qPCR NEWS - August 2010 - focus on Copy Number Variations
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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
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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
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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 123:333â€"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
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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 â€" digital PCR (incl. M Kubista, P Day)
- HRM â€" 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 â€" 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
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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
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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
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