qPCR NEWS - December 2009

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qPCR NEWS - December 2009

qPCR NEWS - free REST 2009 version

Dear qPCR NEWS Reader,

Best Wishes for the Holiday Season and a Happy and Successful New Year 2010

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

- new REST 2009 Version  =>  http://www.REST.eu.com
- Call for Abstracts - qPCR 2010 event in Vienna => http://www.qPCR2010-Vienna.net
- Download Call => http://www.bioeps.com/qpcr2010/call-for-abstracts-qPCR-2010.pdf
- Download course brochure 2010 => http://www.gene-quantification.de/bioeps-course-programm-2010.pdf
- Register here => http://site.bioeps.com/index.php?option=com_seminar&Itemid=6


REST 2009 Software
For gene expression analysis using real-time PCR data from the Rotor-Gene Q and other cyclers

Estimates up and down regulation for gene expression studies
Analysis using randomization and bootstrapping techniques
Graphical data output via whisker-box plots
REST 2009 Software is a standalone software tool, developed by M. Pfaffl (Technical University Munich) and QIAGEN, for analysis of gene expression data from quantitative real-time PCR experiments.

Click the "Resources" tab to download REST 2009 Software free of charge  =>  http://www.REST.eu.com

REST 2009 Software is intended for molecular biology applications. This software is neither intended for the diagnosis, prevention, or treatment of a disease, nor has it been validated for such use either alone or in combination with other products. Therefore, the performance characteristics of the product for clinical use (i.e., diagnostic, prognostic, therapeutic, or blood banking) are unknown.

REST 2009 Software applies a mathematic model that takes into account the different PCR efficiencies of the gene of interest and reference genes. Compared to using a single reference gene, using multiple reference genes for normalization can improve the reliability of results.

Traditional relative quantitation enables estimation of gene expression. However, this method does not provide statistical information that is suitable for comparing expression in groups of treated and untreated samples in a robust manner. The integrated randomization and bootstrapping methods used in REST 2009 Software test the statistical significance of calculated expression ratios and can be used even when the data includes outliers. REST 2009 Software provides additional features for convenient and robust data analysis (see table "Convenient and robust data analysis").

Convenient and robust data analysis
Feature  Description - REST RG mode An optional input method allows users to copy and paste results from a Rotor-Gene Q comparative quantitation analysis rather than importing standard curve and CT results.
Whisker box plots export  - Expression variation for each gene is visualized in a whisker-box plot to highlight potential issues, such as a distribution skew. Whisker-box plots are exported by right-clicking the graph.
Improved randomization - Randomization algorithms have been improved for better confidence intervals and more accurate p values.
Handling of standard curve variation - Improvements have been made to the calculation of confidence intervals and p values. Efficiency is determined using the best fit for the standard curve and is used in the randomization process.

REST 2009 Software is suitable for gene expression analysis using real-time PCR data from the Rotor-Gene Q and other cyclers.

Free Download REST 2009 Software  =>  http://www.REST.eu.com

Download User Guide  =>  REST 2009 Software User Guide - English (PDF)  http://www.gene-quantification.de/REST_2009_Software_User_Guide.pdf


Call for Abstracts - qPCR 2010 event in Vienna
7th – 9th April 2010 in Vienna

The great international interest of the previous International qPCR Events from 2004 to 2009 with up to 600 participants from over 40 countries, and 32 international companies in the Exhibition motivates repeating the success next year in Vienna - qPCR 2010 Vienna international symposium 7th – 9th April 2010. The focus of the qPCR 2010 Event will be “The ongoing evolution of qPCR” representing all new and emerging techniques, applications and data analysis methods:  MIQE Gudelines, HRM, microRNA, CNV, single-cell qPCR, digital PCR, and analysis of circulating nucleic acids will be in the focus of the conference. The talks topics by the keynote lecturer and selected invited academic speakers will be published in a METHODS special qPCR issue with the title “The ongoing evolution of qPCR”, at the meeting in cooperation with Elsevier.

Why Vienna?  The Vienna region is Austria’s largest life sciences location. The Austrian government and the City of Vienna set up a biotechnology network (LISA VR www.lisavr.at) with the aim of having one central body to provide support and advice to start-ups and high-tech companies in the biotec field. Currently 175 life science companies employ 11,000 people in the greater Vienna region. In addition an estimated 4,500 academic researchers work in the life science sector. Vienna is the economic and biotechnology hub for Central and Eastern Europe and has become an innovative center for the life science in recent years.

The event is structured in two parts:
1)  an international qPCR Symposium taking place April 7 - 9, including various talk sessions in the big lecture hall fitting 350 persons, 
2)  a parallel qPCR Industrial Exhibition with 32 companies in the Aula and the Basement of the Juridicum (Juridicum der Universität Wien) directly in the city center of Vienna.

We have the pleasure to announce the Call for Abstracts for the qPCR 2010 Event !

Register and submit your abstract now  =>   http://submission.qPCR2010-Vienna.net   Deadline to submit an abstract is 31st January 2010.

Symposium sessions:

- MIQE and QM strategies in qPCR
- High throughput quantitative PCR – digital PCR
- HRM – High Resolution Melting - Epigenetics
- CNA - Circulating nucleic acids
- Single-cell qPCR
- RNAi - microRNA - siRNA Applications – miRNA normalisation
- qPCR BioStatistics & BioInformatics


Symposium sessions & preliminary titles

MIQE and QM strategies in qPCR
The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments. Following these guidelines will encourage better experimental practice, allowing more reliable and unequivocal interpretation of qPCR results. QM strategies in real-time PCR to guarantee better and more valid results. 
Prof. Stephen Bustin,  “The MIQE Guidelines:  Minimum Information for Publication of Quantitative Real-Time PCR Experiments”
Prof. Christine Mannhalter,  "Standardization efforts of qPCR: Example BCR-ABL Translocation"
IT-IS Lifescience,  "Optical artefacts: Cause, Consequence, Correction"

High throughput quantitative PCR – digital PCR
384 well applications, new high throughput platforms, droplet PCR, qPCR robotics, digital PCR, gene expression real-time RT-PCR arrays (mRNA and microRNA), quantitative multiplexing, …
Prof. Mikael Kubista,  “Digital PCR and intracellular expression profiling”
Dr. Philip Day,  “High throughput droplet PCR”
Dr. Ken Livak,   "High Throughput Gene Expression Profiling of Single Cells"
Dr. Dr. Simone Kreth,  "Prognostic Impact of Gene Expression Analyses in Human Glioblastoma"
Dr. Gudrun Tellmann,  "High-Throughput Gene Expression Analysis Using the LightCycler Platform"

HRM – High Resolution Melting - Epigenetics
SNP analysis, HRM = high resolution melt applications, Epigenetics, methylation markers, HRM platform comparison, …
Prof. Carl Wittwer,  "High Resolution Melting Analysis"
Prof. Claudio Orlando,  “High Resolution Melting Analysis in Cancer Diagnosis”

CNA - Circulating Nucleic Acids
Analysis of circulating RNAs and DNA and microRNAs as diagnostic and prognostic marker, …
Dr. Pamela Pinzani,  “Cell free circulating DNA”
Dr. Alfred Schöller,  "Targeting the human urine RNAome for tumor diagnostics by qPCR”
Dr. Jim Huggett,  "Diagnostic tools for measuring cell free nucleic acids. What can we expect from the next decade?”

Single-cell qPCR
Single-cell sampling, pre-amplification techniques, laser microdissection, sub-cellular PCR, micro-manipulation of cell clusters, cellular micro injection, FACS spotting, single cell handling, pre-amplification…
Dr. Michael W. Pfaffl,  “Quantitative expression analysis after pre-amp in single WBCs”
Dr. Anders Stahlberg,  “Single-cell gene expression profiling”
Dr. Petra Hartmann,  "Analysis of Single Circulating Tumour Cells isolated from Gastro-Intestinal Cancer Patients"

RNAi - microRNA - siRNA Applications – miRNA normalisation
RNAi mechanism, microRNA extraction, qRT-PCR technologies to detect microRNA, microRNA normalisation strategies, siRNA applications in combination with qRT-PCR, microRNA targets and microRNA precursors, new siRNA manipulation and microRNA technologies, ...
Prof. Jo Vandesompele,  “MicroRNA and mRNA gene expression normalization”
Dr. Mirco Castoldi, "Expression profiling of microRNA by quantitative real time PCR, what is available and where to go from there"

qPCR BioStatistics & BioInformatics
software applications, data mining, calculation of relative expression, primer and probe design on mRNA and microRNA level, real-time PCR efficiency determination, mathematical modelling, multivariate expression profiling, statistics in real-time PCR, data management, multiway expression profiling, multiple regression analysis,  3D data visualization, ...
Dr. Ales Tichopad,  “Statistical aspects of quantitative PCR experiment design and qPCR data analysis”
Dr. Jan Hellemans,  “Accurate and objective copy number profiling using real-time quantitative PCR”
Dr. Anders Bergkvist,  “Expression profiling - clusters of possibilities”
Dr. Jan Ruijter,  "Determining PCR efficiency and Cq value after monitoring PCR amplification with hydolysis probes"

BioEPS GmbH - qPCR Application Workshops

Life Science is still a growing sector and new methods and technologies are continously developed. Therefore permanent training and education becomes so important.

With our specific course program we are offering a range of high-quality course modules, in cooperation with different companies to give a general and independent overview of existing qPCR technologies and systems. Our course issues are based on skilled know-how from own research studies and publications.

Our aim is to point out a critical way of thinking to increase the quality and outcome of experimental data.
All courses are held regularly in Freising-Weihenstephan, Germany, in German and English language.
Further customized workshops and specialized trainings will be held as well across Europe and world-wide.
Workshops are powered by BioEPS GmbH, located at the campus of the Technical University of Munich, in Freising-Weihenstephan, very close to the Munich Airport (MUC).
For more information and registration, please see our web page => http://workshops.gene-quantification.info/

Course Occasions 2010:

3-day qPCR Basic Module
2-day BioStatistics & Expression Profiling Module
3-day single-cell qPCR
2-day microRNA qPCR
1-day HRM     NEW !
2-das qPCR-R data analysis   NEW !
1-day Project Management     NEW !
2-day Quality Management    NEW !

Download course brochure 2010 => http://www.gene-quantification.de/bioeps-course-programm-2010.pdf

Register here => http://site.bioeps.com/index.php?option=com_seminar&Itemid=6

Access to our workshops => http://www.gene-quantification.de/bioeps-access.html

Forward Please send the qPCR NEWS to further scientists and friends who are interested in qPCR !

Best regards,

Michael W. Pfaffl
responsible Editor of the Gene Quantification Pages

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