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N A V I G A T I O N K E Y

Dear Bio-IT World Subscriber:

The July/August issue profiles the nine winning projects in the 2010 Bio-IT World Best Practices Awards, highlighting innovation at Merck, MIT, The Scripps Research Institute, Centocor and many others. We also take an in-depth look at pipelining tools, investigating the primary producers of workflow and pipeline software Accelrys and InforSense. Their challenge may not be so much with each other as evolving in step with pharma's needs.

This issue also includes insights into cloud computing for life sciences, a insider's look at the silicon marvel supercomputer at HHMI's Janelia Farm, and a full preview of the program at Bio-IT World Europe in Germany in October.

As you're aware, many business-to-business publishers are moving in the direction of offering digital publications and relying less on the print-model. We hope you enjoy this issue with its new features and future digital editions.

Thank you for your subscription and continued interest in Bio-IT World. Please feel free to share this issue.

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



Meetthe 2010

Best Practices Winners

PIPELINING TOOLS AND SOFTWARE 30

HHMI'S SILICON MARVEL 48

SIGNATURE SERIES:THE BIOCLOUD 35

Click to view video blog

Kevin Davies, Editor of #JPt*58PSME

pages 1628

Full agenda in this issue

See page S1



The Life Sciences Value Chain: Adding Strength through Innovation

The pressures on the life sci-ences value chain are relentless. From staggering R&D costs to constantly changing regulatory

requirements, myriad issues are taking aim at the bottom line.

To overcome the roadblocks on the path from discovery through supply chain, companies are embarking on enterprise cost-reduction and transformation ini-tiatives, focusing their attentionand technologieson moving toward real-time enterprises for improved data management, reduced cycle time for decision-making and improved collaboration with external partners, physi-cians, payors, providers and regulators.

The bottom line? Life sciences companies today can no longer afford to view technology as merely a supporting service designed primarily to automate certain business practices and keep the lights on. To remain competitive, companies must embrace technology as an enabler of innovation and industrialization throughout the value chain.

How canand shouldthis be accom-plished? With the technology solutions landscape changing rapidly and radically, life sciences companies are positioned to exploit these advancements, such as cloud computing, enterprise performance management and virtualization, along with other game-changing shifts tailored for the industry. As a result, companies can achieve greater agility, faster cycle times, stronger collaboration with customers and swift adoption of compliance practicesall through technology-enablement.

Following, we discuss some of the industrys burning platforms and how tech-nology can be used to address them.

Mergers & Acquisitions: A Matter of Months, Not YearsWith product pipelines running dry, compa-nies are looking for mergers, acquisitions and licensing opportunities.

To leverage the synergies the merger or acquisition is intended to create, newly merged companies must integrate IT architecture, applications and processes quickly and effectively. And in the process of integration, it is also expected that the IT portfolio is appropriately right-sized and new programs be launched to sus-tain business imperatives. The industry

benchmark is shrinkinga two- or three-year timeframe for integration is no longer acceptable.

Constructing a holistic view with the right integra-tion framework, enterprise architecture and robust infostructure methodologies is key to addressing this

challenge. In addition, leveraging the next generation application lifecycle services along with strong program governance and change management is essential.

Multi-Channel: New Ways to Reach a Customer SegmentCompanies are seeking new ways to reach customers, including health care providers (HCPs), patients, managed-care organizations and payors. To enhance the effectiveness of interactions, information availability, brand adoption and ultimately quality of care, multiple channels of com-munication are being combined to form a closed-loop, 360-degree view of the cus-tomer interaction. These channels include tablet detailing, product and disease websites, virtual events and conferences, portals, social and professional networks and others.

Executive Viewpoint Capgemini

SPECIAL ADVERTISING SECTION

Serving as Capgeminis Life Sciences Leader in North America, Shakthi Kumar has worked intimately with many of the worlds leading life sci-ences organizations. As a result, he understands that companies today are competing on their abil-

ity to rapidly transform to outpace the market and exploit opportuni-ties.

Mr. Kumaralong with 2,500 experienced professionals who sup-port Capgeminis Life Sciences Practicehelps companies

worldwide embark on business transformation initiatives and successfully leverage technology to serve business needs.

Underpinning all of Capgem-inis Life Sciences offerings is a unique, multi-tiered approach to delivering technology solutions. Built upon innovation and thought leadership, Capgeminis solutions and accelerators combine with world-class technology capabili-ties and industrialization deliv-ered through CELLS (Capgeminis Center of Excellence for Leader-ship in Life Sciences) and a glob-al distributed delivery framework called Rightshore. Together with new and flexible service models, Capgemini offers full lifecycle capabilities that include consult-ing, technology transformation, implementation, hosting and maintenance.

To learn how Capgemini can enable your company to thrive in todays competitive environment, visit us at: us.capgemini.com/lifesciences

Why Capgemini?




Implementing a closed-loop marketing system requires a wide range of technol-ogy platforms and services that must be integrated and rendered operational in a seamless, agile and flexible manner.

Compliance: A New Way of Doing BusinessOf the many issues confounding the industry, compliance is easily one of the most perplexing. At many companies, compliance management is often defined inconsistently among the different levels of the organization depending on its type, be it aggregate spend, clinical trials or marketing reviews.

But as the regulatory, political and societal scrutiny on them grows stronger, companies that continue to define compli-ance this way risk dire consequences. In addition to crippling fines and other puni-tive governmental actions, non-compliant companies can suffer staggering impacts to their reputations.

To mitigate risks, companies must evaluate compliance more broadly and develop an enterprise-wide execution road-

map for transformation. At the heart of it, compliance is enabled through better pro-cess, data and information management, but companies must not underestimate the importance of change management and organizational alignment in designing, developing and managing compliance. Armed with a strategic roadmap to identify all relevant touch-points throughout the organization, companies should then focus on implementing point-solutions (for HCP aggregate spend, ePedigree, clinical trials and others) that will best enable them to stay on course.

It all boils down to this: Compliance is no longer just a reporting issue, but a new way of doing business.

R&D: Better Products FasterThe traditional process of bringing new products to market has become all but impossible with the continued increases in the volume and diversity of data, new FDA approval requirements, and the changing relationships between life science compa-nies, CROs and other stakeholders.

As companies explore new drug dis-

covery paradigms and clinical trial execu-tion models, R&D organizations struggle to locate, retrieve, share, process and distribute information to all stakeholders, both internal and external. Meanwhile, IT departments grapple to create an inte-grated platform of services ranging from data collection, trial management, analysis, safety and adverse events management through submissions. Traditional bound-aries between pharma, CROs and HCPs are disintegrating. As they collaborate in new ways to form an ecosystem, there is a compelling need for innovative technol-ogy solutions and support models that can help accelerate R&D cycles, enhance outcomes and reduce cost.

Tearing Down Burning PlatformsThe many burning platforms confronting life science companies are not going away. And more are undoubtedly on the way. To overcome them, companies should seek innovative and industrialized solutions delivered through new service models to create more agile, leaner and effective IT.

Are you inventing the business model for your future? Your competitors are.

The rising costs of R&D and increasing compliance requirements are butting against intense price pressure driven at the payors reimbursement level and resulting from shortened market exclusivity. This squeeze, further accentuated by the economic crisis, is fueling restructuring across our industry. The industrys leaders will emerge with innovative business models ready to confront the challenges of the future.

As a global leader Capgemini Consulting works with you to unleash your full potential and transform it into tangible outcomes.

The 8th edition of our Vision & Reality research series examines how Life Sciences companies are adjusting their cost base and redening their business model. Learn how your peers are innovating in the downturn and beyond, inventing business models for the future. Access the full report at: www.us.capgemini.com/VRFuturePharma.

And visit www.us.capgemini.com/lifesciences.

Are you transforming the business model for your future? Your competitors are.

The rising costs of R&D and increasing com-pliance requirements are exacerbated by the intense price pressure that results from payors reduced reimbursement levels. The widow of opportunity for market exclusivity has been shortened. This dilemma, further accentuated by the economic crisis, is fueling restructuring across our industry. Now is the time for leader-ship and innovation to confront the demands of today and the challenges of tomorrow.

Across Life Sciences in pharmaceuticals, biotechnology, medical devices, healthcare services and agribusiness Capgemini offers industry-specific solutions and services that cover all components of the value chain from R&D to Sales and Marketing. Our solutions extend from business strategy and process consulting to technology strategy and execu-tion and outsourcing address critical issues and create opportunities for business innovation and growth.

For more information, visit us at: us.capgemini.com/lifesciences



Up Front

7 Consumer Genetics Puts on a ShowBig news from Illumina, GnuBio.

8 Genome Mapping for $4KSequencing as a service from Malay-sian Genomics Center.

10 The Next Big ThingThe Bush Doctrine Which technolo-gies will do the most for drug safety?

7 Briefs

Clinical Trials

12 Early Trial Planning SolutionsMedidata products streamline ran-domization and site selection.

13 Points of Light in Gene Therapy RenaissancePatient success stories drive gene therapy forward.

14 DIA 2010Drug Information Association meet-ing is positive and hopeful.

ComputationalBiology

15 A Bright iDEAIllumina launches data visualization competition.

ComputationalDevelopment

46 No KIDding: Informatics in ReverseParthys Reverse Informatics shifts knowledge to information to data.

IT/Workflow 48 The Silicon Marvel

The new Howard Hughes Medical Institute computing cluster puts a premium on expandability.

52 Australian Supercomputer The IBM machine will reportedly have 64,000 cores.

In Every Issue

5 Reflections on Good Practices

First Base Theres much to be learned from the Best Practices runners up. BY KEVIN DAVIES

58 No Safe Haven for FDAThe Russell Transcript Some are call-ing the FDA to stop worrying about efficacy and focus on safety instead. BY JOHN RUSSELL

6 Company Index6 Advertiser Index

54 Educational Opportunities56 New Products

[4]#*0t*5 803-%+6-:|"6(6452010 www.bio-itworld.com

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BioCloud Computing for Life Sciences

BioCloud Computing for Life Sciences 35

Cloud 3.0: Everything is a Service 40

Cloud Computing for Data Analysis: Toward the Plateau of Productivity 42

Protein-Powered Drug Discovery 18

Creating a One-Stop-Shop for Research 19

Taking the High Road 20

Get Smart 21

Informed Integration 22

Drug Discovery in a Virtual Environment 23

goBalto Grows Matchmaking Portal 24

Spidey Sense: Open Source Chemistry 25

After Further REVIEW at the FDA 26

2010 Best Practices Entries 27

Feature

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www.bio-itworld.com JULY | AUGUST 2010 #*0t*5 803-% [ 5 ]

First Base

One of the undoubted highlights of our professional calendar is the second night of our annual Bio-IT World Conference & Expo, when we host a gala dinner for the announcement and presentation of our Best Practices Awards (see pages 16-28). The winners are profiled elsewhere in this issue, but it is

important to note that our judges decisions were always hard, in some cases contentious even, and it would be a shame to dismiss the dozens of worthy en-tries merely to champion the nine winners.

Basic Research and Discov-ery: Working with JMP Genomics, Greg Gibsons laboratory at the Georgia Institute of Technology is developing a high-throughput workflow to study geographi-cal genomics, or the genetics of gene expression in global popula-tions, with some impressive peer-reviewed publications already. Genstruct, a previous winner, im-pressed again with a causal network model of a liver cancer in a mouse model, in conjunction with Pfizer. And Sigmas partner-ship with Ingenuity to create a free web-based biological search portal had its admirers.

Knowledge Management: Undoubtedly the most dynamic category, this spurred four awards in all. Among those edged

out was Biovista, which is developing a very promising litera-ture-based discovery platform for drug repositioning purposes. The judges were also impressed with HPs ongoing work with the M.D. Anderson Cancer Center in Houston in building a Re-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-ration with the Moffitt Cancer Center, namely the establish-ment of a data usability environment to conduct hypothesis-driven research without the need of IT professionals. Merck also contributed a clinical imaging system being developed with IBM called i-SCORE, to improve and expedite the transfer of patient image files.

The IT & Informatics category was particularly strong. Convey Computer nominated a team at UCSD, for InsPecT, a fast database search tool for post-transitional modified mass spectrometry spectra. The Translational Genomics Research

Institute (TGen) has developed the BIOMAP repository for the Integrated Biobank of Luxembourg.

On the High-Performance Computing side, there were strong entries nominated by companies such as Cycle Comput-ing (Purdue), DataDirect Networks (Cornell), FalconStor Soft-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 data processing pipeline.

The Clinical Trials and Research category was populated with many successful vendor/pharma partnerships, ranging from dashboards and electronic data capture tools to a graphi-cal user interface for trial designs.

As always, we thank everyone who participated in the 2010 competition, and not just the folks who are deservedly spot-lighted elsewhere in this issue. We encourage everyone working on bold, imaginative solutions for managing research and data to consider entering their story when we open the gates for the 2011 competition in a few months time.

Reflections on Good Practices

KEVIN DAVIES

September SpecialThe next issue of %LRv,7:RUOG (September/October) will feature a special report on the march to the $1,000 genome. It will include reports and interviews on many facets of the next-generation sequencing industry, from a preview of third-generation platforms to current-generation software tools, as well as profiles of some key people in the field. It will also coincide with the publication of my new book, 7KH*HQRPH, published by Free Press, which has been gestating over the past three years.

MAR

K G

ABR

ENYA

The CEOs of the sponsors Tessella (Grant Stephan, left) and GenomeQuest (Ron Ronauro, right) helped bestow the 2010 Best Practices Awards last April.




Abbott Laboratories. . . . . . . . . . 17Accelrys . . . . . . . . . . . . . . . . . . 30Almac . . . . . . . . . . . . . . . . . . . . 56Cambridge Healthtech

Institute . . . . . . . . . . . . . . . . . 17AstraZeneca . . . . . . . . . . . . . 5, 46BioFortis . . . . . . . . . . . . . . . . . . 31Biovista. . . . . . . . . . . . . . . . . . . . 5Bristol-Myers Squibb . . . . . . . . . 20Broad Institute . . . . . . . . . . . . . 31Celera Diagnostics . . . . . . . . . . 31Celgene . . . . . . . . . . . . . . . 17, 33CenterPhase Solutions . . . . . . . 14Centocor R&D. . . . . . . . . . . . . . 21ChemSpider . . . . . . . . . . . . . . . 25CHI Insight Pharma Reports . . . 17CLC Bio. . . . . . . . . . . . . . . . . . . 17Collaborative Drug Discovery. . . 25Convey Computer . . . . . . . . . . . . 5Cycle Computing. . . . . . . . . . . . . 5Dana-Farber Cancer Institute. . . 33DataDirect Networks . . . . . . . . . . 5Develotron . . . . . . . . . . . . . . . . 17DNA2.0. . . . . . . . . . . . . . . . . . . 56FalconStor Software . . . . . . . . . . 5Food and Drug

Administration . . . . . . 14, 26, 58Frost & Sullivan. . . . . . . . . . . . . 30GenomeQuest. . . . . . . . . . . . . . 17Genstruct . . . . . . . . . . . . . . . . . . 5Genzyme. . . . . . . . . . . . . . . . . . 30GlobalSubmit . . . . . . . . . . . . . . 26GnuBio . . . . . . . . . . . . . . . . . . . . 7goBalto.com . . . . . . . . . . . . . . . 24Harvard Medical School . . . . . . 17Harvard University.. . . . . . . . . . . . 7

Health Decisions. . . . . . . . . . . . 17Howard Hughes Medical

Institute . . . . . . . . . . . . . . . . . 48HP . . . . . . . . . . . . . . . . . . . . . . . 5IBM. . . . . . . . . . . . . . . . . . 5, 7, 52IDBS. . . . . . . . . . . . . . . . . . . . . 30IDC . . . . . . . . . . . . . . . . . . . . . . 17IDC Health Insights . . . . . . . . . . 17Illumina . . . . . . . . . . . . . . . . 7, 15InforSense . . . . . . . . . . . . . . . . 31Ingenuity. . . . . . . . . . . . . . . . . . . 5Integrated Biobank of

Luxembourg. . . . . . . . . . . . . . . 5invivodata . . . . . . . . . . . . . . . . . 14IO Informatics . . . . . . . . . . . . . . 22Isilon Systems. . . . . . . . . . . . . . . 5James Hogg iCAPTURE Research

Centre . . . . . . . . . . . . . . . . . . 22JMP Genomics . . . . . . . . . . . . . . 5Johnson & Johnson. . . . . . . 21, 32Jubilant Biosys . . . . . . . . . . . . . 46Life Technologies . . . . . . . . . . . . 56Malaysia Genomics Resource

Centre . . . . . . . . . . . . . . . . . . . 8Massachusetts Institute of

Technology. . . . . . . . . . . . . . . 18Max Planck Florida Institute. . . . . 7M.D. Anderson Cancer Center . . . 5Medidata Solutions. . . . . . . . . . 12Merck . . . . . . . . . . . . . . . . . . 5, 23Moffitt Cancer Center . . . . . . . . . 5National Institutes of Health . . . . 7National Technical University of

Athens. . . . . . . . . . . . . . . . . . 18NuGen . . . . . . . . . . . . . . . . . . . 56Panasas . . . . . . . . . . . . . . . . . . . 5

Parthys Reverse Informatics. . . . 46Patients Like Me . . . . . . . . . . . . 16Perceptive Informatics . . . . . . . . 14Pfizer. . . . . . . . . . . . . . . . 5, 17, 31PROOF (Prevention of Organ

Failure) Centre of Excellence . 22Quintiles . . . . . . . . . . . . . . . . . . 14Recombinant Data Corp.. . . . . . 21Roche. . . . . . . . . . . . . . . . . . . . . 7Royal Society of Chemistry . . . . 25Sans Digital . . . . . . . . . . . . . . . 56Sapio Sciences . . . . . . . . . . . . . 56Schering-Plough . . . . . . . . . . . . 23SciQuest . . . . . . . . . . . . . . . . . . 19SciTegic. . . . . . . . . . . . . . . . . . . 31SGI . . . . . . . . . . . . . . . . . . . . . . 52Sigma. . . . . . . . . . . . . . . . . . . . . 5Symyx. . . . . . . . . . . . . . . . . . . . 33Synamatix. . . . . . . . . . . . . . . . . . 8Tahoe Informatics . . . . . . . . . . . 17Teranode. . . . . . . . . . . . . . . . . . 31Tessella. . . . . . . . . . . . . . . . . 5, 17The BioTeam . . . . . . . . . . . . . . . 17The Schooner Group . . . . . . . . . 17The Scripps Research Institute . 19Translational Genomics

Research Institute . . . . . . . . . . 5UCSD . . . . . . . . . . . . . . . . . . . . . 5University of Manchester . . . . . . 31University of Melbourne. . . . . . . 52Vertex Pharmaceuticals . . . . . . . 31Victoria Life Sciences Computation

Initiative. . . . . . . . . . . . . . . 7, 52Virtify . . . . . . . . . . . . . . . . . . . . 14Weizmann Institute . . . . . . . . . . 46Wellcome Trust . . . . . . . . . . . . . . 7

V O L U M E 9 , N O . 4

Editorial, Advertising, and Business Offices: 250 First Avenue, Suite 300, Needham, MA 02494; (781) 972-5400BiorIT World (ISSN 1538-5728) is published bi-monthly by Cambridge Bio Collaborative, 250 First Avenue, Suite 300, Needham, MA 02494.Bio rIT World is free to qualified life science professionals. Periodicals postage paid at Boston, MA, and at additional post offices. The one-year subscription rate is $199 in the U.S., $240 in Canada, and $320 in all other countries (payable in U.S. funds on a U.S. bank only).

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Subscriptions: Address inquires to Bio-IT World, P.O. Box 3414, Northbrook, IL 60065 (888) 835-7302 or e-mail [email protected].

Reprints: Copyright 2010 by Bio-IT World All rights reserved. Reproduction of material printed in Bio rIT World is forbidden without written permission. For reprints and/or copyright permission, please contact the YGS group, 3650 West Market St., York, PA 17404; 800-501-9571 or via email to [email protected].

Company Index

This index is provided as an additional service. The publisher does not assume any liability for errors or omissions.

Indispensable Technologies Driving Discovery, Development, and Clinical Trials

EDITOR-IN-CHIEF

Kevin Davies (781) [email protected]

MANAGING EDITOR

Allison Proffitt (617) [email protected]

ART DIRECTOR

Mark Gabrenya (781) [email protected]

VP BUSINESS DEVELOPMENT

Angela Parsons (781) [email protected]

VP SALES WESTERN US, CANADA, EUROPE, PACIFIC RIM

Alan El Faye (213) [email protected]

ACCOUNT MANAGER, MULTI-MEDIA ADVERTISING

John J. Kistner (781) [email protected]

ACCOUNT MANAGER, MULTI-MEDIA ADVERTISING

Tim Reimer (781) [email protected]

CORPORATE MARKETINGCOMMUNICATIONS DIRECTOR

Lisa Scimemi (781) [email protected]

PROJECT/MARKETING MANAGER

Lynn Cloonan (781) [email protected]

ADVERTISING OPERATIONS COORDINATOR

Stephanie Cline (781) [email protected]

DESIGN DIRECTOR

Tom Norton (781) [email protected]

Contributing EditorsMichael Goldman, Karen Hopkin, Deborah Janssen, John Russell,

Salvatore Salamone, Deborah BorfitzAnn Neuer, Tracy Smith Schmidt

Advisory BoardJeffrey Augen, Mark Boguski, Steve Dickman, Kenneth Getz, Jim Golden, Andrew Hopkins,

Caroline Kovac, Mark Murcko, John Reynders, Bernard P. Wess Jr.

Cambridge Healthtech InstitutePRESIDENT

Phillips Kuhl

Contact [email protected]

250 First Avenue, Suite 300Needham, MA 02494

http://twitter.com/bioitworld

Barnett Educational Services . . . 53barnettinternational.com

Bio-IT World Expo Europe Conference and Expo . . . 44-45Bio-ITWorldExpoEurope.com

Bio-IT World Magazine Subscription Application. . . . 59Bio-ITWorld.com/subscribe

BlueArc . . . . . . . . . . . . . . . . . . . . 51Bio-ITWorld.com/webcasts/index_html

Cambridge Bio Collaborative . . . . 47http://chicorporate.com/Corporate_Content.aspx?id=89096

Capgemini . . . . . . . . . . . . . . . . . 2-3Us.capgemini.com/lifesciences

Cmed Technology. . . . . . . . . . 38-39bio-itworld.com/BioIT/WhitePapers.aspx

Discovery On Target . . . . . . . . . . . 57DiscoveryOnTarget.com

Educational Opportunities. . . 54-55Bio-ITWorld.com

Insight Pharma Reports . . . . . . . . 9insightpharmareports.com/

Medidata. . . . . . . . . . . . . . . . . . . 11mdsol.com

Next-Generation Sequencing . . . . 26Healthtech.com

Perceptive Informatics. . . . . . . . . 43Perceptive.com/eclinical

Surety . . . . . . . . . . . . . . . . . . . . . 41Info.surety.com/content/cloud

Symyx . . . . . . . . . . . . . . . . . . . . . 60Blog.symyx.com

Tessella . . . . . . . . . . . . . . . . . . . . 29tessella.com

Thermo Scientific . . . . . . . . . . . . 37Limsondemand.com

Advertiser IndexAdvertiser Page # Advertiser Page # Advertiser Page #

www.linkedin.com/groupRegistration?gid=3141702

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Up Front News

BY KEVIN DAVIES

BOSTONThe second annual Consumer Genetics Show* was highlighted by some audacious pronouncements regarding the

future cost of human genome sequencing just as one executive announced a sharp cut in the current retail price.

One year after Illumina introduced its personal genome sequencing service, CEO Jay Flatley announced a significant price drop to below $20,000, and poten-tially half that if there is clinical relevance. Illuminas Individual Genome Sequenc-ing (IGS) service launched with a price of $48,000 for a whole genome sequence at 30-fold coverage. The service has to be ordered by a physician, and the results are also delivered back to the physician to discuss with the consumer.

With the introduction of the HiSeq 2000 instrument earlier this year, Illu-mina said the reagent cost of sequencing a full human genome had dropped to the $10,000 mark, which made the original IGS price tag of $48,000 appear a little steep.

The new cost of an individual ge-nome sequence is $19,500. For groups of five people or more, the price drops to $14,500. Flatley also said that for a phy-sician ordering a sequence for genuine clinical relevance, the price falls further to $9,500. The only catch with the new pricing is that the sequence is no longer delivered on an iMac. A little less elegant, a little less cool, Flatley admitted.

Flatley disclosed that the IGS has sequenced at least 14 individuals to date. These include Flatley, venture capitalist Hermann Hauser, Henry Skip Gates and his father; Glenn Close; John West (former Solexa CEO) and his family of four; a cancer patient, two centenarians, and a severely ill child.

New EntryThe latest entry in the next-generation sequencing sweepstakes made its public debut at the show, offering the prospect of a $30 human genome. GnuBio is a company based on the technology of David Weitz, a physics professor at Har-vard University. Weitz did not unveil an instrument or even any dataIm just a physics professor across the river, he said modestly. But he did outline a microfluid-ics platform that could have instrumenta-tion available by the end of 2010 for some very affordable DNA sequencing.

The Weitz group uses microdroplets as microreactors in a way quite similar to the commercially available RainDance platform. The drops are surrounded by inert oil which provides a measure of flu-idics control. A droplet of 10 microns in diameter can contain 10-14 grams reagent. We process drops at 1 million/second, said Weitz. The droplets can be formed, broken apart, sorted, and the contents detected. The size of the device is roughly the thickness of a human hair, so they can be stacked and run in parallel.

Weitz presented some fairly provoca-tive figures for the cost of DNA sequenc-ing using his technology. With an estimat-ed sequencing cost per base of just $10-9,a 30-fold human genome sequence would cost a mere $30 and take about 10 hours. You can quibble about the details of these calculations but the orders of magnitude are not that far off, said Weitz.

Weitz has co-founded a start-up bio-tech called GnuBio Corporation. Advi-sors on the convergence board include George Church, Dietrich Stephan, and Affomix founders Michael Weiner and John Boyce. Weitz hopes to have beta sys-tems ready by the end of 2010. There are already commitments to purchase instru-ments from the Beaulieu-Saucier Uni-versite de Montreal pharmacogenomics center and Stephans Ignite Institute. x

Consumer Genetics Puts on a ShowBig genomics news from Illumina, GnuBio.

Briefs

LIFE SCIENCES SUPERCOMPUTERThe Victoria Life Sciences Compu-tation Initiative (VLSCI) in Victoria, Australia, has announced that it will have the worlds largest life sciences-dedicated supercomputer by 2012. The purchased IBM Blue Gene machine is expected to have around 64,000 cores, says Justin Zobel, professor of computer sci-ence and software engineering at the University of Melbourne, and head of the supercomputer project.

AFRICAN GENOME PROJECTThe Wellcome Trust and the National Institutes of Health have launched The Human Heredity and Health in Africa Project (H3 Africa), a $38 million partner-ship to study how genes and the environment, including diet, work together to affect cancer, heart disease, and other diseases. H3 Africa will receive at least $12 mil-lion from the Wellcome Trust and $5 million a year from the NIH, along with administrative and scientific support, over the next five years. The NIH has provided $750 000 to kick-start the project.

MAX PLANCK FLORIDAThe Max Planck Florida Institutehas broken ground on a 100,000 square foot biomedical research facility in Jupiter, Florida on the John D. MacArthur Campus of Florida Atlantic University. The new institute will focus on cutting-edge research in the neurosciences and integrative biology.

ROCHE, IBM TALK 3RD GENRoche, the manufacturer of the first next-generation sequencing technology to reach the market, originally commercialized by 454 Life Sciences, has backed a promis-ing third-generation sequencing technology under development by IBM. The two firms will jointly develop a nanopore-based sequencing system that IBM has been developing in house.

*Consumer Genetics Show, Boston, June 2-4, 2010.




Up Front News

BY ALLISON PROFFITT

SINGAPOREMalaysia Genomics Re-source Centre (MGRC) has announced a genome mapping pipeline service starting at $4000 per genome.

The target market, said Robert Her-cus, managing director of MGRC, is smaller labs, hospitals, and university researchers who perhaps do not have the facilities or the bioinformaticians but want to do some sequencing.

We want to un-complicate the lives of the researchers who are doing wet lab biology and research, Robert told %LRv,7World in a phone interview. He believes the service will help smaller labs that do not have the time or resources to invest in learning 10-20 open-sources packages or pay for software or hardware.

MGRCs solution is a proprietary pipe-line for processing genomic data. MGRC does the processing and analysis and returns their findings to the lab for vali-dation. The service takes about a week for each genome. Data is sent to MGRC on a terabyte disc by courier. MGRC accepts sequence data from Illumina, 454, and Complete Genomics said Hercus, and, MGRC hopes to later offer Ion Torrent and PacBio as well.

Once the data has arrived, MGRC does pre-processing to clean up the data, maps the reads, and then applies propri-etary mutation and structural variation pipelines. All of the processing is done in-house on MGRC servers, and Hercus said the current capacity is about 100 genomes per month.

Results are returned to the customer on the same terabyte disc one week after receipt. MGRC also offers their own ge-nome browser with which researchers can share and interact with their results.

The processing includes identification of SNPs; inserts and deletions up to three bases; and density mapping to flag copy number variations. With paired end data,

the pipeline can identify structural varia-tions such as insertions, translocations, inversions, and multi-base deletions. As a separate service, MGRC will do com-parative analyses between any number of genomes.

We have comparative results against other systems that do mapping, for ex-ample, Bowtie, SOAP and BWA, and we [make] those statistics available to cus-

tomers so they can see [that] our results are more accurate than whats currently available, Hercus said.

I dont think theres another company in the world that could take a complete human genome at 30x coverage, say 90 gigabases, and process it in one week with complete analysis, 100% finished.

PLoS VettingThe service was launched in early April, and Hercus said that the company has already done some genomes, has 15 com-mitments, and is in talks with another 20 prospects worldwide. When asked for names, he laughed, but then mentioned that Harvard Medical School has sent several genomes. The company website

lists some key customers and partners including Lilly, The Genome Center at Washington University, and Cancer Re-search UK.

In the May 13 issue of 3/R62QH, re-searchers at Brigham & Womens Hospi-tal in Boston published the sequencing of the Mesothelioma tumor genome.

Sequencing was done on a human primary malignant pleural mesothelioma (MPM) tumor and matched normal tissue by using a combination of sequencing-by-synthesis and pyrosequencing methodolo-gies to a 9.6X depth of coverage, said the paper authors including Hercus. Read density analysis uncovered significant aneuploidy and numerous rearrange-ments. Method-dependent informatics rules, which combined the results of different sequencing platforms, were de-veloped to identify and validate candidate mutations of multiple types.

Tool ProviderMGRC has been around for five years and is the services subsidiary of Synamatix, a Malaysian software and bioinformat-ics tools company that Hercus founded in 2001. Synamatix has developed the software and tools; MGRC provides the services to customers and looks after the bioinformatics pipeline. MGRC also has a web portal that provides free online bioinformatics tools to users.

MGRCs services are constantly ex-panding, Hercus explained, as new customers bring new challenges and op-portunities as the technology advances. We plan to eventually offer a sequencing service as well, he said. We have a lot of local Malaysian research institutes that want to do sequencing of human ge-nomes, and at the moment we send that out overseas. So we believe it will be cost effective for us to have our own sequenc-ing centre here, at least for Malaysia, if not the region. x

Malaysian Genomics Center Offers Genome Mapping for $4K4FRVFODJOHBTBTFSWJDFJTBWBJMBCMFXJUI*MMVNJOBBOE$PNQMFUF(FOPNJDT

Robert Hercus



Primary ResearchAnalysisTrendsCompany Activities

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[10]#*0t*5 803-%+6-:| AUGUST 2010 www.bio-itworld.com

Up Front The Bush Doctrine

Although probably not the best topic for your next neighborhood barbecue, the question of which new technologies may contribute to developing safer medicines makes for interesting debate over a beer with professional colleagues. I find it particularly entertaining to ask the question: What happened

to previous Big Things that appeared from prior beer sum-mits one, five or ten years ago?

Perhaps the most talked about Big Thing of the recent 3-5 years has been biomarkers. The discovery and development of biomarkers has been promised to aid in the diagnosis and treatment of diseases as well as in monitoring and predicting safety outcomes.

When the FDA released its Critical Path Opportunities List in March 2006, one could be forgiven for concluding that it was all about biomarkers. Indeed, of the 76 targeted opportu-nities identified, nearly half referred to the identification and validation of new biomarkers. In fact, there was an initial flurry of activity that seemed to promise success, exemplified by the work of the Predictive Safety Testing Consortium of the C-Path Institute and its work in detecting early kidney damage.

Unfortunately, four years later we still have not seen any sig-nificant adoption of new biomarkers for tissue damage or safety evaluation either in clinical studies or pre-clinical safety assess-ment. Of course, validation of new clinical biomarkers has been more difficult than many would have guessed, but even those new preclinical biomarkers which have been accepted by regu-latory authorities, and for which commercial tests are available, are not used appreciably in routine GLP studies.

Before biomarkers, the Big Thing in safety assessment was undoubtedly toxicogenomics. It would be hard to overstate the hype surrounding the introduction of microarrays and their potential impact on toxicology and adverse event prediction. Toxicogenomics spawned many companies and soaked up hun-dreds of millions of dollars of R&D money from VC firms and big pharma companies.

A decade later, it is clear that toxicogenomics has evolved into a valuable mechanistic tool and may yet provide some value in terms of safety evaluation. But as the demise of all those toxicogenomics companies suggests, its value in safety prediction has not panned out.

Another Big Thing worth considering is the rise, fall and

subsequent reappearance of exploratory or mechanistic toxicol-ogy groups. This movement stretches back into the late 1980s. Even 20 years ago, the limitations of conducting safety evalu-ations in GLP animal studies were well recognized. Therefore 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 terms of toxicology prediction. Interestingly, though, after a couple of decades of development and refinement, in vitro (and now in silico) safety testing is enjoying a re-emergence with most major pharma research groups establishing discovery safety functions and implementing new pre-GLP safety predic-tion tools.

What Have We Learned?It is tempting to conclude that the biggest takeaway about next Big Things is to disregard the hype, and maybe even to ignore all new things, as most dont work out as well as promised. Indeed, I would always advise a healthy (scientific) amount of skepti-cism about any claims for new technology promises or routine assay results.

But such simplistic conclusions miss the useful lessons from what our history is trying to teach us. These are:1. The development AND implementation of new technologies

are experimental sciences. If most of your experiments do not turn out as you expect, then you are probably not being creative or daring enough in your science.

2. Real advances in scientific practice, especially in safety pre-diction, take time. Although the vision for early safety evalu-ation stretches back more than 20 years, it took a full two decades for the science and the technology to catch up with that vision. I suspect that biomarkers and toxicogenomics will also one day play important roles in safety assessment, but that is probably another 5-10 years in the future.

3. New technologies in which success depends on catching re-ally small fish in really big oceans are doomed to fail most of the time. If the new technology vision promises, If we look at a large enough number of parameters across a large enough pool of patients/subjects/experiments, we will even-tually find an answer, then be prepared for a very long haul. Endeavors such as building toxicogenomics databases, find-ing the next biomarker from large patient databases, gener-ating huge libraries of compounds through combinatorial chemistry, etc. all fail to acknowledge the nearly unimagina-ble diversity of chemistry and biology on Earth. The ocean of possibilities is really deep and even giant fishing expeditions have a slim chance of catching fish without some guide to where the fish are.

Ernie Bush is VP and scientific director of Cambridge Health Associates. He can be reached at: [email protected].

The Next Big ThingERNIE BUSH



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Clinical Trials

BY ALLISON PROFFITT

Medidata announced two new products at the Drug Informa-tion Association (DIA) meet-ing in Washington, D.C.: an

updated version of Grants Manager and Medidata Balance.

Glen de Vries, Medidata Solutions 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. Theres never been somewhere where I can just go online and turn on a randomization system for a clinical trial, says de Vries. Thats exactly what weve done with Balance.

Balance is a randomization and trial supply management (RTSM) solution that replaces interactive voice response (IVR) and interactive web response (IWR) systems. Study designers and trial managers can use Balance to plan and simulate trials, while sites can use Balance to assign subjects in real-time at enrollment, and begin drug supply plan-ning immediately.

Randomization can become quite complex, de Vries told %LRv,7:RUOG.Youll have a clinical trial where maybe you have 10 different doses or 5 different doses and you need to figure out which one is most effective. There may be other factors, the age of the subjects or their genders. With traditional block random-ization techniques, subjects are assigned in the trial according to a pre-determined schedule.

You load that data into the system and when the inevitable issues occur, for instance a patients gets randomized then drops out of the clinical trial, you hope you hope!that you have balance in the trial, that youve achieved the relative equivalence of study subjects that have gotten the drug or placebo, says de Vries.

The solution is dynamic randomiza-tion, or assigning subjects to the study based on how enrollment is progress-ing in real time while still remaining blinded and nondeterministic. Dynamic randomization is something that has typically been regarded as the more ad-vanced, the more complicated, the more expensive, the more time-intensive way to randomize subjects, and its therefore not used that much, says de Vries. We think dynamic randomization isnt something that should require tons of cost and tons of time and tons of risk.

In addition to one-click dynamic ran-

domization, Balance supports trial simu-lations. If you dont like the way the trial came out if you did it ten times simulated, change the parameters and do it ten times more and see how it comes out, de Vries says. You can do all the design, and then just turn on dynamic randomization in a very streamlined way, without having to implement any custom software to do it.

Balance is not a module for Rave, but works seamlessly with the system. It brings all elements of the design and execution of randomization and supply logistics into the Medidata Rave platform. Giving trial designers and sites a single system for everything from randomiza-tion to EDC helps trials run with fewer subjects and less time, risk, and cost, says de Vries.

How Much and How ComplicatedContinuing with a focus on early-trial planning, Medidata also announced an update to their Grants Manager product.

Grants Manager 3.0 is where users ag-gregate and pool their worldwide grant payments and is a database of actual but anonymized trial costs.

So youre doing a new clinical trial. You decide you want to use some sites in China, but you want to know what, on average, a site in oncology in China in Phase II gets paid to do a blood draw. You use Grants Manager to figure that out, explains de Vries.

Grants Manager 3.0 is now browser-based with a friendly user interface that provides data for more than 80 countries with specific regional groups by country

and has the ability to assign different study arms for countries, regions and site budgets.

But the most exciting thing, de Vries says, is the benchmarking capabilities of not only cost but complexity, a measure based on research that Medidata did with the Tufts Center for Drug Development and that de Vries calls spectacularly useful.

The benchmark that you get out of Grants Manager now shows you the information about complexity. Is your clinical trial one that is harder or easier from an execution standpoint for that site in China than theyre used to?... If I know that I have a particular clinical trial that is hardmeaning its going to take a lot of time and a lot of different proceduresI may want to go and find more experi-enced sites to work on it.

Having access to both complexity and actual cost data allows Grants Manager users to make operational decisions. x

Early Trial Planning Solutions5XPOFXQSPEVDUTGSPN.FEJEBUBTUSFBNMJOFSBOEPNJ[BUJPOBOETJUFTFMFDUJPO

G rants Manager now shows you if your clinical trial is harder or easier than that site in China is used to.

Glen de Vries.FEJEBUB



www.bio-itworld.com+6-:|"6(6452010 #*0t*5 803-% [ 13 ]

BY RICKI LEWIS

WASHINGTON, DCLike the mythical Phoenix that springs anew from its ashes, gene therapy shows signs of re-emerging with a stockpile of safer and more efficient viral vectors. At the annual meeting of the American Society of Gene and Cell Thera-py last May*, optimism was palpable.

The excitement peaked when 9-year old Corey Haas walked onstage at the Presidential symposium. His physician, Jean Bennett, professor at the F. M. Kirby Center for Molecular Ophthalmology at the University of Pennsylvania, an-nounced: Id like to introduce the young-est person ever to speak at ASGCT.

Until his gene therapy in September 2008, Corey was headed for blindness from Leber congenital amaurosis type 2 (LCA2). Today he plays baseball and just recently saw fireflies for the first time. He calmly answered questions from an astonished audience, and afterwards was mobbed by awed scientists, some in tears.

Earlier that day, Corey and his parents joined other emissaries of recent advances in gene therapy at a news conference. It was sparsely attended because across town, Craig Venter had just announced that he had artificially created life.

LCA2 is caused by mutation in the RPE65 gene. RPE65 helps to recharge vitamin A, and without it, there is no vi-sion. The gene therapy idea was simpledeliver the gene to the retinal pigment epithelium, which hugs the photorecep-tors, said Bennett. The pediatric clinical trial at Childrens Hospital of Philadelphia treated 12 patients between the ages of 8 and 24 in one eye. All improved.

The target disease most like the meta-phorical phoenix is severe combined im-mune deficiency (SCID). Gene therapies

for two treated forms had problems. First was ADA deficiency, tried on a 4-year-old in 1990. Her restored health could have been due to concomitant enzyme replace-ment. And gene therapy for SCID-X1 (bubble boy disease) worked, but caused leukemia.

Don Kohn, director of the University of California Los Angeles human gene medicine program, discussed new gene therapy trials for both forms of SCID using safer vectors. A trial to treat 20 boys with SCID-X1 is underway in Paris, London, and three sites in the U.S., using a self-inactivating retroviral vector. And for ADA deficiency, Kohns group is using the chemotherapeutic busulfan to clear space in the bone marrow for replacement cells, and using a lentivirus (HIV), which works in non-dividing cells, carries bigger genetic payloads, and integrates more ef-ficiently than past vectors. To date, four of eight patients have benefited clinically, living at home and doing well, he said. And thats without enzyme replacement.

In the second row at the press con-ference sat three young women who catalyzed gene therapy for their familys

disease, adrenoleukodystrophy (ALD), the genetic disorder portrayed in the film /RUHQ]RV2LO. When Nathalie Cart-ier-Lacave arrived, the four women embraced. Cartier-Lacave is director of research at INSERM in Paris.

The ALD protein normally admits very long chain fatty acids into peroxi-somes, where they are degraded and used to make myelin, which insulates neurons. Behavioral symptoms rapidly progress to seizures, blindness, and incapacita-tion. The only treatment, a stem cell transplant, takes 12 to 18 months for progression to stop, said Cartier-Lacave, but is risky. Gene therapy, also using HIV, exploits the fact that the brain cells af-fected in ALD (the microglia) come from bone marrow. The first two patients made headlines in fall 2009, after they had been making normal ALD protein for many months, as MRIs tracked remyelination. There was no problem with HIV or immunity or insertion into a gene that causes leukemia, said Cartier-Lacave.

Eve (Salzman) Lapin said that after her son Oliver was diagnosed with ALD in 2000, genetic testing found that one brother and a cousin had also inherited the disorder. Sisters Amber Salzman (an executive at GlaxoSmithKline at the time) and Rachel Salzman (a veterinarian) launched Stop-ALD, uniting researchers for a clinical trial. They did everything shy of following us into the mens room, jokes Jim Wilson, professor of pathology and laboratory medicine at the University of Pennsylvania, who helped the sisters.

Lapin had the final word at the news conference. The legacy of Olivers life and death is that gene therapy will be a better way to treat ALD and other terrible diseases. x3JDLJ-FXJTJTUIFBVUIPSPGThe Forever Fix: The Rise, Fall and Rebirth of Gene Therapy and the Boy Who Saved It,UPCFQVCMJTIFECZ4U.BSUJOT1SFTT

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Clinical Trials

BY ANN NEUER

The 46th Annual Meeting of the Drug Information Association (DIA) held in Washington, D.C. sported a decidedly optimistic tone. Exhibitors claimed to have more traffic at their booths this year, and there seemed to be much less discus-sion about the economic climate. In its place were a whole host of sessions and exhibits highlighting strategic partner-ships among multiple stakeholders, the growing role of payers and comparative effectiveness research, electronic health records, continued globalization, and of course, the latest technological solutions.

Virtify Launches Rules-Based SolutionSponsors are scrambling to remain in compliance with an ever-increasing array of regulations put forth by regulatory agencies across the globe. In the U.S., for example, complying with Protocol Reg-istration System (PRS), the Web-based data entry method for www.clinicaltrials.gov, requires companies to conform to thousands of rules that define how data on clinical trial postings and results are to be registered and disclosed to the Web site. Virtify, a provider of enterprise content compliance solutions for the life sciences sector, is addressing this tough challenge head-on with its DIA-announced Clini-cal Trials Registration & Results software solutionCTRR Enterprise 2.0.

Our new CTRR product has a 5,200 rules engine to keep customers compli-ant with PRS requirements while help-ing them mitigate their staffing needs. Companies are anxious to reduce their out-of-compliance status and the cost of adhering to that compliance, says Ste-phen Bergson, Executive Vice President, Commercial Operations at Virtify.

According to Bergson, remaining in compliance with constantly changing regulations and deadlines is a highly complex and burdensome endeavor for most companies, especially since rules-

based database requirements for clinical trial registries are a global phenomenon. For instance, the European Union (EU) is slated to release Version 8 of the Euro-pean Clinical Trials Database (EudraCT) and the EU Clinical Trials Register in September 2010. In addition, the Eu-ropean Commission recently released a draft technical guidance that details how result-related information should be up-

loaded to EudraCT in the future.Virtify maintains a staff that monitors

these sorts of regulatory changes that are happening in many countries. This surveillance allows the company to make updates without having to re-validate the software every time a new rule is es-tablished. Bergson explains, When new rules are put in place, CTRR will be up-dated promptly and appropriately.

Enough with the e!One of the most insightful discussions at this years DIA took place at a breakfast meeting I had with Beth Harper, industry veteran, and Chief Clinical Officer of the newly formed CenterPhase Solutions, a company dedicated to improving clinical trials performance. We got together on the last morning of DIA at the charm-ing Coeur de Lion restaurant in the Park Henley, an 88-year old hotel across the street from the Walter E. Washington Convention Center, this years site for the DIA Annual Meeting.

Just as I was about to dig into my cinnamon brioche French toast, Harper announced, Im e-d out. Theres e-clin-ical, ePRO, eCRF, EDC, but what about people? Harper asks. This is a people business. A relationship business. Many investigative sites tell me they miss the days of being able to call a monitor and ask a question. Today, many sites dont even know who their monitor is for a particular study, and to answer questions, they have to log onto an e-learning portal to look at the study manual. Harper ex-plains that this might work most of the time, but if the site is attempting to enroll a patient right then, it would be easier to simply pick up the phone to ask a ques-tion, but unfortunately, those days are mostly gone.

Significantly, despite, all of the e-improvements, CenterWatch reported in a 2009 study that less than 10% of clinical trials are completed on time. Additional research from CenterWatch indicated that 70% of investigative sites are more than one month behind in enrollment, and only 7% of sites report meeting en-rollment timelines.

E has not solved the root causes of study delay, and its not costing any less to go with e-everything. Products today havent gotten safer with e-tools, and drugs havent become more effective and arent coming to market any faster, Harper points out.

Harper is a specialist in helping spon-sors improve investigative site perfor-mance and is not anti-technology. In fact, she believes in balance and clearly recognizes the tremendous value of elimi-nating the mountains of paperwork and documentation that has typified clinical trials for so long. But as she tells it, tech-nology is no substitute for personal rela-tionships among the many stakeholders. I like interacting with people, and I get exhausted being blackberried all the time. When there is a personal relation-ship, you are more likely to feel a com-mitment to perform. How can you have a commitment or a sense of obligation to someone youve never met? Were losing the human touch. x

Innovation, Issues-Driven, Upbeat%*"QSPWFEQPTJUJWFBOEIPQFGVM

Beth Harper




BY KEVIN DAVIES

In an effort to challenge the life sci-ences community to create more in-formative and accessible ways to look at the wealth of genomic and other

life science data, Illumina is launching what it calls the iDEA (Illumina Data Ex-cellence Award) Challenge. The initiative was first discussed at a small workshop of the Genomics Informatics Alliance, held in early May in Seattle.

Jacques Retief, Illuminas senior manager of scientific affairs, says the goal behind the iDEA Challenge is to find ways to improve the scientific utility of genomics data and provide an intellectual leap for the community.

Illuminas technologies have the po-tential to help us understand diseases and the living world around us at the molecu-lar level. Unlocking that knowledge will enable radical improvements in human health and quality of life over the next decade, states the competition Website, www.illumina.com/landing/idea/. iDEA is a program designed to challenge the scientific community to develop new and creative visualization and data analysis techniques.

The competition is open to all comers and will run for about 9 months, from June 15, 2010, when Illumina released a standard data set for the challenge, until March 15, 2011. The winners will be an-nounced at an iDEA conference in San Diego in June 2011.

Retief says biological sciences have always had a strong observational com-ponent. It is no coincidence we use the word insight to describe improved understanding, he said. In the golden era of biology, scientific breakthroughs by Mendel, Pasteur, Darwin and others were based on sharp observations using small data sets. The size and scope of modern day scientific breakthroughs have changed with the sequencing of the

human genome and the development of next-generation sequencing technology. As a result, we are now entering the sec-ond golden era of biology, an era that is fueled by large amounts of data.

Ironically, Retief says, the sheer size and complexity of modern genomic data that makes them so valuable also makes them very challenging to visualize. The size of the data sets we are dealing with now have a closer resemblance to those generated in high energy physics than those a typical biologist is used to han-dling. Take, for example, the ongoing 1,000 Genomes Project. How do you intuitively display and compare 1,000 genomes? asks Retief. Our challenge to the community is to answer that very question by increasing the utility of next-gen sequencing data through creative integration and visualization.

Software SolutionsThe iDEA contest seeks to recognize creative advances in algorithms and vi-sualization. Algorithms are rarely in the spotlight, but a well-crafted algorithm can play a key role in integrating or improving the display of data, says Retief. The same can be said for data formats. The data formats common in the field today, such

as BAM and FASTQ, are not particularly elegant or compact... you cannot visualize or use the data if you cannot transport or parse it efficiently.

There will be a total of six awards divided into two categoriesacademic and commercial. The overall academic winner will receive a grant for $50,000 from Illumina, while the overall winner in the commercial category receives a one-year co-marketing deal with Illumina. In addition, awards will be given for most creative algorithm and most creative vi-sualization in both categories.

Illumina will provide any interested iDEA contestant a hard drive containing a dataset derived from breast cancer cell lines, including methylation, gene ex-pression, RNA-seq and genotyping data. The data set will include different read-lengths, paired ends on mRNA, small RNA, DNA and methylation, as well as biological information on the breast cell lines (drug response, tumor progression, etc.).

Entries will be judged by a team of five judges on magnitude of the intellectual advance over the present state of the art; novelty or uniqueness of the entry; utility to the typical scientist; intuitiveness of results presented to the user of the algo-rithm or visualization; and integration of data.

Retief expects the visualization cat-egory to be the most exciting aspect of the competition and to generate the most interest.

Illumina is not requiring that the entries be complete, fully functioning software. Entries do not need to have functioning software. For the Algorithm and Visualization judging, storyboards, sketches and cartoons are all eligible, entry details state. Sometimes the best ideas come from unusual sources and we want to encourage the brightest minds to participate, explains Retief. x

A Bright iDEA: Illumina Launches Data Visualization Competition5IFDPNQFUJUJPOTHPBMJTUPJNQSPWFTDJFOUJGJDVUJMJUZPGHFOPNJDTEBUB

S ometimes the best ideas come from unusual sources and we want to encourage the brightest minds to participate.

Jacques Retief*MMVNJOB

Computational Biology




BY KEVIN DAVIES

The fact that guest speaker Jamie Heywood dropped the first F bomb in %LRv,7:RUOGs Best Practices Awards history didnt seem to bother the 200 din-ner guests.

Heywood delivered an impassioned speech advocating the role of IT in drug discovery, reliving his experiences over the past decade dealing with his brother Stephens diagnosis with amyotrophic lateral sclerosis (ALS). Hey-wood played the trailer from the documentary 6R0XFK6RFast. Do you feel the power of the mission were all on? he asked the audience to warm applause.

Heywood, who is the founder and chairman of Patients-LikeMe, said the pharmaceutical and biotech industry was trying to make a difference in what was a very hard and difficult process. But his own prescription was to change the paradigm. You all serve the scientists in your institu-tions Thats backwards. IT should be running the joint! he said. Quite frankly, scientists dont have any idea how to deal with data. They dont understand what it means, how to interpret it, how to find quality in it.

Two days after his brothers ALS diagnosis in 1998, Heywood quit his research job and embarked on a journey to help prolong his brothers life. He recalled typing into PubMed the keywords prognosis and ALS. I computed what would happen to Stephen, he said. The result was a predicted lifespan of 2-5 years. Heywoods then wife sug-gested he read 7XHVGD\V:LWK0RUULH. No way! he said.

Instead, he started the worlds first non-profit biotech company, the ALS Therapy Development Institute, and a few years later, injected Stephen in his spinal cord with first stem cell transplant in ALS at Jefferson University. It didnt do jack, said Heywood. He didnt live a day longer.

Computing Stephen

Jamie Heywood, founder and chairman of PatientsLikeMe




In trying to determine why it didnt work, Heywood needed to break out of the rut that biotech had been in for 20 years, trying to translate so-so data in an animal model and turn it into a thera-peutic. I needed knowledge. I needed to compute what it meant. I needed every clinical trial that had ever been run in ALS. Around 2000, Heywood built one of the first databases for any disease, list-ing every trial, the number of patients, and the outcome.

Would a software engineer ever un-dertake a project if they didnt build a da-tabase of the options? Yet scientists spend $50 billion a year and dont even bother to list the options. So why are we [engi-neers] not in charge?! This is insane.

Heywood found he couldnt replicate published data, and simulation experi-ments suggested many results could be explained by random chance. The people in our lab were not classically trained scientists We came from industries that believed in quality, understood the rigor-ous collection of data. Heywood even banned notebooks, because if you cant put it in the computer and compare it, its not really meaningful.

The challenge now was to think about how these platforms can drive experi-ments so we can compute the results in a meaningful way and no longer make bogus investments in drugs that never worked in the first place. He said: The challenge, the excitement, the opportunity is to stop

serving and start leading. Its about the metadata, the comparison of data.

Trust IssuesIn the end, Stephen Heywood fought ALS for ten years in which he raised a son and lived an incredibly full life. Not be-cause of anything I did, said Jamie. Not because of the stem cell transplant. Not because of the experiments we tried but

because he had an internal avenue that changed the way he lived.

But he also helped Heywood view a new way of thinking about medicine. Quoting Marcia Angell, Heywood said it is simply no longer possible to believe much of the clinical research currently published. Drugs cannot be trusted. Clini-cal decisions cannot be trusted.

Thats why our industry has been los-ing money for 20 years. The way we fix that is we bring rigorous IT and rigorous quality into a system that is a crass indus-try run by people who think they know the answer instead of proving it. Thats why IT should run the damn system. So go make friends with manufacturing en-gineers and stop losing 19/20 drugs, not because biology is hard, but because we are believing BS.

With PatientsLikeMe, Heywood can ask hundreds or thousands of patients with the same disease the same ques-tions. He said: Imagine a world where in real time, every patient knows what will happen to them... the drug companies will be competing not to prove to the FDA they have some drug that modifies a signal to get through the [approval] process, but to convince the patients that they generate enough value to make their lives better.

Thats a world we can make real, if we measure everything, integrate it together, and think about how we connect that, which will only be driven by IT. x

Last October groups were invited to submit outstanding and innovative best practices in industry and aca-demia. We received a record 74 entries Next, we assembled a panel of 15 expert judges drawn from big pharma, academia, and consultants. Together, we debated the merits of every entry, assessing each case in terms of novelty, return on investment (recognizing that in some cases ROI has not yet been fully demonstrated), and the potential transference to other organizations.

In the following pages, youll find profiles of the six category winners

and three other awards: the Editors Choice Award, the Judges Prize, and a Community Service Award.

We extend our thanks to everyone who entered, our 2010 Best Practices Dinner sponsors Tessella and Genom-eQuest, and especially our judges for volunteering their time and expertise:t"M%PJHCHI Insight Pharma Reportst"MBO-PVJFIDC Health Insightst#JMM7BO&UUFOThe BioTeamt$SBJH-JQTFUPfizert%FSFL%FCFAbbott Laboratoriest+POBUIBO6TVLBCelgenet+PTFQI$FSSPThe Schooner Group

t.BSUJO(PMMFSZTahoe Informaticst.JDIBFM3PTFOCFSHHealth Decisionst/PFNJ(SFZ[EPSGIDCt1IJMMJQT,VIMCambridge Healthtech

Institutet4BOEZ"SPOTPOHarvard Medical

Schoolt4BVM,SBWJU[CLC Biot4UFQIFO'PHFMTPODevelotront4VTBO8BSEConsultant

Were very proud of the quality of this years entries (see the full list online), and are looking forward to the 2011 competition.

Allison Proffitt, Kevin Davies

Last April, we handed out the#JPt*58PSME 2010 Best Practices Awardsat a lavish awards ceremony in Boston during the Bio-IT World Conference & Expo.

WinnersResearch & Discovery:.BTTBDIVTFUUT

Institute of TechnologyClinical Trials: '%"(nominated by

GlobalSubmit)IT & Informatics: The Scripps Research

Institute (nominated by SciQuest)IT & Informatics/HPC:#SJTUPM.ZFST

Squibb, Research & DevelopmentKnowledge Management: Centocor

R&D, a subsidiary of Johnson & Johnson (nominated by Recombinant Data Corp)

Personalized & Translational Medicine:1300'J$"1563&$FOUSFof Excellence (nominated by IO Informatics)

Judges Prize: goBalto.comEditors Choice Award:.FSDLBOE$PCommunity Service Prize: Royal

Society of Chemistrys ChemSpider (nominated by Collaborative Drug Discovery)

MAR

K G

ABR

ENYA

A complete list of entries is on pages 27-28:




BY ALISSA POH

Whole-genome methods have garnered a lot of attention in target-based drug discovery, leaving their protein-based

counterparts somewhat squeezed in the shuffle. Nevertheless, one promising pro-teomics approach received the Best Prac-tices Award for Research and Discovery.

This new tool for understanding how drugs work uses novel algorithms that deconvolute data derived from phosphoproteomicsa branch of large-scale proteomic studies that identifies

and characterizes protein activity. Details were published in the December 2009 issue of PLoS Computational Biology.

Alexander Mitsos and Leonidas Alex-opoulos, the papers lead and senior authors respectively, describe phosphop-roteomic measurements as the ultimate reporters of a drugs action on signaling networks. Changes in phosphorylation status almost always reflect changes in protein activity, which provides clues as to what molecular pathway(s) are activated and what proteins might be potential drug targets.

As a postdoc at MIT and Harvard Medical School, Alexopoulos and col-league Julio Saez-Rodriguez pursued ways to create cell signaling topologies, or pathway maps, using high-throughput phosphoproteomic data.

Shortly before returning to his home country, Greece, in 2008where he is now a lecturer and group leader of the Systems Biology and Bioengineering Laboratory at the National Technical University of AthensAlexopoulos struck up a conversation with Mitsos, then a re-search group leader at Germanys RWTH Aachen University.

Mitsos had developed what Alexo-poulos called some neat computational approaches, and they both saw an op-portunity to use these to generate cell signaling topologies.

Despite their different scientific back-grounds, they found a good niche for collaboration. Alexopoulos pooled his training as a biological engineer with Mit-sos computational knowledge. Together, they created a two-step system: first build pathways simulating cell function, then identify drug-induced alterations of those pathways.

Mitsos, Alexopoulos, Saez-Rodriguez, and other team members Ioannis Melas, Paraskeuas Siminelakis, and Aikaterini Chairakaki used their method to evalu-ate the effects of four drugs on HepG2, a liver cancer cell line. They picked 13 key interaction points, identified by phosphorylation of specific proteins. They then tracked these under different conditions, treating the cells with various combinations of cytokine ligands, kinase inhibitors, and four anti-cancer drugs:

Lapatinib, Erlotinib, Gefitinib (all three block EGFR), and Sorafenib, a dirty inhibitor that blocks signaling via several kinases, including RAF.

The researchers were able to build a HepG2-specific map which confirmed known effects such as signaling responses to ligands, and the drugs main targets. They also uncovered an intriguing off-target effect of Gefitinib, observing that the drug inhibits signaling downstream of the protein cJUN along the interleukin-1 alpha pathway, possibly by interacting with molecules upstream of cJUN.

This was pretty surprising, Alexo-poulos says. Gefitinib is known as a pure EGFR inhibitor, and I wouldnt have thought that it would also act along a totally different pathway.

This strategy, Alexopoulos says, is significantly different from others cur-rently implemented for drug screeningfor instance, high-throughput in vitroassayswhich generally identify binding partners for drugs of interest. Its more of a physiologic approach. Were answer-ing the same question from an alternate point of view; both are complementary methods, he says.

The key strengths of this tool lie in its scalability and reproducibility; it al-lows precise, defined measurements to be made within a well-curated system. Besides being useful for validating known

drug actions, it has the potential to identify drug effects missed by cur-rent screening procedures, as dem-onstrated by detection of Gefitinibs off-target activity against cJUN.

So what was the biggest chal-lenge they faced in developing this system? Definitely language, chuckles Mitsos, now an assis-tant professor of mechanical engineering at MIT. Hes a math person, while Alexopou-los focuses more on biological systems. We talked a lot and

tried to solve problems as they came, while always trying to not

impose any particular method or point of view. x

Protein-Powered Drug Discovery

Winner: Massachusetts Institute of 5FDIOPMPHZ

Project:*EFOUJGZJOH%SVH&GGFDUTWJB1BUIXBZ"MUFSBUJPOTVTJOHBO*OUFHFS-JOFBS1SPHSBNNJOH0QUJNJ[BUJPO'PSNVMBUJPOPO1IPTQIPQSPUFPNJD%BUB

Research & Discovery

Alexander Mitsos, Massachusetts Institute of 5FDIOPMPHZ




BY ALLISON PROFFITT

The Scripps Research Institute (TSRI) boasts 534 faculty, 735 post doctoral researchers, 218 graduate students and 1,445 lab

and supporting employees in its two locations in California and Florida, and keeping all of those researchers busy and equipped means a huge procure-to-pay process. Automating that process with SciQuests eProcurement product has saved TSRI over 8,000 man hours and won %LRv,7:RUOGs Best Practices Award in IT & Informatics.

Before the SciQuest rollout, labs searched through numerous paper cata-logs and on suppliers Web sites. They filled out the required paperwork and requisitions. Written approval was re-quired to make purchases of more than $1,000 or that included regulated ma-

terials. The process could take up to two weeks or more and required 17 people to touch the necessary paperwork all before the order could be placed.

June Lombardi, director of procure-ment, and Dennis Gilliland, senior sourc-ing manager for IT liked that the SciQuest shopping platform allowed TSRI to create its own online marketplaceAmazon for their researchers needs, Lombardi saysrepresenting 1080 catalogs. Prior to the SciQuest model of searching, researchers would have to pull off the manufacturers catalogs one by one and some are 200, 300, 400 pages thick, explains Lom-bardi. [SciQuest] allows researchers to search by chemical attribute, by descrip-tion, and compare across product lines and look for a particular item.

The new process not only streamlined the process of finding supplies and re-agents, but it dramatically improved the actual ordering process. Before SciQuest our entire procurement system was a paper process, says Gilliland. This proved particularly cumbersome when TSRI opened a new facility in Florida, but all procurement was still done in La Jolla. With the deployment of the SciQuest system throughout the organization, not only has that been able to speed up processing time, but also has been able to

gain greater efficiency. The new system went live in January

2007. With no mandatory requirement to use itresearchers typically own the grants they work withleadership at the Institute expected scientists to adopt it gradually, but word of the benefits it deliv-ered spread quickly. By September 2009 95% of all labs, and 1,327 active employ-ees were using the SciQuest system.

Today more than 90 percent of spend-ing at the Institute (thousands of pur-chases) flows through the new electronic, on-demand procurement system and all facets of the purchasing cyclefrom gaining approvals to the payment of suppliersare dramatically faster.

SciQuest lets researchers spend more time doing what we do best... researching! Before we had it, we wasted countless hours shuffling papers instead. And there is no way to know how much money we lost through redundant purchases, rush orders and the like, said Bruce Beutler, professor and chair of the department of genetics in the Best Practices entry.

Labs now spend 85 percent less time ordering supplies and managing their orders. Many have gained 20 hours of re-search time each week by eliminating the administrative tasks once associated with the purchasing process, while the average requisition to delivery cycle takes half the time it did before the transformation and continues to accelerate.

The new system has saved hundreds of thousands of dollars. Many labs can report saving of seven percent or more on their supplies and purchases, allowing researchers to achieve far more with exist-

ing funding. Labs can now easily ac-cess TSRIs negotiated rates and

invoices can be automatically checked against these rates.

Lombardi is proud of the efforts Best Practices win. An administrative pro-curement function can have a significant contri-bution to the accelera-tion of science to drug discovery. x

Creating a One-Stop-Shop for Research

Winner:5IF4DSJQQT3FTFBSDI*OTUJUVUFOPNJOBUFECZ4DJ2VFTU

Project:1SPDVSFNFOU5SBOTGPSNBUJPO

IT & Informatics

-UP3%FOOJT(JMMJMBOE+VOF-PNCBSEJ5IF4DSJQQT3FTFBSDIInstitute; and Max -FJTUFO4DJ2VFTU

A complete list of entries is on pages 27-28




BY ALISSA POH

Like most technologies that produce reams of information, high content screening necessitates finding ways to efficiently manage and analyze

large, image-intensive data sets. At Bristol-Myers Squibb (BMS), researchers decided to handle HCS separately. They designed and built HCS Road, a spe-cific data management system that won %LRv,7:RUOGs 2010 Best Practices award for IT and Informatics: HPC.

BMS now employs HCS along differ-

ent stages of its drug discovery process, but the company took some time to fully implement this technology, says James Gill, one of the companys directors and leader of the HCS Road project. We dont tend to jump whole-hog into something until were certain it can pay back, Gill says. BMS began with one HCS instrument, then, noting that the industry was growing quickly and different instrument vendors had very diverse capabilities, gradually expanded its fleet.

At that point, Gills team recognized that the in-formatics [compo-nent] was actually impairing our abil-ity to explore the science. So we were awarded some financing to build what we originally c a l l e d H C S Footpath, and that helped our

science community to really button down on [using] the technology. Later, the de-cision was made to forge a single resource for all of BMSs HCS databasically, ex-panding the footpath to a road.

HCS Road starts by collecting de-tails about an experimenttype(s) of cell line(s), dyes, fluorescent antibodies, what aspect of biology is being tracked and so on, tying all this information into our existing database and re

bio-it world aug 2010

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