Bio-IT World Aug 2010

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Turn on the Power of
Information-Driven R&D
ELECTRONIC LAB NOTEBOOKS DECISION SUPPORT SOFTWARE SCIENTIFIC DATABASES

Experience Life in the Electronic Lab at blog.symyx.com



Meet
the 2010
Best Practices
Winners
pages 16—28
Full agenda
in this issue

PIPELINING TOOLS
AND SOFTWARE 30
HHMI'S SILICON
MARVEL 48
See page S1
SIGNATURE SERIES:
THE BIOCLOUD 35

Click to view video blog

Kevin Davies, Editor of


S P E C I A L A DV E R T I S I N G S E C T I O N

Executive Viewpoint Capgemini

Why Capgemini? The Life Sciences Value Chain:
Adding Strength through Innovation
S
erving as Capgemini’s Life
Sciences Leader in North
America, Shakthi Kumar

T
he pressures on the life sci- Mergers & Acquisitions:
has worked intimately with many
ences value chain are relentless. A Matter of Months, Not Years
of the world’s leading life sci-
From staggering R&D costs to With product pipelines running dry, compa-
ences organizations. As a result,
constantly changing regulatory nies are looking for mergers, acquisitions
he understands that companies
requirements, myriad issues are taking and licensing opportunities.
today are competing on their abil-
aim at the bottom line. To leverage the synergies the merger
ity to rapidly transform
To overcome the roadblocks on the or acquisition is intended to create, newly
to outpace the market
path from discovery through supply chain, merged companies must integrate IT
and exploit opportuni-
companies are embarking on enterprise architecture, applications and processes
ties.
cost-reduction and transformation ini- quickly and effectively. And in the process
Mr. Kumar—along
tiatives, focusing their attention—and of integration, it is also expected that the
with 2,500 experienced
technologies—on moving toward real-time IT portfolio is appropriately “right-sized”
professionals who sup-
enterprises for improved data management, and new programs be launched to sus-
port Capgemini’s Life
reduced cycle time for decision-making and tain business imperatives. The industry
Sciences Practice—
improved collaboration with benchmark is shrinking—a
helps companies
external partners, physi- two- or three-year timeframe
worldwide embark on business cians, payors, providers and for integration is no longer
transformation initiatives and regulators. acceptable.
successfully leverage technology The bottom line? Life Constructing a holistic
to serve business needs. sciences companies today view with the right integra-
Underpinning all of Capgem- can no longer afford to view tion framework, enterprise
ini’s Life Sciences offerings is a technology as merely a architecture and robust
unique, multi-tiered approach to supporting service designed infostructure methodologies
delivering technology solutions. primarily to automate certain is key to addressing this
Built upon innovation and thought business practices and “keep the lights challenge. In addition, leveraging the next
leadership, Capgemini’s solutions on.” To remain competitive, companies generation application lifecycle services
and accelerators combine with must embrace technology as an enabler of along with strong program governance and
world-class technology capabili- innovation and industrialization throughout change management is essential.
ties and industrialization deliv- the value chain.
ered through CELLS (Capgemini’s How can—and should—this be accom- Multi-Channel: New Ways to
Center of Excellence for Leader- plished? With the technology solutions Reach a Customer Segment
ship in Life Sciences) and a glob- landscape changing rapidly and radically, Companies are seeking new ways to
al distributed delivery framework life sciences companies are positioned reach customers, including health care
called Rightshore®. Together with to exploit these advancements, such as providers (HCPs), patients, managed-care
new and flexible service models, cloud computing, enterprise performance organizations and payors. To enhance the
Capgemini offers full lifecycle management and virtualization, along with effectiveness of interactions, information
capabilities that include consult- other game-changing shifts tailored for availability, brand adoption and ultimately
ing, technology transformation, the industry. As a result, companies can quality of care, multiple channels of com-
implementation, hosting and achieve greater agility, faster cycle times, munication are being combined to form a
maintenance. stronger collaboration with customers and closed-loop, 360-degree view of the cus-
To learn how Capgemini can swift adoption of compliance practices—all tomer interaction. These channels include
enable your company to thrive in through technology-enablement. tablet detailing, product and disease
today’s competitive environment, Following, we discuss some of the websites, virtual events and conferences,
visit us at: us.capgemini.com/ industry’s burning platforms and how tech- portals, social and professional networks
lifesciences nology can be used to address them. and others.


S P E C I A L A DV E R T I S I N G S E C T I O N

Implementing a closed-loop marketing map for transformation. At the heart of it, covery paradigms and clinical trial execu-
system requires a wide range of technol- compliance is enabled through better pro- tion models, R&D organizations struggle
ogy platforms and services that must be cess, data and information management, to locate, retrieve, share, process and
integrated and rendered operational in a but companies must not underestimate distribute information to all stakeholders,
seamless, agile and flexible manner. the importance of change management both internal and external. Meanwhile, IT
and organizational alignment in designing, departments grapple to create an inte-
Compliance: A New Way of developing and managing compliance. grated platform of services ranging from
Doing Business Armed with a strategic roadmap to identify data collection, trial management, analysis,
Of the many issues confounding the all relevant touch-points throughout the safety and adverse events management
industry, compliance is easily one of the organization, companies should then focus through submissions. Traditional bound-
most perplexing. At many companies, on implementing point-solutions (for HCP aries between pharma, CROs and HCPs
compliance management is often defined aggregate spend, ePedigree, clinical trials are disintegrating. As they collaborate in
inconsistently among the different levels and others) that will best enable them to new ways to form an ecosystem, there is
of the organization depending on its type, stay on course. a compelling need for innovative technol-
be it aggregate spend, clinical trials or It all boils down to this: Compliance is ogy solutions and support models that
marketing reviews. no longer just a reporting issue, but a new can help accelerate R&D cycles, enhance
But as the regulatory, political and way of doing business. outcomes and reduce cost.
societal scrutiny on them grows stronger,
companies that continue to define compli- R&D: Better Products Faster Tearing Down Burning Platforms
ance this way risk dire consequences. In The traditional process of bringing new The many burning platforms confronting
addition to crippling fines and other puni- products to market has become all but life science companies are not going
tive governmental actions, non-compliant impossible with the continued increases in away. And more are undoubtedly on
companies can suffer staggering impacts the volume and diversity of data, new FDA the way. To overcome them, companies
to their reputations. approval requirements, and the changing should seek innovative and industrialized
To mitigate risks, companies must relationships between life science compa- solutions delivered through new service
evaluate compliance more broadly and nies, CROs and other stakeholders. models to create more agile, leaner and
develop an enterprise-wide execution road- As companies explore new drug dis- effective IT.

Are you transforming the business model
Are you inventing the business model for
for your future? Your competitors are.
your future? Your competitors are.
The rising costs of R&DR&D increasing com-
The rising costs of and and increasing
pliance requirements are exacerbated by the
compliance requirements are butting against
intense price pressure that results from payors’
intense price pressure driven at the payors’
reduced reimbursement and resulting from
reimbursement level levels. The widow of
opportunity market exclusivity. Thishas been
shortened for market exclusivity squeeze,
shortened. This dilemma, further accentuated
further accentuated by the economic crisis, is
by the economic crisis, is fueling restructuring
fueling restructuring across our industry. The
across our industry.will emerge time for leader-
industry’s leaders Now is the with innovative
ship and innovation to confront the demandsthe
business models ready to confront of
today and the challenges’ of tomorrow.
challenges of the future.

Across Lifeleader Capgemini Consulting works
As a global Sciences in pharmaceuticals,
biotechnology, medical devices, healthcare
with you to unleash your full potential and
services and agribusiness Capgemini offers
transform it into tangible outcomes.
industry-specific solutions and services that
cover all components ofour Vision chain from
The 8th edition of the value & Reality
research series examines how Life Sciences
R&D to Sales and Marketing. Our solutions
extend from business strategycost base and
companies are adjusting their and process
redeﬁning their business model. Learn how
consulting to technology strategy and execu-
your peers are innovating in the downturn
tion and outsourcing address critical issues and
create beyond, inventingbusiness innovation
and opportunities for business models
for the future. Access the full report at:
and growth.
www.us.capgemini.com/VRFuturePharma.
For more information, visit us at:
And visit www.us.capgemini.com/lifesciences.
us.capgemini.com/lifesciences
®



Contents [ ]

Computational
Biology
15 A Bright iDEA
Illumina launches data
visualization competition.

Computational
Development
46 No KIDding: Informatics
in Reverse
Parthys Reverse Informatics shifts
knowledge to information to data.

48 IT / Workflow
48 The Silicon Marvel
The new Howard Hughes Medical
Computing Stephen Institute computing cluster puts a
premium on expandability.

16 52 Australian Supercomputer
The IBM machine will reportedly
Protein-Powered Drug Discovery 18 goBalto Grows Matchmaking have 64,000 cores.
Portal 24
Creating a One-Stop-Shop
for Research 19 Spidey Sense: Open Source In Every Issue
Chemistry 25 5 Reflections on Good
Taking the High Road 20
After Further REVIEW at Practices
Get Smart 21 the FDA 26 First Base There’s much to be learned
from the Best Practices runners up.
Informed Integration 22 2010 Best Practices Entries 27 BY KEVIN DAVIES
Drug Discovery in a Virtual
Environment 23 58 No Safe Haven for FDA
The Russell Transcript Some are call-
ing the FDA to stop worrying about
Feature efficacy and focus on safety instead.
BY JOHN RUSSELL
Workflow’s Towering Aspirations 6 Company Index
6 Advertiser Index
54 Educational Opportunities
as evolving in step with pharma’s needs. 30 56 New Products

Up Front Clinical Trials SPECIAL ADVERTISING SECTION

7 Consumer Genetics 12 Early Trial Planning BioCloud Computing
Puts on a Show Solutions for Life Sciences
Big news from Illumina, GnuBio. Medidata products streamline ran-
domization and site selection. BioCloud Computing for Life
8 Genome Mapping for $4K Sciences 35
Sequencing as a service from Malay- 13 Points of Light in Gene
sian Genomics Center. Therapy Renaissance Cloud 3.0: Everything is a
Patient success stories drive Service 40
10 The Next Big Thing gene therapy forward.
The Bush Doctrine Which technolo- Cloud Computing for Data
gies will do the most for drug safety? 14 DIA 2010 Analysis: Toward the Plateau of
Drug Information Association meet- Productivity 42
7 Briefs ing is positive and hopeful.

[4 ] | 2010 www.bio-itworld.com



First Base

out was Biovista, which is developing a very promising litera-

Ref lections on ture-based discovery platform for drug repositioning purposes.
The judges were also impressed with HP’s ongoing work with
the M.D. Anderson Cancer Center in Houston in building a Re-

Good Practices search Station platform to integrate genomic, transcriptomic
and proteomic data. And Tessella presented CrysIS, an X-ray
crystallography workflow tool now in worldwide deployment
among drug design chemists across AstraZeneca.
In Personal and Translational Medicine, Merck followed
up its 2008 Best Practice Award with phase two of its collabo-
KEVIN DAVIES ration with the Moffitt Cancer Center, namely the establish-
ment of a “data usability environment” to conduct hypothesis-

O
ne of the undoubted highlights of our professional driven research without the need of IT professionals. Merck
calendar is the second night of our annual Bio-IT also contributed a clinical imaging system being developed
World Conference & Expo, when we host a gala with IBM called i-SCORE, to improve and expedite the transfer
dinner for the announcement and presentation of of patient image files.
our Best Practices Awards (see pages 16-28). The The IT & Informatics category was particularly strong.
winners are profiled elsewhere in this issue, but it is Convey Computer nominated a team at UCSD, for InsPecT, a
important to note that our judges’ decisions were always hard, fast database search tool for post-transitional modified mass
in some cases contentious even, and it would be a shame to spectrometry spectra. The Translational Genomics Research
dismiss the dozens of worthy en-
tries merely to champion the nine
winners.
Basic Research and Discov-
ery: Working with JMP Genomics,
Greg Gibson’s laboratory at the
Georgia Institute of Technology
is developing a high-throughput
workflow to study “geographi-
MARK GABRENYA

cal genomics,” or the genetics of
gene expression in global popula-
tions, with some impressive peer-
The CEOs of the sponsors Tessella (Grant Stephan, left) and GenomeQuest (Ron Ronauro, right)
reviewed publications already.
helped bestow the 2010 Best Practices Awards last April.
Genstruct, a previous winner, im-
pressed again with a causal network model of a liver cancer in a Institute (TGen) has developed the BIOMAP repository for the
mouse model, in conjunction with Pfizer. And Sigma’s partner- Integrated Biobank of Luxembourg.
ship with Ingenuity to create a free web-based biological search On the High-Performance Computing side, there were
portal had its admirers. strong entries nominated by companies such as Cycle Comput-
Knowledge Management: Undoubtedly the most dynamic ing (Purdue), DataDirect Networks (Cornell), FalconStor Soft-
category, this spurred four awards in all. Among those edged ware (Baylor College of Medicine), Isilon Systems (Oklahoma
Medical Research Foundation) and Panasas (Uppsala Univer-
sity). TGen also described its experiences building its next-gen
September Special data processing pipeline.
The next issue of (September/October) will The Clinical Trials and Research category was populated
feature a special report on the march to the $1,000 genome. with many successful vendor/pharma partnerships, ranging
It will include reports and interviews on many facets of the from dashboards and electronic data capture tools to a graphi-
next-generation sequencing industry, from a preview of cal user interface for trial designs.
third-generation platforms to current-generation software As always, we thank everyone who participated in the 2010
tools, as well as profiles of some key people in the field. It competition, and not just the folks who are deservedly spot-
will also coincide with the publication of my new book, lighted elsewhere in this issue. We encourage everyone working
, published by Free Press, which has been on bold, imaginative solutions for managing research and data
gestating over the past three years. to consider entering their story when we open the gates for the
2011 competition in a few months’ time.

www.bio-itworld.com JULY | AUGUST 2010 [5]



Company Index ®

Indispensable Technologies Driving
Discovery, Development, and Clinical Trials

EDITOR-IN-CHIEF
Abbott Laboratories. . . . . . . . . . 17 Health Decisions. . . . . . . . . . . . 17 Parthys Reverse Informatics. . . . 46
Accelrys . . . . . . . . . . . . . . . . . . 30 Howard Hughes Medical Patients Like Me . . . . . . . . . . . . 16 Kevin Davies (781) 972-1341
kevin_davies@bio-itworld.com
Almac . . . . . . . . . . . . . . . . . . . . 56 Institute . . . . . . . . . . . . . . . . . 48 Perceptive Informatics . . . . . . . . 14
Cambridge Healthtech HP . . . . . . . . . . . . . . . . . . . . . . . 5 Pfizer. . . . . . . . . . . . . . . . 5, 17, 31 MANAGING EDITOR
Institute . . . . . . . . . . . . . . . . . 17 IBM. . . . . . . . . . . . . . . . . . 5, 7, 52 PROOF (Prevention of Organ Allison Proffitt (617) 233-8280
AstraZeneca . . . . . . . . . . . . . 5, 46 IDBS. . . . . . . . . . . . . . . . . . . . . 30 Failure) Centre of Excellence . 22 aproffitt@healthtech.com
BioFortis . . . . . . . . . . . . . . . . . . 31 IDC . . . . . . . . . . . . . . . . . . . . . . 17 Quintiles . . . . . . . . . . . . . . . . . . 14
ART DIRECTOR
Biovista. . . . . . . . . . . . . . . . . . . . 5 IDC Health Insights . . . . . . . . . . 17 Recombinant Data Corp.. . . . . . 21
Mark Gabrenya (781) 972-1349
Bristol-Myers Squibb . . . . . . . . . 20 Illumina . . . . . . . . . . . . . . . . 7, 15 Roche. . . . . . . . . . . . . . . . . . . . . 7 mark_gabrenya@bio-itworld.com
Broad Institute . . . . . . . . . . . . . 31 InforSense . . . . . . . . . . . . . . . . 31 Royal Society of Chemistry . . . . 25
Celera Diagnostics . . . . . . . . . . 31 Ingenuity. . . . . . . . . . . . . . . . . . . 5 Sans Digital . . . . . . . . . . . . . . . 56 VP BUSINESS DEVELOPMENT
Celgene . . . . . . . . . . . . . . . 17, 33 Integrated Biobank of Sapio Sciences. . . . . . . . . . . . . 56 Angela Parsons (781) 972-5467
CenterPhase Solutions . . . . . . . 14 Luxembourg. . . . . . . . . . . . . . . 5 Schering-Plough . . . . . . . . . . . . 23 aparsons@healthtech.com
Centocor R&D. . . . . . . . . . . . . . 21 invivodata . . . . . . . . . . . . . . . . . 14 SciQuest . . . . . . . . . . . . . . . . . . 19 VP SALES – WESTERN US,
ChemSpider . . . . . . . . . . . . . . . 25 IO Informatics . . . . . . . . . . . . . . 22 SciTegic. . . . . . . . . . . . . . . . . . . 31 CANADA, EUROPE, PACIFIC RIM
CHI Insight Pharma Reports . . . 17 Isilon Systems. . . . . . . . . . . . . . . 5 SGI . . . . . . . . . . . . . . . . . . . . . . 52 Alan El Faye (213) 300-3886
CLC Bio. . . . . . . . . . . . . . . . . . . 17 James Hogg iCAPTURE Research Sigma. . . . . . . . . . . . . . . . . . . . . 5 alan_elfaye@bio-itworld.com
Collaborative Drug Discovery. . . 25 Centre . . . . . . . . . . . . . . . . . . 22 Symyx. . . . . . . . . . . . . . . . . . . . 33 ACCOUNT MANAGER,
Convey Computer . . . . . . . . . . . . 5 JMP Genomics . . . . . . . . . . . . . . 5 Synamatix. . . . . . . . . . . . . . . . . . 8 MULTI-MEDIA ADVERTISING

Cycle Computing. . . . . . . . . . . . . 5 Johnson & Johnson. . . . . . . 21, 32 Tahoe Informatics . . . . . . . . . . . 17 John J. Kistner (781) 972-1354
Dana-Farber Cancer Institute. . . 33 Jubilant Biosys . . . . . . . . . . . . . 46 Teranode. . . . . . . . . . . . . . . . . . 31 jkistner@healthtech.com
DataDirect Networks . . . . . . . . . . 5 Life Technologies . . . . . . . . . . . . 56 Tessella. . . . . . . . . . . . . . . . . 5, 17 ACCOUNT MANAGER,
MULTI-MEDIA ADVERTISING
Develotron . . . . . . . . . . . . . . . . 17 Malaysia Genomics Resource The BioTeam . . . . . . . . . . . . . . . 17
DNA2.0. . . . . . . . . . . . . . . . . . . 56 Centre . . . . . . . . . . . . . . . . . . . 8 Tim Reimer (781) 972-1342
The Schooner Group . . . . . . . . . 17
treimer@healthtech.com
FalconStor Software . . . . . . . . . . 5 Massachusetts Institute of The Scripps Research Institute . 19
Food and Drug Technology. . . . . . . . . . . . . . . 18 Translational Genomics CORPORATE MARKETING
COMMUNICATIONS DIRECTOR
Administration . . . . . . 14, 26, 58 Max Planck Florida Institute. . . . . 7 Research Institute . . . . . . . . . . 5 Lisa Scimemi (781) 972-5446
Frost & Sullivan. . . . . . . . . . . . . 30 M.D. Anderson Cancer Center . . . 5 UCSD . . . . . . . . . . . . . . . . . . . . . 5 lscimemi@healthtech.com
GenomeQuest. . . . . . . . . . . . . . 17 Medidata Solutions. . . . . . . . . . 12 University of Manchester . . . . . . 31
PROJECT/MARKETING MANAGER
Genstruct . . . . . . . . . . . . . . . . . . 5 Merck . . . . . . . . . . . . . . . . . . 5, 23 University of Melbourne. . . . . . . 52
Genzyme. . . . . . . . . . . . . . . . . . 30 Moffitt Cancer Center . . . . . . . . . 5 Vertex Pharmaceuticals . . . . . . . 31 Lynn Cloonan (781) 972-1352
lcloonan@healthtech.com
GlobalSubmit . . . . . . . . . . . . . . 26 National Institutes of Health . . . . 7 Victoria Life Sciences Computation
GnuBio . . . . . . . . . . . . . . . . . . . . 7 National Technical University of Initiative. . . . . . . . . . . . . . . 7, 52 ADVERTISING OPERATIONS COORDINATOR
goBalto.com . . . . . . . . . . . . . . . 24 Athens. . . . . . . . . . . . . . . . . . 18 Virtify . . . . . . . . . . . . . . . . . . . . 14 Stephanie Cline (781) 972-5465
Harvard Medical School . . . . . . 17 NuGen . . . . . . . . . . . . . . . . . . . 56 Weizmann Institute . . . . . . . . . . 46 scline@healthtech.com
Harvard University.. . . . . . . . . . . . 7 Panasas . . . . . . . . . . . . . . . . . . . 5 Wellcome Trust . . . . . . . . . . . . . . 7 DESIGN DIRECTOR
Tom Norton (781) 972-5440
tnorton@healthtech.com
Advertiser Index
Contributing Editors
Advertiser Page # Advertiser Page # Advertiser Page # Michael Goldman, Karen Hopkin,
Barnett Educational Services . . . 53 Capgemini . . . . . . . . . . . . . . . . . 2-3 Next-Generation Sequencing . . . . 26 Deborah Janssen, John Russell,
barnettinternational.com Us.capgemini.com/lifesciences Healthtech.com Salvatore Salamone, Deborah Borfitz
Bio-IT World Expo Europe Cmed Technology. . . . . . . . . . 38-39 Perceptive Informatics. . . . . . . . . 43 Ann Neuer, Tracy Smith Schmidt
Conference and Expo . . . 44-45 bio-itworld.com/BioIT/WhitePapers. Perceptive.com/eclinical
Bio-ITWorldExpoEurope.com aspx Surety . . . . . . . . . . . . . . . . . . . . . 41 Advisory Board
Bio-IT World Magazine Discovery On Target . . . . . . . . . . . 57 Info.surety.com/content/cloud Jeffrey Augen, Mark Boguski,
Subscription Application. . . . 59 DiscoveryOnTarget.com Symyx . . . . . . . . . . . . . . . . . . . . . 60
Bio-ITWorld.com/subscribe Steve Dickman, Kenneth Getz,
Educational Opportunities. . . 54-55 Blog.symyx.com
Jim Golden, Andrew Hopkins,
BlueArc . . . . . . . . . . . . . . . . . . . . 51 Bio-ITWorld.com Tessella . . . . . . . . . . . . . . . . . . . . 29
Bio-ITWorld.com/webcasts Caroline Kovac, Mark Murcko,
Insight Pharma Reports . . . . . . . . 9 tessella.com
/index_html insightpharmareports.com/ John Reynders, Bernard P. Wess Jr.
Thermo Scientific . . . . . . . . . . . . 37
Cambridge Bio Collaborative . . . . 47 Medidata. . . . . . . . . . . . . . . . . . . 11 Limsondemand.com
http://chicorporate.com/Corporate_ mdsol.com
Cambridge Healthtech Institute
Content.aspx?id=89096 PRESIDENT
This index is provided as an additional service. The publisher does not assume any liability for errors or omissions. Phillips Kuhl

VO L U M E 9 , N O. 4
Contact Information
editor@healthtech.com
Editorial, Advertising, and Business Offices: 250 First Avenue, Suite 300, Needham, MA 02494; (781) 972-5400
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Up Front News Briefs

Consumer Genetics LIFE SCIENCES SUPERCOMPUTER
The Victoria Life Sciences Compu-
tation Initiative (VLSCI) in Victoria,

Puts on a Show Australia, has announced that it
will have the world’s largest life
sciences-dedicated supercomputer
by 2012. The purchased IBM Blue
Big genomics news from Illumina, GnuBio. Gene machine is expected to have
around 64,000 cores, says Justin
BY KEVIN DAVIES New Entry Zobel, professor of computer sci-
The latest entry in the next-generation

B
OSTON—The second annual ence and software engineering at
Consumer Genetics Show* was sequencing sweepstakes made its public the University of Melbourne, and
highlighted by some audacious debut at the show, offering the prospect head of the supercomputer project.
pronouncements regarding the of a $30 human genome. GnuBio is a
future cost of human genome sequencing company based on the technology of AFRICAN GENOME PROJECT
just as one executive announced a sharp David Weitz, a physics professor at Har- The Wellcome Trust and the
cut in the current retail price. vard University. Weitz did not unveil an National Institutes of Health have
One year after Illumina introduced instrument or even any data—“I’m just a launched The Human Heredity
its personal genome sequencing service, physics professor across the river,” he said and Health in Africa Project (H3
CEO Jay Flatley announced a significant modestly. But he did outline a microfluid- Africa), a $38 million partner-
price drop to below $20,000, and poten- ics platform that could have instrumenta- ship to study how genes and the
tially half that if there is clinical relevance. tion available by the end of 2010 for some environment, including diet, work
Illumina’s Individual Genome Sequenc- very affordable DNA sequencing. together to affect cancer, heart
ing (IGS) service launched with a price The Weitz group uses microdroplets disease, and other diseases. H3
of $48,000 for a whole genome sequence as microreactors in a way quite similar Africa will receive at least $12 mil-
at 30-fold coverage. The service has to be to the commercially available RainDance lion from the Wellcome Trust and $5
ordered by a physician, and the results platform. The drops are surrounded by million a year from the NIH, along
are also delivered back to the physician to inert oil which provides a measure of flu- with administrative and scientific
discuss with the consumer. idics control. A droplet of 10 microns in support, over the next five years.
With the introduction of the HiSeq diameter can contain 10-14 grams reagent. The NIH has provided $750 000 to
2000 instrument earlier this year, Illu- “We process drops at 1 million/second,” kick-start the project.
mina said the reagent cost of sequencing said Weitz. The droplets can be formed,
a full human genome had dropped to the broken apart, sorted, and the contents MAX PLANCK FLORIDA
$10,000 mark, which made the original detected. “The size of the device is roughly The Max Planck Florida Institute
IGS price tag of $48,000 appear a little the thickness of a human hair, so they can has broken ground on a 100,000
steep. be stacked and run in parallel.” square foot biomedical research
The new cost of an individual ge- Weitz presented some fairly provoca- facility in Jupiter, Florida on the
nome sequence is $19,500. For groups tive figures for the cost of DNA sequenc- John D. MacArthur Campus of
of five people or more, the price drops to ing using his technology. With an estimat- Florida Atlantic University. The new
$14,500. Flatley also said that for a phy- ed sequencing cost per base of just $10-9, institute will focus on cutting-edge
sician ordering a sequence for genuine a 30-fold human genome sequence would research in the neurosciences and
clinical relevance, the price falls further cost a mere $30 and take about 10 hours. integrative biology.
to $9,500. The only catch with the new “You can quibble about the details of these
pricing is that the sequence is no longer calculations but the orders of magnitude ROCHE, IBM TALK 3RD GEN
delivered on an iMac. “A little less elegant, are not that far off,” said Weitz. Roche, the manufacturer of the
a little less cool,” Flatley admitted. Weitz has co-founded a start-up bio- first next-generation sequencing
Flatley disclosed that the IGS has tech called GnuBio Corporation. Advi- technology to reach the market,
sequenced at least 14 individuals to date. sors on the “convergence board” include originally commercialized by 454
These include Flatley, venture capitalist George Church, Dietrich Stephan, and Life Sciences, has backed a promis-
Hermann Hauser, Henry “Skip” Gates Affomix founders Michael Weiner and ing third-generation sequencing
and his father; Glenn Close; John West John Boyce. Weitz hopes to have beta sys- technology under development
(former Solexa CEO) and his family of tems ready by the end of 2010. There are by IBM. The two firms will jointly
four; a cancer patient, two centenarians, already commitments to purchase instru- develop a nanopore-based
and a severely ill child. ments from the Beaulieu-Saucier Uni- sequencing system that IBM has
versite de Montreal pharmacogenomics been developing in house.
*Consumer Genetics Show, Boston, June 2-4, 2010. center and Stephan’s Ignite Institute.

www.bio-itworld.com JULY | AUGUST 2010 [7]



Up Front News

Malaysian Genomics Center
Offers Genome Mapping for $4K

BY ALLISON PROFFITT the pipeline can identify structural varia- lists some key “customers and partners”
SINGAPORE—Malaysia Genomics Re- tions such as insertions, translocations, including Lilly, The Genome Center at
source Centre (MGRC) has announced a inversions, and multi-base deletions. As Washington University, and Cancer Re-
genome mapping pipeline service starting a separate service, MGRC will do com- search UK.
at $4000 per genome. parative analyses between any number In the May 13 issue of , re-
“The target market, said Robert Her- of genomes. searchers at Brigham & Women’s Hospi-
cus, managing director of MGRC, “is “We have comparative results against tal in Boston published the sequencing of
smaller labs, hospitals, and university other systems that do mapping, for ex- the Mesothelioma tumor genome.
researchers who perhaps do not have the ample, Bowtie, SOAP and BWA, and we Sequencing was done on a “human
facilities or the bioinformaticians but [make] those statistics available to cus- primary malignant pleural mesothelioma
want to do some sequencing.” (MPM) tumor and matched normal tissue
“We want to un-complicate the lives by using a combination of sequencing-by-
of the researchers who are doing wet lab synthesis and pyrosequencing methodolo-
biology and research,” Robert told gies to a 9.6X depth of coverage,” said the
World in a phone interview. He believes paper authors including Hercus. “Read
the service will help smaller labs that do density analysis uncovered significant
not have the time or resources to invest in aneuploidy and numerous rearrange-
learning 10-20 open-sources packages or ments. Method-dependent informatics
pay for software or hardware. rules, which combined the results of
MGRC’s solution is a proprietary pipe- different sequencing platforms, were de-
line for processing genomic data. MGRC veloped to identify and validate candidate
does the processing and analysis and mutations of multiple types.”
returns their findings to the lab for vali-
dation. The service takes about a week for Tool Provider
each genome. Data is sent to MGRC on a MGRC has been around for five years and
terabyte disc by courier. MGRC accepts is the services subsidiary of Synamatix,
sequence data from Illumina, 454, and a Malaysian software and bioinformat-
Complete Genomics said Hercus, and, Robert Hercus ics tools company that Hercus founded
“MGRC hopes to later offer Ion Torrent in 2001. Synamatix has developed the
and PacBio as well.” tomers so they can see [that] our results software and tools; MGRC “provides the
Once the data has arrived, MGRC does are more accurate than what’s currently services to customers and looks after the
pre-processing to “clean up” the data, available,” Hercus said. bioinformatics pipeline.” MGRC also has
maps the reads, and then applies propri- “I don’t think there’s another company a web portal that provides free online
etary mutation and structural variation in the world that could take a complete bioinformatics tools to users.
pipelines. All of the processing is done human genome at 30x coverage, say 90 MGRC’s services are constantly ex-
in-house on MGRC servers, and Hercus gigabases, and process it in one week with panding, Hercus explained, as new
said the current capacity is about 100 complete analysis, 100% finished.” customers bring new challenges and op-
genomes per month. portunities as the technology advances.
Results are returned to the customer PLoS Vetting “We plan to eventually offer a sequencing
on the same terabyte disc one week after The service was launched in early April, service as well,” he said. “We have a lot
receipt. MGRC also offers their own ge- and Hercus said that the company has of local Malaysian research institutes
nome browser with which researchers can already done some genomes, has 15 com- that want to do sequencing of human ge-
share and interact with their results. mitments, and is in talks with another nomes, and at the moment we send that
The processing includes identification 20 prospects worldwide. When asked for out overseas. So we believe it will be cost
of SNPs; inserts and deletions up to three names, he laughed, but then mentioned effective for us to have our own sequenc-
bases; and density mapping to flag copy that Harvard Medical School has sent ing centre here, at least for Malaysia, if
number variations. With paired end data, several genomes. The company website not the region.”




Primary Research…Analysis…Trends…Company Activities

CLOUD COMPUTING
IN LIFE SCIENCES R&D
Insight Pharma’s Cloud Computing in Life Sciences R&D
report was motivated by the rapidly growing importance of cloud
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This 128-page market research study provides you with:
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www.InsightPharmaReports.com



Up Front The Bush Doctrine

The Next
subsequent reappearance of exploratory or mechanistic toxicol-
ogy groups. This movement stretches back into the late 1980’s.
Even 20 years ago, the limitations of conducting safety evalu-
ations in GLP animal studies were well recognized. Therefore

Big Thing and at least in part based on the success of the Aims type gene
tox testing systems, there was a trend in pharma companies to
establish in vitro toxicology functions/groups focused on creat-
ing the next generation of safety evaluation.
Unfortunately, these groups did not contribute much in
ERNIE BUSH terms of toxicology prediction. Interestingly, though, after a
couple of decades of development and refinement, in vitro (and

A
lthough probably not the best topic for your next now in silico) safety testing is enjoying a re-emergence with
neighborhood barbecue, the question of which new most major pharma research groups establishing discovery
technologies may contribute to developing safer safety functions and implementing new pre-GLP safety predic-
medicines makes for interesting debate over a beer tion tools.
with professional colleagues. I find it particularly
entertaining to ask the question: What happened What Have We Learned?
to previous “Big Things” that appeared from prior beer sum- It is tempting to conclude that the biggest takeaway about next
mits one, five or ten years ago? Big Things is to disregard the hype, and maybe even to ignore all
Perhaps the most talked about Big Thing of the recent 3-5 new things, as most don’t work out as well as promised. Indeed,
years has been biomarkers. The discovery and development I would always advise a healthy (scientific) amount of skepti-
of biomarkers has been promised to aid in the diagnosis and cism about any claims for new technology promises or routine
treatment of diseases as well as in monitoring and predicting assay results.
safety outcomes. But such simplistic conclusions miss the useful lessons from
When the FDA released its Critical Path Opportunities List what our history is trying to teach us. These are:
in March 2006, one could be forgiven for concluding that it 1. The development AND implementation of new technologies
was all about biomarkers. Indeed, of the 76 targeted opportu- are experimental sciences. If most of your experiments do
nities identified, nearly half referred to the identification and not turn out as you expect, then you are probably not being
validation of new biomarkers. In fact, there was an initial flurry creative or daring enough in your science.
of activity that seemed to promise success, exemplified by the 2. Real advances in scientific practice, especially in safety pre-
work of the Predictive Safety Testing Consortium of the C-Path diction, take time. Although the vision for early safety evalu-
Institute and its work in detecting early kidney damage. ation stretches back more than 20 years, it took a full two
Unfortunately, four years later we still have not seen any sig- decades for the science and the technology to catch up with
nificant adoption of new biomarkers for tissue damage or safety that vision. I suspect that biomarkers and toxicogenomics
evaluation either in clinical studies or pre-clinical safety assess- will also one day play important roles in safety assessment,
ment. Of course, validation of new clinical biomarkers has been but that is probably another 5-10 years in the future.
more difficult than many would have guessed, but even those 3. New technologies in which success depends on catching re-
new preclinical biomarkers which have been ‘accepted’ by regu- ally small fish in really big oceans are doomed to fail most
latory authorities, and for which commercial tests are available, of the time. If the new technology vision promises, “If we
are not used appreciably in routine GLP studies. look at a large enough number of parameters across a large
Before biomarkers, the Big Thing in safety assessment was enough pool of patients/subjects/experiments, we will even-
undoubtedly toxicogenomics. It would be hard to overstate the tually find an answer,” then be prepared for a very long haul.
hype surrounding the introduction of microarrays and their Endeavors such as building toxicogenomics databases, find-
potential impact on toxicology and adverse event prediction. ing the next biomarker from large patient databases, gener-
Toxicogenomics spawned many companies and soaked up hun- ating huge libraries of compounds through combinatorial
dreds of millions of dollars of R&D money from VC firms and chemistry, etc. all fail to acknowledge the nearly unimagina-
big pharma companies. ble diversity of chemistry and biology on Earth. The ocean of
A decade later, it is clear that toxicogenomics has evolved possibilities is really deep and even giant fishing expeditions
into a valuable mechanistic tool and may yet provide some have a slim chance of catching fish without some guide to
value in terms of safety evaluation. But as the demise of all where the fish are.
those toxicogenomics companies suggests, its value in safety
prediction has not panned out. Ernie Bush is VP and scientific director of Cambridge Health
Another Big Thing worth considering is the rise, fall and Associates. He can be reached at: ebush@chacorporate.com.

[10 ] | AUGUST 2010 www.bio-itworld.com



Technology for a healthy world.®
www.mdsol.com
1.212.918.1847



Clinical Trials

Early Trial Planning Solutions
The solution is dynamic randomiza- Grants Manager 3.0 is where users ag-
tion, or assigning subjects to the study gregate and pool their worldwide grant
based on how enrollment is progress- payments and is a database of actual but
ing in real time while still remaining anonymized trial costs.
blinded and nondeterministic. “Dynamic “So you’re doing a new clinical trial.
randomization is something that has You decide you want to use some sites in
typically been regarded as the more ad- China, but you want to know what, on
BY ALLISON PROFFITT vanced, the more complicated, the more average, a site in oncology in China in
expensive, the more time-intensive way to Phase II gets paid to do a blood draw. You

M
edidata announced two new
products at the Drug Informa- randomize subjects, and it’s therefore not use Grants Manager to figure that out,”
tion Association (DIA) meet- used that much,” says de Vries. “We think explains de Vries.
ing in Washington, D.C.: an dynamic randomization isn’t something Grants Manager 3.0 is now browser-
updated version of Grants Manager and that should require tons of cost and tons based with a friendly user interface that
Medidata Balance. of time and tons of risk.” provides data for more than 80 countries
Glen de Vries, Medidata Solutions In addition to one-click dynamic ran- with specific regional groups by country
president, says that Balance will do for
clinical trial randomization what Medida-
ta Rave did for data transfer from site to
sponsor 11 years ago. “There’s never been
somewhere where I can just go online
and turn on a randomization system for a
clinical trial,” says de Vries. “That’s exactly
what we’ve done with Balance.”
Balance is a randomization and trial
‘G rants Manager now shows
you if your clinical trial is
harder or easier than that site
in China is used to.”
supply management (RTSM) solution
that replaces interactive voice response Glen de Vries
(IVR) and interactive web response
(IWR) systems. Study designers and
trial managers can use Balance to plan domization, Balance supports trial simu- and has the ability to assign different
and simulate trials, while sites can use lations. “If you don’t like the way the trial study arms for countries, regions and site
Balance to assign subjects in real-time at came out if you did it ten times simulated, budgets.
enrollment, and begin drug supply plan- change the parameters and do it ten times But the most exciting thing, de Vries
ning immediately. more and see how it comes out,” de Vries says, is the benchmarking capabilities of
“Randomization can become quite says. “You can do all the design, and then not only cost but complexity, a measure
complex,” de Vries told . just turn on dynamic randomization in a based on research that Medidata did with
“You’ll have a clinical trial where maybe very streamlined way, without having to the Tufts Center for Drug Development
you have 10 different doses or 5 different implement any custom software to do it.” and that de Vries calls “spectacularly
doses and you need to figure out which Balance is not a module for Rave, useful.”
one is most effective. There may be other but works seamlessly with the system. “The benchmark that you get out
factors, the age of the subjects or their It brings all elements of the design and of Grants Manager now shows you the
genders.” With traditional block random- execution of randomization and supply information about complexity. Is your
ization techniques, subjects are assigned logistics into the Medidata Rave platform. clinical trial one that is harder or easier
in the trial according to a pre-determined Giving trial designers and sites a single from an execution standpoint for that site
schedule. system for everything from randomiza- in China than they’re used to?... If I know
“You load that data into the system tion to EDC helps trials run with fewer that I have a particular clinical trial that
and when the inevitable issues occur, for subjects and less time, risk, and cost, says is hard—meaning it’s going to take a lot of
instance a patients gets randomized then de Vries. time and a lot of different procedures—I
drops out of the clinical trial, you hope— may want to go and find more experi-
you hope!—that you have balance in the How Much and How Complicated enced sites to work on it.”
trial, that you’ve achieved the relative Continuing with a focus on early-trial Having access to both complexity and
equivalence of study subjects that have planning, Medidata also announced an actual cost data allows Grants Manager
gotten the drug or placebo,” says de Vries. update to their Grants Manager product. users to make operational decisions.




Points of Light in Gene
Therapy Renaissance
BY RICKI LEWIS disease, adrenoleukodystrophy (ALD),
WASHINGTON, DC—Like the mythical the genetic disorder portrayed in the
Phoenix that springs anew from its ashes, film . When Nathalie Cart-
gene therapy shows signs of re-emerging ier-Lacave arrived, the four women
with a stockpile of safer and more efficient embraced. Cartier-Lacave is director of
viral vectors. At the annual meeting of the research at INSERM in Paris.
American Society of Gene and Cell Thera- The ALD protein normally admits
py last May*, optimism was palpable. very long chain fatty acids into peroxi-
The excitement peaked when 9-year somes, where they are degraded and used
old Corey Haas walked onstage at the to make myelin, which insulates neurons.
Presidential symposium. His physician, Behavioral symptoms rapidly progress
Jean Bennett, professor at the F. M. Kirby to seizures, blindness, and incapacita-
DANIEL BURKE PHOTOGRAPHY

Center for Molecular Ophthalmology tion. “The only treatment, a stem cell
at the University of Pennsylvania, an- transplant, takes 12 to 18 months for
nounced: “I’d like to introduce the young- progression to stop,” said Cartier-Lacave,
est person ever to speak at ASGCT.” but is risky. Gene therapy, also using HIV,
Until his gene therapy in September exploits the fact that the brain cells af-
Jean Bennett
2008, Corey was headed for blindness fected in ALD (the microglia) come from
from Leber congenital amaurosis type 2 for two treated forms had problems. First bone marrow. The first two patients made
(LCA2). Today he plays baseball and just was ADA deficiency, tried on a 4-year-old headlines in fall 2009, after they had been
recently saw fireflies for the first time. in 1990. Her restored health could have making normal ALD protein for many
He calmly answered questions from an been due to concomitant enzyme replace- months, as MRIs tracked remyelination.
astonished audience, and afterwards ment. And gene therapy for SCID-X1 “There was no problem with HIV or
was mobbed by awed scientists, some in (“bubble boy disease”) worked, but caused immunity or insertion into a gene that
tears. leukemia. causes leukemia,” said Cartier-Lacave.
Earlier that day, Corey and his parents Don Kohn, director of the University Eve (Salzman) Lapin said that after
joined other emissaries of recent advances of California Los Angeles human gene her son Oliver was diagnosed with ALD
in gene therapy at a news conference. medicine program, discussed new gene in 2000, genetic testing found that one
It was sparsely attended because across therapy trials for both forms of SCID brother and a cousin had also inherited
town, Craig Venter had just announced using safer vectors. A trial to treat 20 the disorder. Sisters Amber Salzman (an
that he had artificially created life. boys with SCID-X1 is underway in Paris, executive at GlaxoSmithKline at the time)
LCA2 is caused by mutation in the London, and three sites in the U.S., using and Rachel Salzman (a veterinarian)
RPE65 gene. “RPE65 helps to recharge a “self-inactivating” retroviral vector. And launched Stop-ALD, uniting researchers
vitamin A, and without it, there is no vi- for ADA deficiency, Kohn’s group is using for a clinical trial. “They did everything
sion. The gene therapy idea was simple— the chemotherapeutic busulfan to clear shy of following us into the men’s room,”
deliver the gene to the retinal pigment space in the bone marrow for replacement jokes Jim Wilson, professor of pathology
epithelium,” which hugs the photorecep- cells, and using a lentivirus (HIV), which and laboratory medicine at the University
tors, said Bennett. The pediatric clinical works in non-dividing cells, carries bigger of Pennsylvania, who helped the sisters.
trial at Children’s Hospital of Philadelphia genetic payloads, and integrates more ef- Lapin had the final word at the news
treated 12 patients between the ages of 8 ficiently than past vectors. “To date, four conference. “The legacy of Oliver’s life
and 24 in one eye. All improved. of eight patients have benefited clinically, and death is that gene therapy will be a
The target disease most like the meta- living at home and doing well,” he said. better way to treat ALD and other terrible
phorical phoenix is severe combined im- And that’s without enzyme replacement. diseases.”
mune deficiency (SCID). Gene therapies In the second row at the press con-
The Forever Fix: The Rise, Fall
- ference sat three young women who and Rebirth of Gene Therapy and the Boy Who Saved It,
catalyzed gene therapy for their family’s

www.bio-itworld.com | 2010 [ 13 ]


Bio-IT World Aug 2010

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