Jonathan Izant AAAS Annual Meeting 2012-02-18


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Jonathan Izant Feb 18, 2012 AAAS Annual Meeting Vancouver, BC

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Jonathan Izant AAAS Annual Meeting 2012-02-18

  1. 1. “Secrecy is a!Public Health Problem”! Jonathan G. Izant Sage Bionetworks @SageBio AAAS 18 February 2012
  2. 2. denial
  3. 3. 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
  4. 4. 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
  5. 5. genetic regulation circa 1970
  6. 6. Genetic networks
  7. 7. 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
  8. 8. Network biology collaborations involve multiplespecialized labs, big data, sophisticated methods andthe results are often published in open access journalsCollaboration -  Multiple labs; specialized; -  Biologists, clinicians, statisticians, engineers, etcTechnology - Sophisticated technologiesData -  >5x108 data pointsMethods -  Computationally intensive (5000 node cluster)Publish -  Open access journal -  18 figures, 19 tables -  Gigabytes of data
  9. 9. Catalytic nonprofit formed in 2009Vision: to create a “Commons” where integrative bionetworks are evolvedby contributor scientists with a sharedvision to accelerate the elimination of human disease
  10. 10. PrinciplesUnderstanding 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.
  11. 11. What is Sage Bionetworks? - People •  Stephen Friend, MD, PhD •  Jonathan Derry, PhD >20 research scientists with Rosetta •  Adam Margolin, PhD PhDs/MDs. •  Jonathan Izant, PhD Inpharmatics, •  Solly Sieberts, PhD •  Xia Yang, PhD 537 peer-reviewed scientific Merck & Co •  Eric Huang, MD PhD publications. •  Christine Suver, PhD University of Washington Research •  Thea Norman, PhD Duke University •  Zhi Wang, PhD 385 combined years of •  Chris Gaiteri, PhD biomedical research Broad Institute of MIT and Harvard •  Charles Ferte, MD PhD •  Elias Neto, PhD experience in academia and B&M Gates Foundation industry. •  Lara Mangravite, PhD Jackson Labs •  Justin Guinney, PhD •  Qingying Meng, PhD 7 software engineers. ------ University of California Davis •  Mette Peters, PhD University of Michigan •  Vitalina Komashko, PhD •  Brig Mecham, PhD 90 years of industry Ambryx •  Andrew Twister, MD PhD experience: Deployment of Software University of Pittsburgh •  Matt Furia professional software •  Brian Bot applications to over 100 Mayo Clinic •  In Sock Jang, PhD million users. University of Wisconsin • Mike Kellen, PhDChildren’s Hospital of Oakland Institute • Nicole Deflaux, PhD 5,000 node in-house • Bruce Hoff, PhD Columbia University supercomputer cluster, and • Dave Burdick • John Hill tight integration with cloud- Institute for Systems Biology • Xa Schildwachter compute vendors. Teranode • Brian Holt Amazon
  12. 12. What is Sage Bionetworks? - PartnersFunders &Nonprofits Pharma & ITResearchPartners
  13. 13. SynapseSage Synapse : Contribute to the Cure •  Open computational resource offering network models of disease and the underlying datasets REGISTER LOGIN and algorithms used to construct them. WELCOME TO SYNAPSE Synapse is an online community built for a new biology... more open, more collaborative, more data-driven, and more reproducible. •  Synapse integrates a data and network repository, the IT infrastructure in which the data are housed and the tools that allow manipulation Everything SEARCH Development Update Synapse is currently in Alpha development. This prototype has been developed to demonstrate our vision for the technology and solicit feedback from the community. The ability to create accounts and download Sage-hosted data is operational now. Call for ALPHA USERS Are you interested in working with Sage to start a pilot project on Synapse? Please let us know at and analysis. Some of the other functionality of the site is still under development. CREATE AN ACCOUNT Projects in the Spotlight FEDERATION AGING SAGEBIOCURATION START YOUR OWN •  Synapse is an innovation space where researchers can compute and collaborate on Project spotlight description... PROJECT PROJECT! The Sage Bio Curation project is an The Federation Aging project is umbrella for all Sage Bionetworks- Get started using Synapse today by exploring the large effect of age on curated projects. creating your own Project. START A PROJECT human gene expression by genomic datasets, use tools to build models of exploring a set of genes whose expression levels are tightly associated with age. Synapse News Top Synapse Contributors human disease, and modify those built by others. Whats happening on Synapse Synapse users who are actively contributing data New Normalization Analysis Charles Sawyers et al, MSKCC •  Contributors are active participants that build 12-Apr-2011: A new analysis method for Schadts New Diabetes Model DNA copy number, mRNA expression profiles, candidate gene resequencing, and normalizing data was published by Brig 08-Apr-2011: Eric Schadt and colleagues clinical traits from 218 prostate tumors. Mecham. have published an article on a new model for diabetes. Amanda Myers, University of Miami collective content in effect ‘crowdsourcing’ the Genotypes, mRNA expression profiles, and clinical traits from 176 Alzheimer disease and 188 non-diseased brain samples. Beatriz Carvalho & Gerrit Meijer, VUMC evolution of disease models creating an DNA copy number, mRNA expression, and tumor traits from 36 colorectal adenocarcinoma and 33 adenoma tumors. See all contributors... WITH SUPPORT FOLLOW CONTACT INFO accelerated mechanism for the dissemination of knowledge. FROM US ON Sage Bionetworks 1100 Fairview Ave N Seattle, WA 98109 Copyright 2011 Sage Bionetworks Home / Privacy Policy / Platform support / Creative Commons License / FAQ / Submit feedback1 of 1 2/16/12 1:26 PM
  14. 14. “WE CONSENT” Portable Legal ConsentsCompliant and standardized tool for engaging with and empowering citizens and patients
  15. 15. 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 16
  16. 16. The Federation Experiment Stephen Friend Sage Bionetworks Andrea Califano Columbia U.Gary Nolan Eric Schadt Stanford Mount Sinai Trey Ideker UCSD
  17. 17. Lessons •  Building transformative technology is (relatively) easy •  Transforming people is hard
  18. 18. Why is it so hard to share data?
  19. 19. Traitwise Survey Congress Participants
  20. 20. Biomedical research lives in a cottageindustry tradition
  21. 21. Academic researchers live in a complexprofessional ecosystem
  22. 22. “Secrecy is a!Public Health Problem”!
  23. 23. “If you move the food bowl the cats will follow”! -Sharon Terry! Sage Bionetworks @SageBio