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Unlocking Our Treasures Enhancing Access to Tissue for Genomics Research Henry Chueh Massachusetts General Hospital Harvard Medical School Internet2 Member Meeting Austin, Texas September 30, 2004
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“ Be careful of reading health books. You may die of a misprint.” Mark Twain
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Genetic alphabet AT GC
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Mutations Image credit: U.S. Department of Energy Human Genome Program, http://www.ornl.gov/hgmis
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Molecular foundation of disease Image credit: U.S. Department of Energy Joint Genome Institute
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Epithelial Growth Factor Receptor Angiogenesis Metastasis EGFR Tyrosine Kinase Receptor Invasion Proliferation K K EGFR-TK Inhibitor Cell membrane Image credit: Modified from Astra-Zeneca educational materials
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Lynch, T. J. et al. N Engl J Med 2004;350:2129-2139 Clustering of Mutations in the EGFR Gene at Critical Sites within the ATP-Binding Pocket
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Genomics research Clinical research in the genomics era requires, at a minimum: Access to diseased and healthy tissue Clinical information associated with the tissue (demographics, outcomes, etc)
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Shared Pathology Information Network
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SPIN Collaborators National Cancer Institute (NCI) Children’s Hospital Massachusetts General Hospital Brigham and Women’s Hospital Dana-Farber Cancer Institute Beth Israel Hospital UCLA Medical Center Regenstrief Institute Univ. of Pittsburgh Medical Center
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SPIN Themes Think “framework” Specifications clear enough to develop products independently Local control Network planning
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SPIN: p2p Model Assumptions No ongoing aggregation of data, no central repository to govern Provision of data into a SPIN node from systems internal to the institution is managed locally with SPIN tools Any information search by any SPIN Query Tool is HIPAA Privacy Rule compliant
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SPIN Network Today MGHUCLA HMS CH BI BWH UPMC HMS Tissue Banks (other) OliveViewCedars RI SPIN VSL Running type A SPIN node software Running type B SPIN software Link established Link planned VA
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SPIN: Key Activities Join: Become a member of the network Host: Provision clinical, specimen data Search: Locate specimens Acquire: Obtain specimens
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SPIN Host / Search: Data Flow SPIN node De-identified Limited Data Set Institutional Firewall SPIN Query SPIN Response Anonymous or De-identified Data Set InternetIntranet SPIN ProtocolsSPIN Node Software Source Systems Identified Data SPIN Loading Tools Source Systems Clinical Systems Codebook Internal Threshold
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Clinical reports to coded annotations … Right colon Chronic colitis Active Mild …
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SPIN Query Propagation and Response MGHUCLA BI BWH Query Server SPIN CH SPIN XML request Compose query using a Web browser SPIN request propagates SPIN peer responses return directly to originating SuperNode UPMC RI Cedars SPIN (aggregate) XML Response
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Clinical Research Scenarios ? Rare subset of non-small cell lung cancer (NSCLC) shares common mutation that would make it more susceptible to certain novel therapeutics ? Infection with herpes zoster (chickenpox) virus enhances mutagenicity in lung cancer
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SPIN Open Architecture Accommodates alternative node and query server implementations Will accommodate additional data models and schema: Clinical data (symptoms, outcomes, etc) Clinical imaging data (MRI, CT scans, etc) Molecular biology data (microarray data, etc) Pathology imaging
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What’s ahead? Bringing phenotypes in juxtaposition with genotypic information NIH roadmap initiatives to include integrated biomedical computing In silico experiments and analysis
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Acknowledgements Jules Berman (NCI) Isaac Kohane Clem McDonald Jonathan Braun Michael Becich Ulysses Balis David Berkowicz David Korn (AAMC) Elias Zerhouni (NIH)
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Image credit: U.S. Department of Energy Human Genome Program, http://www.ornl.gov/hgmis
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