“Secrecy is a !Public Health Problem”!

Jonathan G. Izant Sage Bionetworks

www.sagebase.org @SageBio AAAS 18 February 2012

denial

What is the real problem? •  Profit margin too low? •  No one willing to pay? •  No one able to pay? •  Internal research costs too high? •  Low hanging fruit picked? •  Genome has not delivered? •  Companies can’t execute on strategy? •  Regulatory hurdles too high? •  Clinical trials too difficult and expensive?

In fact, all are true but none is the real problem

the real problem

•  We need to rebuild the drug discovery process so that we better understand disease biology

•  We need to reshape the way researchers, citizens, companies and funders interact

genetic regulation circa 1970

Genetic networks

The opportunity

•  Stunning technologies are generating heaps of genomic and clinical data

•  Bionetworks using integrative genomic approaches can highlight the non-redundant components- can find drivers of the disease and of therapies

•  Need to develop ways to host massive amounts of data, evolving representations of disease as represented by these probabilistic causal disease models

Network biology collaborations involve multiple specialized labs, big data, sophisticated methods and the results are often published in open access journals

Collaboration -  Multiple labs; specialized; -  Biologists, clinicians,

statisticians, engineers, etc Technology

- Sophisticated technologies Data

-  >5x108 data points

Methods -  Computationally intensive

(5000 node cluster)

Publish -  Open access journal -  18 figures, 19 tables -  Gigabytes of data

Catalytic nonprofit formed in 2009

Vision: to create a “Commons” where integrative bionetworks are evolved

by contributor scientists with a shared vision to accelerate the elimination of

human disease

Principles Understanding human biology requires a new community-based vision of open access innovation that

respects and links all stakeholders and supports a new culture of cooperative, data-intensive science.

We pledge to take up this challenge and have drafted the Sage Bionetworks Commons Principles to guide the development of an open source community where computational biologists can develop and test competing models built from common resources.

1.  The purpose of the Commons is to expedite the pathway to knowledge, treatment, and prevention of disease.

2.  We will promote collaborative discovery through the creation and support of a broadly accessible digital Commons consisting of curated data and methodological tools in which analytical results are shared in a transparent, open fashion.

3.  The Commons will respect the rights and interests of all contributors including individuals from whom data are derived, researchers who collect and analyze data, and scientists and physicians who develop and implement healthcare advances. Those not respecting these rights will be excluded from the Commons.

4.  Contributions to the Commons shall be appropriately acknowledged and attributed.

5.  The Commons will promote data and tool sharing and distribution using standards that enable efficient reuse, compilation and comparison.

6.  The Commons will hold no intellectual property rights in, and will not permit encumbrances on, data and other elements within the Commons. This will not, however, preclude individuals from protecting new goods and services developed using data and other elements from the Commons.

•  Stephen Friend, MD, PhD •  Jonathan Derry, PhD •  Adam Margolin, PhD •  Jonathan Izant, PhD •  Solly Sieberts, PhD •  Xia Yang, PhD •  Eric Huang, MD PhD •  Christine Suver, PhD •  Thea Norman, PhD •  Zhi Wang, PhD •  Chris Gaiteri, PhD •  Charles Ferte, MD PhD •  Elias Neto, PhD •  Lara Mangravite, PhD •  Justin Guinney, PhD •  Qingying Meng, PhD •  Mette Peters, PhD •  Vitalina Komashko, PhD •  Brig Mecham, PhD •  Andrew Twister, MD PhD •  Matt Furia •  Brian Bot •  In Sock Jang, PhD

• Mike Kellen, PhD • Nicole Deflaux, PhD • Bruce Hoff, PhD • Dave Burdick • John Hill • Xa Schildwachter • Brian Holt

Rosetta Inpharmatics, Merck & Co

Duke University

Broad Institute of MIT and Harvard

University of Michigan

University of Pittsburgh

University of Washington

Mayo Clinic

University of California Davis

Jackson Labs

Amazon Teranode

Institute for Systems Biology

University of Wisconsin

Children’s Hospital of Oakland Institute

Research ------ Softw

are

>20 research scientists with PhDs/MDs.

537 peer-reviewed scientific publications.

385 combined years of biomedical research experience in academia and industry.

7 software engineers.

90 years of industry experience: Deployment of professional software applications to over 100 million users.

5,000 node in-house supercomputer cluster, and tight integration with cloud-compute vendors.

Columbia University

What is Sage Bionetworks? - People

B&M Gates Foundation

Ambryx

What is Sage Bionetworks? - Partners

Pharma & IT

Funders & Nonprofits

Research Partners

Synapse

WELCOME TO SYNAPSESynapse is an online community built for a new biology... more open, more collaborative, more data-driven, and more reproducible.

SEARCH

Development UpdateSynapse is currently in Alpha development. This prototype has been developed todemonstrate our vision for the technology and solicit feedback from the community.The ability to create accounts and download Sage-hosted data is operational now.Some of the other functionality of the site is still under development. CREATE AN ACCOUNT

Call for ALPHA USERSAre you interested in working with Sage to start a pilot project on Synapse? Please letus know at synapseInfo@sagebase.org

START A PROJECT

Projects in theSpotlightProject spotlight description...

FEDERATION AGINGPROJECTThe Federation Aging project isexploring the large effect of age onhuman gene expression byexploring a set of genes whoseexpression levels are tightlyassociated with age.

SAGEBIOCURATIONThe Sage Bio Curation project is anumbrella for all Sage Bionetworks-curated projects.

START YOUR OWNPROJECT!Get started using Synapse today bycreating your own Project.

New Normalization Analysis12-Apr-2011: A new analysis method for

normalizing data was published by Brig

Mecham.

Schadt's New Diabetes Model08-Apr-2011: Eric Schadt and colleagues

have published an article on a new model for

diabetes.

Synapse NewsWhat's happening on Synapse

Charles Sawyers et al, MSKCCDNA copy number, mRNA expression profiles, candidate gene resequencing, and

clinical traits from 218 prostate tumors.

Amanda Myers, University of MiamiGenotypes, mRNA expression profiles, and clinical traits from 176 Alzheimer

disease and 188 non-diseased brain samples.

Beatriz Carvalho & Gerrit Meijer, VUMCDNA copy number, mRNA expression, and tumor traits from 36 colorectal

adenocarcinoma and 33 adenoma tumors.

Top Synapse ContributorsSynapse users who are actively contributing data

See all contributors...

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1100 Fairview Ave N

Seattle, WA 98109

synapseInfo@sagebase.org

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•  Open computational resource offering network models of disease and the underlying datasets and algorithms used to construct them.

•  Synapse integrates a data and network repository, the IT infrastructure in which the data are housed and the tools that allow manipulation and analysis.

•  Synapse is an innovation space where researchers can compute and collaborate on genomic datasets, use tools to build models of human disease, and modify those built by others.

•  Contributors are active participants that build collective content in effect ‘crowdsourcing’ the evolution of disease models creating an accelerated mechanism for the dissemination of knowledge.

“WE CONSENT” Portable Legal Consents

Compliant and standardized tool for engaging with and empowering citizens and patients

16

Clinical Trial Comparator Arm Partnership (CTCAP)

  Description: Collate, Annotate, Curate and Host Clinical Trial Data with Genomic Information from the Comparator Arms of Industry and Foundation Sponsored Clinical Trials: Building a Site for Sharing Data and Models to evolve better Disease Maps.

  Public-Private Partnership of leading pharmaceutical companies, clinical trial groups and researchers.

  Neutral Conveners: Sage Bionetworks and Genetic Alliance [nonprofits].

  Initiative to share existing trial data (molecular and clinical) from non-proprietary comparator and placebo arms to create powerful new tool for drug development.

Started Sept 2010

Andrea Califano Columbia U. Columbia U.

Eric Schadt Mount Sinai

Gary Nolan Stanford

Trey Ideker UCSD

Stephen Friend Sage Bionetworks

Stephen Friend

The Federation Experiment

Lessons

•  Building transformative technology is (relatively) easy

•  Transforming people is hard

Why is it so hard to share data?

Traitwise Survey Congress Participants

Biomedical research lives in a cottage industry tradition

Academic researchers live in a complex professional ecosystem

“Secrecy is a !Public Health Problem”!

“If you move the food bowl the cats will follow”!

-Sharon Terry!

Sage Bionetworks www.sagebase.org @SageBio