qPCR NEWS - September 2010 - focus on MIQE guidelines

Editor www.Gene-Quantification.info via methods%40net.bio.net (by editor from gene-quantification.info)
Mon Sep 27 09:02:32 EST 2010


qPCR NEWS - September 2010 - focus on MIQE guidelines
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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:

- The MIQE guidelines - all NEWS and Press releases
- qPCR Symposium USA in November 2010
- qPCR Application Workshops  -  and more ... ... ...


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The MIQE Guidelines - Minimum Information for Publication of
Quantitative Real-Time PCR Experiments

Stephen A. Bustin,  Vladimir Benes,  Jeremy A. Garson,  Jan
Hellemans,  Jim Huggett, Mikael Kubista,  Reinhold Mueller,  Tania
Nolan,  Michael W. Pfaffl,  Gregory L. Shipley, Jo Vandesompele,  and
Carl T. Wittwer
Clinical Chemistry 2009, 55(4): 611-622

BACKGROUND:  Currently, a lack of consensus exists on how best to
perform and interpret quantitative real-time PCR (qPCR) experiments.
The problem is exacerbated by a lack of sufficient experimental detail
in many publications, which impedes a reader's ability to evaluate
critically the quality of the results presented or to repeat the
experiments.
CONTENT:  The Minimum Information for Publication of Quantitative Real-
Time PCR Experiments (MIQE) guidelines target the reliability of
results to help ensure the integrity of the scientific literature,
promote consistency between laboratories, and increase experimental
transparency. MIQE is a set of guidelines that describe the minimum
information necessary for evaluating qPCR experiments. Included is a
checklist to accompany the initial submission of a manuscript to the
publisher. By providing all relevant experimental conditions and assay
characteristics, reviewers can assess the validity of the protocols
used. Full disclosure of all reagents, sequences, and analysis methods
is necessary to enable other investigators to reproduce results. MIQE
details should be published either in abbreviated form or as an online
supplement.
SUMMARY:  Following these guidelines will encourage better
experimental practice, allowing more reliable and unequivocal
interpretation of qPCR results.


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Why the need for qPCR publication guidelines? - The case for MIQE

Stephen A. Bustin
Methods.  2010 April    in       qPCR special issue - The ongoing
evolution of qPCR
Institute of Cell and Molecular Science, Barts and the London School
of Medicine and Dentistry
Queen Mary University of London, Whitechapel, London E1 1BB, UK

The polymerase chain reaction (PCR) has matured from a labour- and
time-intensive, low throughput qualitative gel-based technique to an
easily automated, rapid, high throughput quantitative technology. Real-
time quantitative PCR (qPCR) has become the benchmark technology for
the detection and quantification of nucleic acids in a research,
diagnostic, forensic and biotechnology setting. However, ill-assorted
pre-assay conditions, poor assay design and inappropriate data
analysis methodologies have resulted in the recurrent publication of
data that are at best inconsistent and at worst irrelevant and even
misleading. Furthermore, there is a lamentable lack of transparency of
reporting, with the "Materials and Methods" sections of many
publications, especially those with high impact factors, not fit for
the purpose of evaluating the quality of any reported qPCR data. This
poses a challenge to the integrity of the scientific literature, with
serious consequences not just for basic research, but potentially
calamitous implications for drug development and disease monitoring.
These issues are being addressed by a set of guidelines that propose a
minimum standard for the provision of information for qPCRexperiments
("MIQE"). MIQE aims to restructure to-day's free-for-all qPCR methods
into a more consistent format that will encourage detailed auditing of
experimental detail, data analysis and reporting principles. General
implementation of these guidelines is an important requisite for the
maturing of qPCR into a robust, accurate and reliable nucleic acid
quantification technology.


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MIQE precis: Practical implementation of minimum standard guidelines
for fluorescence-based quantitative real-time PCR experiments

Stephen A Bustin, Jean-Francois Beaulieu, Jim Huggett, Rolf Jaggi,
Frederick SB Kibenge, Pal A Olsvik, Louis C Penning email and Stefan
Toegel     BMC Molecular Biology 2010 - Published:     21 September
2010
The conclusions of thousands of peer-reviewed publications rely on
data obtained using fluorescence-based quantitative real-time PCR
technology. However, the inadequate reporting of experimental detail,
combined with the frequent use of flawed protocols is leading to the
publication of papers that may not be technically appropriate. We take
the view that this problem requires the delineation of a more
transparent and comprehensive reporting policy from scientific
journals. This editorial aims to provide practical guidance for the
incorporation of absolute minimum standards encompassing the key assay
parameters for accurate design, documentation and reporting of qPCR
experiments (MIQE precis) and guidance on the publication of pure
'reference gene' articles.


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



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MIQE PRESS REVIEW   on  http://MIQE-press.gene-quantification.info/

Making the most of MIQE
BMC Molecular Biology 2010, 11:74
The Editorial Board of BMC Molecular Biology endorse a new set of
essential MIQE-light guidelines for the reporting of quantitative PCR
data: "MIQE precis", and provide guidance for the suitability of pure
reference gene papers to the journal.

MIQE precis: with reference to reference genes
BioMed Central Blog - Tuesday Sep 21, 2010
Genes that maintain constant expression under a variety of
circumstances are known as =91reference genes=92. They are vital for
researchers who need to quantify gene expression changes in other
genes and need a =91reference point=92 against which to do so. BMC
Molecular Biology, has to date published around 200 reference gene-
related papers from researchers working in such diverse models as
peaches, sharks, barnacles and glioblastoma to name but a few.
However, to be a true reference gene you need to fulfil a certain list
of criteria and the research field is now united in requesting that
all work be performed to the same accuracy and in accordance with
recommended guidelines. The Minimum Information for Publication of
Quantitative Real-Time PCR Experiments (MIQE) guidelines were launched
over a year ago by an international team of researchers. The aim of
these guidelines was to enable the benchmark technology for measuring
gene expression (quantitative PCR - qPCR) to become standardised when
reported in research papers. The MIQE guidelines advise on good assay
design and appropriate data analyses for nucleic acid detection and
quantification. BioMed Central supports and promotes initiatives aimed
at improving the reporting of biomedical research, and refers authors
to the MIBBI Portal (of which MIQE is part of) for reporting
biological and biomedical research. Whilst some authors have included
MIQE checklists as supplemental files with their work (for example
here), there has been some debate as to the utility and ease in doing
this in all cases.
After working with several Editorial Board Members from BMC Molecular
Biology, we propose that all researchers wishing to publish qPCR work
do so by adhering to our simpler and more abridged 'light' guidelines
=96 MIQE pr=E9cis. We also propose that the majority of reference gene
papers are no longer suitable for publication as =91pure reference gene
papers=92, but this information will need to be incorporated as part of
a larger study. Alternatively, authors may publish these more
incremental (but still potentially useful) pure reference gene
articles in BMC Research Notes to contribute to our topical series:
=93Quantitative Real Time PCR normalization and optimization=94



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MIQE WEBINAR

The Future of qPCR: Best practices, Standardization, and the MIQE
Guidelines
Thursday, September 30, 2010 - 12 noon Eastern, 9 a.m. Pacific, 4 p.m.
GMT

Quantitative polymerase chain reaction (qPCR) has emerged as a
powerful tool in molecular biology laboratories, both in research and
in diagnostic settings. Even as qPCR grows in popularity, it is being
recognized that there are some challenges associated with the
technology, particularly with respect to reproducibility within and
between laboratories. Fortunately, many of these limitations can be
addressed through a standardized set of best practices. Using the
recently published MIQE guidelines as a foundation, our expert panel
will address the best practices of qPCR, with the goal of providing
researchers with more consistent and reliable data.

During the webinar, the panelists will:

provide an overview of the MIQE guidelines
address qPCR applications and primary challenges
outline best practices and assay design to get the best out of your
qPCR
describe the essential quality control steps, including nucleic acid
quantification
answer your questions during the live Q&A session
Participants:

Stephen A. Bustin, Ph.D.;  Queen Mary, University of London;  London,
UK
Gregory L. Shipley, Ph.D.;  University of Texas Health Science Center
at Houston;  Houston, TX
Manju R. Sethi;  Thermo Fisher Scientific;  Wilmington, DE



and much more MIQE NEWS on  http://MIQE-press.gene-quantification.info/


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qPCR Symposium USA
1. - 4 November 2010
San Francisco Bay Area, Millbrae, CA , USA
Clarion Hotel San Fransisco Airport
http://www.qPCRsymposium.com


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).
We are inviting scientific papers to present during the Symposium. The
scientific sessions will be held on November 1-2, 2010.
Please email your abstract to =3D> presentation from qPCRsymposium.com  to be
reviewed by the committee.
The Symposium features keynote speech, scientific sessions, poster
presentations, industrial exhibition, courses and networking events.


Scientific Committee Members:
- Stephen A Bustin, Ph.D.
- Gregory L. Shipley, Ph.D.
- Michael W. Pfaffl, Ph.D.
- Mikael Kubista Ph.D.
- Kevin L. Knudtson, Ph.D
- Prasad Jaladi, MS


The focus of the Symposium is on:

- Preanalytics =96 Sample preparation, extraction and purification
- Standardization and quality control
- High throughput qPCR =96 digital PCR, integration, workflow
- High Resolution Melting (HRM) =96 Epigenetics, mutation analysis, copy
number variation
- Molecular diagnostics of complex diseases =96 detection and profiling
of tumor cells
- Single-cell and subcellular expression profiling
- Non coding RNAs
- qPCR experimental design
- qPCR data mining
- Next generation sequencing techniques =96 complement or competitor to
qPCR?



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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 =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.)
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 =3D> http://www.gene-quantification.de/bioeps=
-course-programm-2010.pdf

Register here =3D> http://site.bioeps.com/index.php?option=3Dcom_seminar&It=
emid=3D6

Access to our workshops =3D> http://www.gene-quantification.de/bioeps-acces=
s.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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