qPCR NEWS - August 2010 - focus on Copy Number Variations --------------------------------------------------------------------------------
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: - UPDATE - Copy Number Variations => http://CNV.gene-quantification.info - eConference with high quality 50 talks presented at the "International qPCR 2010 Symposium in Vienna" - View our eSeminar and eConference demo videos http://eseminars.bioeps.com/player/?action=demo - qPCR Symposium USA in November 2010 => http://events.gene-quantification.info - qPCR Application Workshops => http://workshops.gene-quantification.info -------------------------------------------------------------------------------- The gene copy number (also "copy number variants" or CNVs) is the number of copies of a particular gene in the genotype of an individual. Recent evidence shows that the gene copy number can be elevated in cancer cells. The human genome is comprised of 6 billion chemical bases (or nucleotides) of DNA packaged into two sets of 23 chromosomes, one set inherited from each parent. The DNA encodes roughly 27,000 genes. It was generally thought that genes were almost always present in two copies in a genome. However, recent discoveries have revealed that large segments of DNA, ranging in size from thousands to millions of DNA bases, can vary in copy-number. Such copy number variations (or CNVs) can encompass genes leading to dosage imbalances. For example, genes that were thought to always occur in two copies per genome have now been found to sometimes be present in one, three, or more than three copies. In a few rare instances the genes are missing altogether (see figure). Why are CNVs important? Differences in the DNA sequence of our genomes contribute to our uniqueness. These changes influence most traits including susceptibility to disease. It was thought that single nucleotide changes (called SNPs) in DNA were the most prevalent and important form of genetic variation. The current studies reveal that CNVs comprise at least three times the total nucleotide content of SNPs. Since CNVs often encompass genes, they may have important roles both in human disease and drug response. Understanding the mechanisms of CNV formation may also help us better understand human genome evolution. How does the new CNV map help? The new global CNV map will transform medical research in four areas. The first and most important area is in hunting for genes underlying common diseases. To date, attempts to identify these genes have not really considered the role CNVs may play in human health. Second, the CNV map is being used to study familial genetic conditions. Third, there are thousands of severe developmental defects caused by chromosomal rearrangements. The CNV map is being used to exclude variation found in unaffected individuals, helping researchers to target the region that might be involved. The data generated will also contribute to a more accurate and complete human genome reference sequence used by all biomedical scientists. http://CNV.gene-quantification.info -------------------------------------------------------------------------------- Finding copy-number variants. Nicol Rusk Nature Methods 2008 5(11) 917 Large-scale copy number variants (CNVs): Distribution in normal subjects and FISH/real-time qPCR analysis. Ying Qiao, Xudong Liu, Chansonette Harvard, Sarah L Nolin, W Ted Brown, Maryam Koochek, Jeanette JA Holden, ME Suzanne Lewis, and Evica Rajcan-Separovic BMC Genomics 2007, 8: 167-177 Global variation in copy number in the human genome. Richard Redon, Shumpei Ishikawa, Karen R. Fitch, Lars Feuk, George H. Perry, T. Daniel Andrews, Heike Fiegler, Michael H. Shapero, ......et al. Nature (2006) Vol 444. 444-454 Accurate and objective copy number profiling using real-time quantitative PCR Barbara D’haene, Jo Vandesompele, Jan Hellemans Methods Vol 50, Issue 4, Pages 262-270 Taking qPCR to a higher level: Analysis of CNV reveals the power of high throughput qPCR to enhance quantitative resolution Suzanne Weaver, Simant Dube, Alain Mir, Jian Qin, Gang Sun, Ramesh Ramakrishnan, Robert C. Jones, Kenneth J. Livak Methods Vol 50, Issue 4, Pages 271-276 Copy number variation and evolution in humans and chimpanzees. Perry GH, Yang F, Marques-Bonet T, Murphy C, Fitzgerald T, Lee AS, Hyland C, Stone AC, Hurles ME, Tyler-Smith C, Eichler EE, Carter NP, Lee C, Redon R. Genome Res. 2008 18(11): 1698-1710 Methods to detect and analyze copynumber variations at the genome- wideand locus-specific levels. J.H. Lee and J.T. Jeon Cytogenet Genome Res 123:333–342 (2008) Methods and strategies for analyzing copy number variation using DNA microarrays. Carter NP. Nat Genet. 2007 39(7 Suppl): S16-21. Review. Simultaneous mutation and copy number variation (CNV) detection by multiplex PCR-based GS-FLX sequencing. Goossens D, Moens LN, Nelis E, Lenaerts AS, Glassee W, Kalbe A, Frey B, Kopal G, De Jonghe P, De Rijk P, Del-Favero J. Hum Mutat. 2009 30(3): 472-476 Genome-wide analysis of transcript isoform variation in humans. Kwan T, Benovoy D, Dias C, Gurd S, Provencher C, Beaulieu P, Hudson TJ, Sladek R, Majewski J. Nat Genet. 2008 40(2): 225-231. Transcript copy number estimation using a mouse whole-genome oligonucleotide microarray. Mark G Carter, Alexei A Sharov, Vincent VanBuren, Dawood B Dudekula, Condie E Carmack, Charlie Nelson and Minoru S H Ko Genome Biology 2005, 6:R61 Comparative study of three PCR-based copy number variant approaches, CFMSA, M-PCR, and MLPA, in 22q11.2 deletion syndrome. Yang C, Zhu X, Yi L, Shi Z, Wang H, Hu Y, Wang Y. Genet Test Mol Biomarkers. 2009 13(6): 803-808 Copy-number variation genotyping of GSTT1 and GSTM1 gene deletions by real-time PCR. Rose-Zerilli MJ, Barton SJ, Henderson AJ, Shaheen SO, Holloway JW. Clin Chem. 2009 55(9): 1680-1685 High-throughput genotyping of copy number variation in glutathione S- transferases M1 and T1 using real-time PCR in 20,687 individuals. Nørskov MS, Frikke-Schmidt R, Loft S, Tybjaerg-Hansen A. Clin Biochem. 2009 42(3): 201-209 Candidate gene copy number analysis by PCR and multicapillary electrophoresis. Szantai E, Elek Z, Guttman A, Sasvari-Szekely M. Electrophoresis. 2009 30(7): 1098-1101. Statistical tools for transgene copy number estimation based on real- time PCR. Joshua S Yuan, Jason Burris, Nathan R Stewart, Ayalew Mentewab and C Neal Stewart BMC Bioinformatics 2007, 8(): S6 Copy number variation goes clinical. A meeting report Le Caignec C, Redon R. Genome Biol. 2009;10(1): 301-303 http://CNV.gene-quantification.info -------------------------------------------------------------------------------- qPCR 2010 in Vienna International qPCR Symposium & Exhibition 7-9th April 2010 http://www.qpcr2010-vienna.net/ Topic: "The ongoing evolution of qPCR" BioEPS is now presenting the qPCR 2010 eConference online via video stream! With our new eConference streaming server a world-wide know-how transfer becomes possible in a fast and simple way! During the symposium almost all presented talks (50 in total) were recorded in excellent sound quality and high movie resolution. They are available NOW as eConfernce qPCR 2010 on our streaming server => http://eConference.qPCR2010-Vienna.net You can watch an in-depth demo presentation of our seminars and talks right here! => http://eseminars.bioeps.com/player/?action=demo Our offers include: - 20 days free online access to all the talks as often as you want ! - Online access from any computer at any time ! - High resolution streaming technology with great sound quality and high movie resolution ! - Please take a look at the system requirements for our video streams before making a purchase. => http://eConference.bioeps.com The qPCR 2010 eConference package contains 50 talks in high resolution from the qPCR Symposium 2010 in Vienna with the following sessions: - MIQE and QM strategies in qPCR (incl. SA Bustin) - High throughput quantitative PCR – digital PCR (incl. M Kubista, P Day) - HRM – High Resolution Melting - Epigenetics (incl. C Wittwer, C Orlando) - CNA - Circulating nucleic acids (incl. P Pinzani, J Huggett) - Single-cell qPCR (incl. K Livak) - RNAi - microRNA - siRNA Applications – miRNA normalisation (incl. J Vandesompele, M Castoldi, MW Pfaffl) - qPCR data analysis - BioStatistics & BioInformatics (incl. J Hellemans, M Kubista, A Tichopad) - detailed info about all talks and the speakers => http://sessions.qpcr2010-vienna.net - To get connected - visit our web shop => http://eConference.bioeps.com -------------------------------------------------------------------------------- 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 2-das qPCR-R data analysis NEW ! 1-day Project Management NEW ! 2-day Quality Management NEW ! Course dates 2010: 4 - 6 October 2010 (E) 3-day qPCR Basic Module (Mon. - Wed.) 7 October 2010 (E) 1-day HRM Module (Thu.) 11 - 12 October 2010 (E) 2-day qPC-R - data analysis using R packages (Mon.-Tue.) 18 - 20 October 2010 (E) 3-day single-cell & qPCR (Mon. - Wed.) 21 - 22 October 2010 (E) 2-day Experiment Design & qPCR data processing (Thu. - Fri.) 8 - 9 November 2010 (E) 2-day microRNA & qPCR (Mon.-Tue.) 29 November - 1 December 2010 (E) 3-day Experiment Design & qPCR data processing (Mon. - Wed.) 2 - 3 December 2010 (E) 2-day BioStatistics Module (Thu. - Fri.) 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 http://www.gene-quantification.info -------------------------------------------------------------------------------- If this newsletter is not displayed correctly by your email client, please use following link: http://qPCRnews.gene-quantification.info/ 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. Copyright © 2005 - 2010 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:newslet...@gene- quantification.info?subject=SUBSCRIBE _______________________________________________ Methods mailing list Methods@net.bio.net http://www.bio.net/biomail/listinfo/methods
