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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
- qPCR Symposium USA in November 2010
- qPCR Application Workshops - and more ... ... ...
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.
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
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qPCR
2010 in Vienna
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BioEPS is now presenting the
qPCR 2010 eConference online via video stream! During
the symposium almost all presented talks (50 in total) were
recorded in excellent sound quality and high movie resolution. You can watch an in-depth demo presentation of our seminars and talks right here! Our offers include:
Please take a look at the system requirements for our video streams before making a purchase. |
| The complete qPCR 2010
eConference package contains 50 talks in high resolution from the qPCR Symposium 2010 in Vienna with all sessions To get connected
- Visit our web shop |
Or you can visit the single sessions including following keynote speakers:
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The talks by the plenary lecturer, selected invited academic and industrial speakers are published in METHODS special qPCR Vol 50 issue 4 (April 2010) with the title “The ongoing evolution of qPCR” => http://evolution.gene-quantification.info |
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qPCR SYMPOSIUM USA
CALL for papers
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On behalf of Scientific
Committee it is my pleasure to invite you to attend 4th qPCR Symposium
USA from November 1-4, 2010 at Millbrae, CA (very close to San
Francisco International Airport). |
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qPCR Symposium USA
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The focus of the Symposium is on:
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workshops
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 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 BioEPS workshops are based on the MIQE guidelines (Minimum Information for Publication of Quantitative real-time PCR Experiments), the first guidelines for quality assurance within qPCR technology => MIQE.gene-quantification.info
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
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Course modules 2010:
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Course dates 2010:
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Best regards,
Michael W. Pfaffl
responsible Editor of the Gene
Quantification Pages
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