InteView

Conducting good science in a

bad economic environment
with Prof. Janet Thornton
From qPCR to microarrays
with Integromics

Interpreting the
$1,000 genome
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InteView
Contents
Good science in a bad
environment
Schering-Plough – From qPCR
to microarrays with Integromics
Ingenuity and Integromics offer
integration for comprehensive
genomics analysis
Setting standards in proteomics
An affordable approach to
managing gene expression data
Interpreting the $1,000 genome
From microarrays to clinical
breakthroughs
Moving into the Asia Pacific
market
Face of Integromics –
Howard Bilofsky – The road
from GSK to Integromics
Time matters in real-time PCR
Spotting new discoveries in
RT-PCR data
Contact Details
Dear readers,
Welcome to the first edition of InteView, a periodic scientific newsletter from
2-3 Integromics®. As another summer arrives we continue to work hard to deliver what were
once considered ‘expert’ tools to the wider research community, enabling streamlined
research workflows in fields such as gene expression. Our challenge now lies in providing
4 user-friendly data analysis for proteomics and next generation sequencing. In the next
few pages, we hope to give you a sneak preview of what is yet to come.
4 We would like to thank our contributors for their hard work, and trust you will gain new
insight from their wealth of knowledge on various topics. Thank you to all our faithful
customers who continue to work and publish using our tools, and please
5 keep your feedback coming in, this is what drives us forward.
5 Enjoy your journey.
Imad I. Yassin, Global Commercial Director
6
7
7
Good science in a bad
8
economic environment
with Prof. Janet Thornton
Although many of the most important scientific discoveries are made in relatively inexpensive laboratories,
the recent downturn in the global economy potentially means troubled times are ahead for scientific
8
research and development in both the public and private sectors. Although the long-term nature of the
9 grants system means academia has, so far, been relatively insulated from the impact of the economic
slowdown, we can expect some sources of funding to dry up over the next few years. In this situation, one
of the most important tasks for scientists to do is pressure the government to invest in science now for the
10 future economic health of the country.
CONTINUED ON PAGE 3 >
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InteView
Good science in a bad economic environment
This has been very effective in the US, where a significant amount of extra
state funding for scientific research is now available to ensure future
innovation.
It is vital that the scientific community supports this long-term strategic
planning, but it is equally important that we adapt to the way scientific R&D,
particularly in the pharmaceutical sector, is evolving as a result.
Pharmaceutical manufacturers, which historically attempted to develop
in-house solutions for all their experimental and analytical needs, are now
finding new ways to work. This has resulted in large manufacturers –
competitors in the marketplace – working collaboratively for the good of
mankind. This fresh attitude is also benefiting public domain resources, with
pharmaceutical companies increasingly keen to use these services in their
research and development workflows.
This desire by pharmaceutical manufacturers to work more collaboratively is
changing the way the academic bioinformatics sector interacts with industry,
and many projects are now underway to encourage the development of new
tools and technologies for use by both the public and private sectors. The
European Bioinformatics Institute (EBI) is involved in several such projects
through its industry program, and this approach provides new stimulus for
advancement of many fields of bioinformatics. For example, using
computational techniques to identify the most probable candidate compounds
for development can reduce the need for large scale experimental trials,
offering significant cost savings. In addition, this strategy can reduce the
likelihood of candidate compounds proceeding, at great cost, to the validation
stage, only to fail in phase two or phase three trials. However, this is still an
extremely complex and difficult task, driving development of new and
improved predictive tools.
Another benefit of closer collaboration with the pharmaceutical industry is that
we are now seeing a large increase in demand for bioinformatics support
across many sectors, and the latest generation of genetic sequencing
platforms is further contributing to this trend. These platforms allow whole
genome screens to be performed in a matter of hours, yet generate a huge
amount of data that must be carefully analyzed. Although the cost of
sequencing experiments is getting lower and lower, an extensive
computational infrastructure is still required to translate the resulting data into
biologically relevant information. Through the ELIXIR project, the EBI is
coordinating Europe’s efforts to build a bioinformatics infrastructure to both
cope with the unprecedented barrage of data brought about by
next-generation sequencing, and build a more secure future for public domain
biological data resources on which both academic and industrial research
depends. This is leading to a new wave of bioinformatics expansion, driven by
a need for more computational biologists and better analytical packages.
Therefore, while we are seeing large cutbacks and lay-offs in the
pharmaceutical sector, there is also a wealth of expertise, coming directly from
industry, that can be recruited into these roles. This brings new perspectives
to academic research, ultimately offering long term benefits for everyone.
Overall, scientists are very adaptable people, and while there may be tougher
times ahead, research will no doubt continue until the situation improves. In
the meantime, it is important that the academic community seizes the new
opportunities that arise from these difficult economic times.
Professor Janet Thornton
Janet has been Director of the EMBL-EBI since October 2001. Her
research group focuses on understanding biological processes from a
structural perspective, using computational approaches. After a physics
degree, she moved into biophysics at the National Institute for Medical
Research, London. Before moving to the EMBL-EBI she held a joint
appointment at University College London and the Bernal Chair in the
Crystallography Department at Birkbeck College. She is a Fellow of the
Royal Society, a Member of EMBO and a foreign associate of the US
National Academy of Sciences. As Director of the EBI, Janet coordinates
the ELIXIR project which aims to establish a sustainable infrastructure for
life science information in Europe.
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InteView
Schering-Plough
From qPCR to microarrays with Integromics
Schering-Plough’s Genomics Group is using Integromics’
RealTime StatMiner® to standardise results and improve data
analysis workflow at its Kenilworth site in New Jersey. Eric
Gustafson, Head of Genomics at Kenilworth, explained: “My
group conducts a large number of gene expression analyses and,
before using RealTime StatMiner, one of the key challenges we
were facing was standardizing analysis of the functional gene
expression data that we generate. We also use TIBCO
Spotfire®, and having RealTime StatMiner fully integrated into
the Spotfire workflow is a huge advantage, allowing it to form
part of the genomics decision site. The software’s unique
visualizations also make it very easy to pick out results of
interest, making analysis of large data sets much faster.”
“Alongside our qPCR work, we
also perform a lot of microarray
experiments, and are planning
on switching to Integromics
Biomarker Discovery™ (IBD)
for this application”, Eric
continued. “This will allow us to
achieve the same approach to
microarray data analysis as we
have been able to adopt with
qPCR using RealTime
StatMiner, offering a unified
platform to look at gene
expression.”
Ingenuity and
Integromics
offer integration for
comprehensive genomics analysis
Integromics, S.L. and Ingenuity Systems announced the integration of RealTime
StatMiner and Integromics Biomarker Discovery for TIBCO Spotfire with Ingenuity
Pathway Analysis (IPA). The resulting platform provides a uniform solution for
researchers to visualize and statistically assess genomics data, and then identify
relevant biological processes and pathways. Researchers can now leverage a
streamlined workflow to send the data from RealTime StatMiner a step-by-step
workflow-oriented solution for RT-qPCR data analysis and IBD for TIBCO Spotfire
an application to pre-process, normalize, and interpret raw microarray gene
expression data directly into IPA for better modeling, analysis, and understanding of
their biological data.
“Integromics’ data analysis solutions have been well adopted in the market as easy
to use tools for researchers to analyze their expression data for statistical and
biological significance”, said Alberto Pascual, VP, Research and Development,
Integromics S.L. “Once significant genes are identified, researchers can now easily
leverage the analysis capabilities and content in IPA to gain a deeper understanding
of biological context and functions involved in their dataset.”
“Our main objective is to provide our joint customers with
relevant workflows that help them best understand their gene
expression data” said Tuan Nguyen, VP, Partner and Professional Services,
Ingenuity Systems. “We felt it was important to provide a streamlined way for
researchers to move from raw data analysis to understanding relevant biology.
RealTime StatMiner and IBD for TIBCO Spotfire, together with IPA, offer a complete
and reliable platform to provide researchers with confidence in their data analysis
and interpretation.”
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InteView
Setting standards in proteomics An affordable
Professor Juan Pablo Albar, head of the Proteomics Laboratory at the Centro Nacional de Biotecnología approach to
(CNB-CSIC) and general Coordinator of ProteoRed (www.proteored.org) in Madrid, Spain, has witnessed the
evolution of proteomics research into the high throughput technique that it is today, and is taking an active role in
managing gene
the management of the data produced by the latest instruments.
expresssion data
Juan Pablo explained: “As part of the HUPO-PSI community, I am involved in the development of guidelines like Looking for an affordable
MIAPE (Minimum Information About a Proteomics Experiment). At the ProteoRed consortium, which Integromics is microarray LIMS that is easy to
also a collaborative entity of, we have developed web tools to help fulfill these guidelines for gel electrophoresis, install and maintain? ArrayHub®
gel informatics, mass spectrometry (MS) and MS informatics. The community is now promoting the use of these is an off-the-shelf LIMS that offers
guidelines; good quality data is crucial and, hopefully, MIAPE reporting will soon be made mandatory for publishing laboratories straightforward
proteomics experiments.” management of microarray
experimental data from the
“During the last decade, protein separation and identification technologies have improved, in parallel with the moment of installation. In addition,
progress of genome sequencing projects. Proteomics today involves high throughput studies and, in response, a Core Facility Web Module helps
computational proteomics has undergone dramatic development. Modern instruments produce data much more microarray service facilities track
quickly than the speed of analysis, so we need efficient management of data, while effectively incorporating customers’ requests and results.
standards to facilitate sharing and comparison of high quality results between laboratories. HUPO-PSI’s mzML ArrayHub is a flexible easy-to- use
standard has recently been implemented for all new MS instruments, and mzIdentML, a new standard format for system, providing rapid access to
MS informatics, is being developed. If MS vendors develop instruments that output data in mzIdentML format, experimental data for greater
data management and analysis can be performed without limitations of proprietary restrictions from any laboratory efficiency. Don't hesitate to contact
or from any instrument.” us at arrayhub@integromics.com
for an individual consultation or to
“We are in close collaboration with Integromics on its Proteomics OmicsHub*, developing an automated see how ArrayHub can help meet
laboratory workflow based, at least in the first stage, on PRIDE standard.” He concluded: “It is critical that your specific needs.
current and future technologies are trustable, independent of the laboratory, so that high throughput screening
technologies like genomics, transcriptomics, proteomics and metabolomics can be integrated to contribute to the
growing field of systems biology.”

*An Integromics proteomics consortium, aimed at addressing the need to manage, integrate and
analyze proteomics data in a flexible and automated way, is now available to a limited number of
early access members. To find out more contact us at proteomics@integromics.com.

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InteView
Interpreting the $1,000 genome
In the pursuit of affordable genomic analysis, next generation sequencing (NGS) platforms are creating ever greater amounts of
data in shorter times, widening the gulf between data acquisition and data analysis. For his latest book, ‘The thousand dollar
genome’, BioIT World Editor-in-Chief Kevin Davies is following this international race towards the $1,000 milestone, and the
future of NGS technologies in medicine.

Where did the idea for this book come from?

“It’s sort of a follow-up to my last book, Cracking the Genome, which covered the race to sequence the first human genome.
This is kind of the book about your genome! Genome sequencing is exploding right now – there is currently an unofficial
global contest between the big genome centres in the UK, US and China to achieve the largest throughput. However, high
throughput sequencing is just the beginning, and we need to consider how these datasets can be used. The installation of so many sequencing machines
internationally is driving demand for data management and analytical solutions, such as those provided by Integromics, particularly for smaller labs that might
not have the resources for bespoke analytical packages.”

Why do you think there is so much interest in genomics at the moment?

“As I discuss in my book, the use of genetics in medicine is changing for the 21st century. In the next few years, the price of sequencing a complete genome drops
below the $1,000 mark, making access to these technologies possible for the general public, either through national health care systems, or consumer operations
such as 23andme, Navigenics, and Decode Me. This will obviously be big business, and create a lot of demand for user-friendly, accessible analytical software
because as I’ve experienced presenting a clinician with sequence data is useless. Analysis requires expertise and the right tools for proper interpretation; it’s like
drinking from a fire hose and you need to be careful!”

Do you think the economic crisis will push us towards a $1,000 genome faster?
“I think it will. The economic crisis has prompted governments around the world, particularly the US, to investment more in science and technology. President
Obama has gained a lot of support for saying that we must put science before ideology. There are obviously ethical and privacy considerations, but we need to
consider these and how they will impact on the future provision of health care. In the mean time, this stimulus has researchers falling over themselves to file
grant applications, many of which will be for sequencing instruments. Companies like Integromics now have a huge opportunity for their products become key
factors in the genomics pipeline, allowing customers to take full advantage of the sequencing capacity that they will have available.”

What is the future for sequencing technologies?

“With so much data being generated, the focus is now on what this technology can tell us. If you do a genetic scan, can it really tell you meaningful information
about your risk of common diseases such as heart disease or diabetes? As we sequence more and more genomes, and learn more and more about the genetic
variations that contribute to genetic disease, those answers are becoming clearer, but there is so much more to learn. Really we’re still just seeing the tip of the
iceberg as far as understanding the genetics.”

For more information about Integromics Next Generation Sequencing solution, please contact ngs@integromics.com

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InteView
From microarrays Moving into the
Asia Pacific market
to clinical breakthroughs After opening its distribution channel in Japan
(CeresBiosciences) in 2007, Integromics is pleased
Genetic profiling has moved beyond simply identifying and cataloguing genetic to announce that its products are available to
differences, with many laboratories now recognizing the importance of linking microarray laboratories across the Asia Pacific market through
gene expression profiles to clinical data. Effective clinical profiling requires large libraries Molecule Scientific Company (MSC) Ltd. Dr Pei-Li
of samples to be matched to relevant patient information including treatments, outcomes Li, Vice President of MSC, explained: “There are a
and family histories. Integromics Biomarker Discovery (IBD) for Spotfire allows researchers lot of software solutions available for genomics
to quickly analyze huge volumes of microarray data, identifying gene signatures and research – both commercial and open source –
biological markers in patient data to improve drug development. however most require a strong bioinformatics
background to operate them successfully.
For 15 days trial or more information Integromics offers a unique solution to this
write to ibd@integromics.com common yet complex problem, allowing research
scientists to harness powerful analytical tools
through
a user-friendly
interface. We have
had very positive
responses from
everyone that has
tested Integromics’
products, and are
excited to be
introducing these
products to the Asia
Pacific market.”

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InteView
Face of Integromics – Howard Bilofsky Time matters in
The road from GSK to Integromics real-time PCR
The US arm of Integromics is headed by Dr Howard Bilofsky,
Applied Biosystems’ real-time PCR
Vice President, Integromics, Inc. Howard has brought a wealth
instruments, with ‘Fast PCR’ option, can
of experience to the Company, including developing the first
reduce the run time for a 384-well plate to
immunoglobulin sequence database, first project manager for
just 55 minutes. Real-time PCR providers
GenBank, three years at EMBL in Heidelberg, Germany where
are investing a lot of efforts in reducing
he was involved in founding the EBI (European Bioinformatics
the time taken to complete a project, but
Institute) in Cambridge, UK, and a decade leading software
users need months to analyze the data.
engineering teams at GSK.
RealTime StatMiner is a unique data
analysis solution, compatible with all
Howard explained: “As an early pioneer in bioinformatics, along
Applied Biosystems’ real-time PCR
with Professor José-María Carazo, I have been involved in
instruments, providing ready-to-publish
information technology and life science research for over three
results within minutes, via a user-friendly
decades, before there was even a notion of bioinformatics. I’ve
interface. RealTime StatMiner makes a
known José-María for many years, and I was intrigued when he and his colleagues started an
real difference, because time matters in
exciting bioinformatics software company in Spain, creating very sophisticated and powerful
real-time PCR.
products. Later, when it became clear that Integromics needed a presence in the US, it made sense
for me to be involved. Based at the Science Center in Philadelphia, which provides a stimulating and
For 15 days trial or more information write
supportive environment, we are especially close to many large pharmaceutical companies, several
to realtimestatminer@integromics.com
biotechs and prominent non-profit research institutions, as well as potential customers throughout
the Eastern US.

“Compared to a big pharma, Integromics has a different set of

constraints; our focus is very clear and we can move more quickly.
We are in a very dynamic field – at the confluence of advanced
technology and biotech business: IT and genomics – so there’s a lot
to be done to make sure that our products continue to be the best in
their class, and to make people aware of that.”

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InteView
Spotting new discoveries
in RT-PCR data
The Translational Medicine Research Collaboration (TMRC)
is a unique collaboration established in 2006, partnering
four Scottish universities, four NHS trusts, Scottish
Enterprise and Wyeth, with the aim of developing a
world-leading network of clinical and scientific excellence.

As part of this initiative, the TMRC Genomics group is

involved with several projects, predominantly concentrating
on global and targeted expression profiling on a range of
different tissues and clinical sources, and includes
RealTime StatMiner to analyze the qRT-PCR data. It relies
on several analyzers and techniques, as Ross Haggart,
scientific officer within the Genomics group, explained: “We
didn’t want project design to be influenced by what
equipment we had available so we have a few options,
including Affymetrix GeneChip® arrays for global
transcriptional profiling, and an Applied Biosystems 7900HT
Fast Real-Time PCR System. As automation increased
throughput, qRT-PCR analysis was becoming more of a
time burden. These methods produce quite dense data sets
and we were looking for a way to run quick, robust analysis, to give us a good idea of
what we are looking at without getting lost in the data.”

“RealTime StatMiner is quick to use, and the workflows were exactly what we were
looking for. The QC tools are really good; we can choose how we display the information
and the visualizations are something that you don’t routinely see on other available
software. Importantly, it allows us to identify trends in the data and we often spot things
that we maybe wouldn’t have spotted if we were just looking at a list of numbers. Overall,
RealTime StatMiner offers options for qRT-PCR that other software just does not have,
and the technical support is fantastic.”

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InteView
Where to buy Integromics products
Asia Pacific:
Molecule Scientific Co., Ltd
Taipei City, Taiwan
Phone: +886 2 2713 2977
Fax: +886 2 8712 5221
msc-support@molsci.com.tw
Japan:
CeresBio Inc.
Toda, Saitama, Japan
Phone: +81 48 424 3146
Fax: +81 48 424 3148
sales@ceresbio.co.jp
www.ceresbio.co.jp
Support
Asia-Pacific:
apac.support@integromics.com
Europe and North America:
support@integromics.com
Japan:
japan.support@integromics.com
Europe and rest of the world:
Integromics, S.L.
Madrid, Spain
Phone: +34 91 128 24 11
Fax: +34 91 804 62 81
sales@integromics.com
USA and Canada:
Integromics, Inc.
Philadelphia, PA, USA
Phone: +1 215 966 6078
Fax: +1 215 386 3970
sales@integromics.com
Partnership
Our current partners include
Applied Biosystems (Life
Technologies), Ingenuity
and TIBCO Spotfire.
To discuss partnership
opportunities, please contact
partners@integromics.com
www.integromics.com
Free training
Live webinars
Free web training for RealTime StatMiner® and IBD are
available, and can be requested online. On-site training is
also available by emailing training@integromics.com.
Recorded webinars
Breaking the qPCR frontiers (with Novartis). How to get the
most value out of your qPCR data at credit crunch times
(with Applied Biosystems).
Events
Events where you can find Integromics:
BioC 2009
Seattle - July 27-28, 2009
Advances in qPCR
Berlin, Germany - September 17-18, 2009
8th HUPO World Congress
Toronto - September 26-30, 2009
qPCR Congress
London, UK - November 16-18, 2009
10% DISCOUNT VOUCHER
For a 10% discount on ITG listed prices, quote
the discount voucher code ITG0609 when
ordering. The offer is valid until July 31, 2009.
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