qPCR NEWSLETTER - May 2007

1 post / 0 new
gene-quantification
gene-quantification's picture
qPCR NEWSLETTER - May 2007

qPCR NEWSLETTER - May 2007

If this newsletter is not displayed correctly by your email client, please use following LINK:
http://www.gene-quantification.de/qpcr-news.html

Dear researcher,
dear Gene Quantification page reader,

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 papers on PCR efficiency
- Update of the qPCR Talk and Webinar Page - PODCASTS
- qPCR data analysis
- Update on qPCR INFOPORTAL
- qPCR Symposium USA in October/November 2007
- STILL AVAILIBILITY => Real-time qPCR course from 2nd-6th July 2007 in Freising, Germany

--------------------------------------------------------------------------------

http://www.gene-quantification.de/efficiency03.html

Efficiency Overview article - Comprehensive Algorithm for Quantitative Real-Time Polymerase Chain Reaction
Sheng Zhao and Russell D. Fernald, 2005 download PDF

Technical Note - Evaluation of Real-Time PCR Amplification Efficiencies to Detect PCR Inhibitors
Elias J. Kontanis and Floyd A. Reed, 2006 download PDF

Estimation of the reaction efficiency in polymerase chain reaction
Nadia Lalam, 2006 download PDF

Molelling the PCR amplification process by a size-dependent branching process and estimation of the efficiency
Lalam et al., 2004 download PDF

Statistical Inference for Quantitative Polymerase Chain Reaction Using a Hidden Markov Model: A Bayesian Approach Lalam, 2007 download PDF

Evaluation of absolute quantitation by nonlinear regression in probe-based real-time PCR
Goll et al., 2006 download PDF

Mathematical Model of Real-Time PCR Kinetics
Gevertz et al., 2005 download PDF

--------------------------------------------------------------------------------

qPCR data analysis

http://www.gene-quantification.de/main-bioinf.shtml

Statistical analysis of real-time PCR data.

BMC Bioinformatics. 2006 (7): 85. Yuan JS, Reed A, Chen F, Stewart CN Jr.
Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996, USA.

Data Analysis Methods

There are two methods, both equally valid, for analyzing data obtained from real time PCR: Relative Standard Curve Method and Comparative CT Method. The first, relative standard curve method, is useful for investigators that have a limited number of cDNA samples and a large number of genes of interest. The comparative CT method is useful for investigators who have a large number of cDNA samples and a limited number of genes of interest (RRC Core Genomics Facility, University of Illinois at Chicago)

Data Analysis Methods
- Relative Standard Curve Method
- Comparative CT Method
- Data Analysis

Tools and Technologies for Real-Time PCR

Biocompare's qPCR Tutorial presents researchers with an overview of real-time qPCR, identifies the advantages and disadvantages of the various detection technologies, outlines the key issues for optimizing experimental design and offers a brief description of the various methods used for data analysis.

Evaluation of real-time PCR data.

Vaerman JL, Saussoy P, Ingargiola I. J Biol Regul Homeost Agents. 2004 18(2): 212-214.
UCL, Cliniques Saint Luc, Bruxelles, Belgium.

If real-time PCR is to be of much worth to its user, some idea regarding the reliability of its data is essential. We discuss here some of the problems associated with interpreting numerical real-time PCR data that lend themselves to analytical evaluation. We translate into the language of molecular biology some of the criteria which are used to evaluate the performance of any new method (linearity, precision, specificity, limit of detection and quantification).

Real-time PCR gene expression profiling
Mikael Kubista, Bjrn Sjgreen, Amin Forootan, Radek Sindelka and Jiri Jonák, and José Manuel Andrade

Real-time PCR has rapidly become the preferred technique for quantitative analysis of nucleic acids. Its superior sensitivity, reproducibility and dynamic range make it the preferred choice for expression profiling in scientific, as well as routine, applications. => Link to GenEx software

Statistical practice in high-throughput screening data analysis.

Malo N, Hanley JA, Cerquozzi S, Pelletier J, Nadon R. Nat Biotechnol. 2006 24(2): 167-75.
McGill University and Genome Quebec Innovation Centre, 740 avenue du Docteur Penfield, Montreal, Quebec, Canada

High-throughput screening is an early critical step in drug discovery. Its aim is to screen a large number of diverse chemical compounds to identify candidate 'hits' rapidly and accurately. Few statistical tools are currently available, however, to detect quality hits with a high degree of confidence. We examine statistical aspects of data preprocessing and hit identification for primary screens. We focus on concerns related to positional effects of wells within plates, choice of hit threshold and the importance of minimizing false-positive and false-negative rates. We argue that replicate measurements are needed to verify assumptions of current methods and to suggest data analysis strategies when assumptions are not met. The integration of replicates with robust statistical methods in primary screens will facilitate the discovery of reliable hits, ultimately improving the sensitivity and specificity of the screening process.

Addressing fluorogenic real-time qPCR inhibition using the novel custom Excel file system to attain consistently high fidelity qPCR reactions

Jack M. Gallup and Mark R. Ackermann
Department of Veterinary Pathology, College of Veterinary Medicine, Iowa State University. Ames, Iowa 50011-1250. USA
Biol. Proced. Online 2006 (8): 87-152.

The purpose of this manuscript is to discuss fluorogenic real-time quantitative polymerase chain reaction (qPCR) inhibition and to introduce/define a novel Microsoft Excel-based file system which provides a way to detect and avoid inhibition, and enables investigators to consistently design dynamically-sound, truly LOG-linear qPCR reactions very quickly. The qPCR problems this invention solves are universal to all qPCR reactions, and it performs all necessary qPCR set-up calculations in about 52 seconds (using a pentium 4 processor) for up to seven qPCR targets and seventy-two samples at a time calculations that commonly take capable investigators days to finish. We have named this custom Excel-based file system "FocusField2-6GallupqPCRSet-upTool-001" (FF2-6-001 qPCR set-up tool), and are in the process of transforming it into professional qPCR set-up software to be made available in 2007. The current prototype is already fully functional.

--------------------------------------------------------------------------------

TALKS Update of the qPCR Talk and Webinar page

A lot of interesting TALKs, WEBINARs, SLIDE SHOWs, and PODCASTs from various speakers, biotec companies, qPCR Events, and international journals (Nature and Science) are FREE for download. Have a look and you will definitely something interesting for your scientific work !
http://talks.gene-quantification.info/
http://webinar.gene-quantification.info/

--------------------------------------------------------------------------------

INFOPORTAL Protocols on qPCR INFOPORTAL

http://infoportal.gene-quantification.info/

Protocols online is a resource for protocols, including authoritative, peer-reviewed 'protocols and an interactive network.

NEW => qPCR and Molecular Biology - Discussion Forums

--------------------------------------------------------------------------------

Upcoming Events World-wide academic and commercial qPCR Events
http://events.gene-quantification.info/

Symposia, Meetings, Conferences, Workshops, Seminars, Online-Seminars, qPCR Education Program, ...etc...
Please submit your qPCR event here => eval(unescape('%64%6f%63%75%6d%65%6e%74%2e%77%72%69%74%65%28%27%3c%61%20%68%72%65%66%3d%22%6d%61%69%6c%74%6f%3a%65%76%65%6e%74%73%40%67%65%6e%65%2d%71%75%61%6e%74%69%66%69%63%61%74%69%6f%6e%2e%69%6e%66%6f%22%3e%65%76%65%6e%74%73%40%67%65%6e%65%2d%71%75%61%6e%74%69%66%69%63%61%74%69%6f%6e%2e%69%6e%66%6f%3c%2f%61%3e%27%29%3b'))

--------------------------------------------------------------------------------

qPCR Symposium USA
http://www.qPCRsymposium.com

Symposium Focus:
Markers, Stem Cells, Single Cell, siRNA, miRNA, Diagnostics, Immuno-qPCR, Expression Profiling,
Poster Presentation, Workshops in qPCR

--------------------------------------------------------------------------------

WORKSHOP

Opening Opening of TATAA Biocenter, Prague => http://www.img.cas.cz/ge/TATAAPrague.html
Real time open qPCR course from 21th - 25th May 2007 => download flyer

TATAA Biocenter Germany - qPCR Application workshops

At the TATAA Biocenter Germany we offer qPCR application workshops, the 3-day Core Module and a 2-day Biostatistics Module. qPCR courses are held in regularly in Gteborg, Sweden, in English and in Freising-Weihenstephan, Germany, in German and English, and in Prague, Czech Republic in English and Czech.
Depending on the occasion the workshop language and the different prices may apply. Further customized workshops and specialized trainings will be held as well across Europe and world-wide. TATAA Biocenter Germany courses are held in cooperation with the Institute of Physiology, located at the Technical University of Munich, in Freising-Weihenstephan, near Munich, very close to the Munich Airport (MUC). For more information and to register for the qPCR application workshops, please see our web page:

http://tataa.gene-quantification.info/

Course Occasions 2007:
3-day qPCR Core Module (Mon. - Wed.) and 2-day BioStatistics Module (Thu. - Fri.)

2 - 6th July 2007 (in Freising, Germany, English language)
24 - 28th September 2007 (in Freising, Germany, Kurs wird in DEUTSCH gehalten, German language)
22 - 26th October 2007 (in Freising, Germany, English language)
26 - 30th November 2007 (in Freising, Germany, English language)
Please register here => http://www.tataa.com/

--------------------------------------------------------------------------------

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
http://www.gene-quantification.info

--------------------------------------------------------------------------------

If this newsletter is not displayed correctly by your email client, please use following LINK
The qPCR NEWS and the Gene Quantification Pages are educational sites with the only purpose of facilitating access to qPCR related information on the internet. The qPCR NEWS and the Gene Quantification Pages are edited by Michael W. Pfaffl and powered by BioScience Events. Copyright 2005 - 2007 All rights reserved. Any unauthorized use, reproduction, or transfer of this message or its contents, in any medium, is strictly prohibited. Disclaimer & Copyrights are displayed on the homepage www.gene-quantification.com To subscribe or change your e-mail address in qPCR NEWS, and if you would like to receive future issues FREE of charge, please send an e-mail with the subject SUBSCRIBE to mailto:newsletter@gene-quantification.info?subject=SUBSCRIBE

--------------------------------------------------------------------------------
If this newsletter is not displayed correctly by your email client, please use following LINK:
http://www.gene-quantification.de/qpcr-news.html

The qPCR NEWS and the Gene Quantification Pages are educational sites with the only purpose of facilitating access to qPCR related information on the internet. The qPCR NEWS and the Gene Quantification Pages are edited by Michael W. Pfaffl and powered by BioScience Events. Copyright 2005 - 2007 All rights reserved. Any unauthorized use, reproduction, or transfer of this message or its contents, in any medium, is strictly prohibited. Disclaimer & Copyrights are displayed on the homepage www.gene-quantification.com To subscribe or change your e-mail address in qPCR NEWS, and if you would like to receive future issues FREE of charge, please send an e-mail with the subject SUBSCRIBE