 R-based and 5 tools from other platforms. Reviewed packages and tools support the analysis of different qPCR applications, such as RNA quantification, DNA methylation, genotyping, identification of copy number variations, and digital PCR. We report an overview of the functionality, features and specific requirements of the individual software tools, such as data exchange formats, availability of a graphical user interface, included procedures for graphical data presentation, and offered statistical methods. In addition, we provide an overview about quantification strategies, and report various applications of qPCR. Our comprehensive survey showed that most tools use their own file format and only a fraction of the currently existing tools support the standardized data exchange format RDML. To allow a more streamlined and comparable analysis of qPCR data, more vendors and tools need to adapt the standardized format to encourage the exchange of data between instrument software, analysis tools, and researchers.

... more about qPCR data analysis bioinformatics.gene-quantification.info

 

Register for
qPCR & NGS 2015

qPCR & NGS 2015 Event
"Advanced Molecular Diagnostics for Biomarker Discovery"
7th international qPCR & NGS Event -- Symposium  &  Industrial Exhibition  &  Application Workshops
23-27 March 2015, Technical University of Munich - School of Life Sciences, in Freising-Weihenstephan, Germany
www.qPCR-NGS-2015.net

The great international interest in the previous qPCR & NGS Events from 2004 till 2013 with a constant audience of more than 500 participants from all over the world motivates repeating the success next year in March 2015. We broaden our focus in genomics applications from quantitative RT-PCR, over digital PCR to the latest Next Generation Sequencing technologies. The date for the 7th International qPCR Symposium & Exhibition & Application Workshops is from the 23rd to the 27th March 2015. Parallel to the scientific symposium an industrial exhibition will take place where around 35-40 international companies will be presenting their newest qPCR, dPCR and NGS services and technologies. The symposium will be followed by various qPCR & NGS Workshops taking place March 26th and 27th powered by TATAA Biocenter, Bio-Rad, Genomatix and other leaders in the field.
Event location is the central lecture hall complex and the foyer at TUM (Technical University of Munich) in Freising Weihenstephan, Germany. The TUM and the Biotech region around Munich are part of the largest Biotech cluster in Europe, located close to the Munich airport (MUC) directly in the heart of Bavaria.

The focus of the qPCR & NGS 2015 Event is "Advanced Molecular Diagnostics for Biomarker Discovery"

The symposium is based on around 60-70 lectures and 100 posters presented by international recognised experts in their application fields. The emphasis will be on unbiased, didactic and scientific information exchange. One third of the talks will be presented by invited speakers, one third of the speakers will be selected from the submitted abstracts and one third will be given to qPCR and NGS company R&D representatives. Various poster sessions will be held in parallel in a separate poster exhibition hall. All scientific contributions will be published in an abstract book (qPCR & NGS 2015 Proceedings incl. ISBN). All talks will be recorded and made public in autumn 2015 via the www.eConferences.de streaming platform together with around 200 talks from qPCR 2010 onwards.

Leading academic researchers and industrial contributors in the field will participate in the symposium, which will be an arena for fruitful discussions between researchers of different backgrounds. The Symposium Talks, Poster Sessions, Industrial Exhibition and associated qPCR & NGS Application Workshops offer an overview of the present knowledge and future developments in qPCR, next generation sequencing and gene expression measurement technology and its wide applications in research.

As usual the qPCR & NGS Event is structured in three parts: 

  1. Symposium & Poster Sessions, taking place March 23 - 25   Sessions.qPCR-NGS-2015.net
  2. Industrial Exhibition with around 40 companies, taking place March 23 - 25   Exhibition.qPCR-NGS-2015.net  -- the exhibition is fully booked!
  3. qPCR & NGS Application Workshops, taking place March 26 - 27    Workshops.qPCR-NGS-2015.net

Up to now confirmed speakers => Talks.qPCR-NGS-2015.net


 

Symposium Talk & Poster Sessions:

  • Main topic:   Advanced Molecular Diagnostics
  • Main topic:   Biomarker Discovery
  • Main topic:   Next Generation Sequencing (NGS)
     - NGS overview talks - information technology in the era of NGS
     - Pre NGS - sample prep & setup & library generation
     - NGS – new sequencing technologies (e.g. single molecule and pore sequencing)
     - NGS – data analysis (data management, mapping, alignment algorithms, data de novo assembly )
     - NGS – diagnostic applications
  • MicroGenomics & Single-cells diagnostics
  • Circulating Nucleic Acids
  • Molecular Diagnostics in Agriculture, Veterinary Medicine, Food & Environmental Science
  • MIQE & QM & Standardisation strategies in molecular diagnostics
  • Digital PCR  &  Nano-fluidics
  • Non-coding RNAs -- microRNA, small RNAs, long non-coding RNAs
  • qPCR Data Analysis -- BioStatistics & BioInformatics

Register for the symposium and the workshops => Registration.qPCR-NGS-2015.net

Download the latest event flyer => Event-announcement.qPCR-NGS-2015.net

Event location on Google maps  http://goo.gl/maps/3p3gx

View our previous talks and the event trailer on our streaming server -- www.eConferences.de

 
 

NEW Journal -- "Biomolecular Detection and Quantification" -- Call for submissions

Biomolecular Detection and Quantification (BDQ) is an open access, peer-reviewed international journal dedicated to championing excellence in molecular study design, measurement, data analysis and reporting. Its focus is on the application of qualitative and quantitative molecular methodologies to all areas of clinical and life sciences. Download the recent BDQ papers on Elsevier Science Direct.

The journal has two main aims:

  • to provide a forum for discussion and recommendation of guidelines designed to improve the accuracy of molecular measurement, its data analysis and the transparency of its subsequent reporting;
  • to publish molecular biology based studies that adhere to best practice guidelines, both current and future.

Benefits of publishing open access with Elsevier's Biomolecular Detection and Quantification - www.journals.elsevier.com/biomolecular-detection-and-quantification/

  • Peer-reviewed journal indexed by Scopus and supporting ORCID and Crossref to help maintain your publication record.
  • A renowned and respected editorial team with extensive knowledge of your research field. BDQ was established by a group of scientists based on their experience developing and publishing the Minimum Information for Publication of Quantitative Real-Time (and Digital) PCR Experiments (the MIQE and digital MIQE guidelines).
  • Reaching key audiences with 10 million active users per month using our publishing platform ScienceDirect.
  • Choice of user licenses so authors can decide how best to publish open access.
  • A discount on the publication fee for a limited time.

For more information about publishing Open Access with Elsevier, including funding body arrangements, institutional agreements and more, visit: www.elsevier.com/openaccess

We look forward to receiving your paper!

Kind regards,

The Editors
Stephen Bustin, Jim Huggett, Justin O'Grady, Michael W. Pfaffl, Carl Wittwer, Ron Cook

View full editorial board

 

GenEx 6:
real-time PCR data analysis software
 

GenEx 6 available - The most powerful tool for complex qPCR data analysis
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. Download GenEx User Guide

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 analysis of qPCR data compliant with current Clinical Laboratory Standards Institute (CLSI) guidelines.

The new analyses in GenEx 6 include: Estimating PCR efficiency, testing for outliers, testing linear model, estimating dynamic range, estimating random error, estimating limit of detection, estimating limit of quantification, estimating concentrations of unknowns, evaluation of precision, and verification of precision. For all estimates confidence intervals are calculated.
Additional new features include: Transcript distribution for single cell analysis, Survival Analysis, Receiver Operator Characteristics (ROC), Wizard for ProSeek protein analysis, and reader for 3DGene microRNA analysis.

View our GenEx webpage and download a FREE GenEx 6 trial version => GenEx.Gene-Quantification.info

Join all GenEx talks by Prof. Mikael Kubista held at recent qPCR & NGS Events => www.eConferences.de/multid/

 

Best regards,

Michael W. Pfaffl
responsible Editor of the Gene Quantification Pages

 

   

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