qPCR NEWS - August 2010 - focus on Copy Number Variations

Editor www.Gene-Quantification.info via methods%40net.bio.net (by editor from gene-quantification.info)
Thu Aug 5 07:09:21 EST 2010

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  =3D>  http://CNV.gene-quantification.inf=
- 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  =3D>  http://events.gene-quantificat=
- qPCR Application Workshops  =3D>  http://workshops.gene-quantification.in=


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

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
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
Nature (2006) Vol 444. 444-454

Accurate and objective copy number profiling using real-time
quantitative PCR
Barbara D=92haene, 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=96342 (2008)

Methods and strategies for analyzing copy number variation using DNA
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.
N=F8rskov 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
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



qPCR 2010 in Vienna
   International qPCR Symposium & Exhibition
   7-9th April 2010
   Topic:   "The ongoing evolution of qPCR"

BioEPS is now presenting the qPCR 2010 eConference online via video
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During the symposium almost all presented talks (50 in total) were
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They are available NOW as eConfernce qPCR 2010 on our streaming
server  =3D>  http://eConference.qPCR2010-Vienna.net

You can watch an in-depth demo presentation of our seminars and talks
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=3D> http://eseminars.bioeps.com/player/?action=3Ddemo

Our offers include:

- 20 days free online access to all the talks as often as you want !
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- 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.

=3D>  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 =96 digital PCR   (incl. M Kubista, P
- HRM =96 High Resolution Melting - Epigenetics  (incl. C Wittwer, C
- CNA - Circulating nucleic acids    (incl. P Pinzani, J Huggett)
- Single-cell qPCR  (incl. K Livak)
- RNAi - microRNA - siRNA Applications =96 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 =3D> http://sessions.qpcr2=

- To get connected - visit our web shop  =3D>  http://eConference.bioeps.co=


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technologies are continously developed. Therefore permanent training
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With our specific course program we are offering a range of high-
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All courses are held regularly in Freising-Weihenstephan, Germany, in
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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 =3D> 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
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8 - 9  November 2010  (E)   2-day microRNA & qPCR (Mon.-Tue.)
29 November - 1 December 2010  (E)   3-day Experiment Design  &  qPCR
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2 - 3 December 2010  (E)   2-day BioStatistics Module (Thu. - Fri.)

Download course brochure 2010 =3D> http://www.gene-quantification.de/bioeps=

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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


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