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proteomicsncer

http://proteomics.cancer.gov. CPTC: Additional Highlights. Henry Rodriguez, PhD, MBA Director, CPTC. CPTC: Additional Highlights. Clinical Proteomic Technology Assessment for Cancer (CPTAC) Network (U24) FDA – development of prototype 510k

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proteomicsncer

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  1. http://proteomics.cancer.gov CPTC: Additional Highlights Henry Rodriguez, PhD, MBA Director, CPTC

  2. CPTC: Additional Highlights • Clinical Proteomic Technology Assessment for Cancer (CPTAC) Network (U24) • FDA – development of prototype 510k • Advanced Proteomic Platforms and Computational Sciences (R01, R21, R33): • Data analysis and sharing • Technology development • Reagents and Resources Core (IAA & contract): • High quality reagents (protein and antibody reagents) CPTAC (U24) R01, R21,R33 IAA, Contract

  3. CPTAC (U24): Working with FDA to Enable Bridge Technology • MOU - 2006 • Interagency Oncology Task Force workshop - 2008 • Goal: • Identify analytical validation needs for proteomic technologies in the context of intended use. • Multiplex mass spec (MRM) • Multiplex affinity array • Deliverables: • White paper • Two mock 510k pre-applications that serve as guidance documents to the proteomics community October 30, 2008 “There’s really no guidance for multiplex proteomic assays. ….There are unique issues when you start to do a multiple test in a single tube or platform.” Elizabeth Mansfield, Ph.D., Senior Policy Analyst, Office of In Vitro Diagnostic Devices, FDA

  4. R01: Data Analysis and Sharing(discovery-stage technologies) Existing Proteomic Pipelines Software developed at CPTC RAW files from LC-MS/MS Biomarker Candidate Analysis Biomarker Candidate Analysis Intensity-based differentiation ID-based differentiation Protein ID Peptide ID Data pre- processing MS Inspect Protein / Peptide Prophet MASCOT, Sequest, etc. Distiller, ReAdW www.massqc.com PICQuant PEPPeR fPEPPeR XAlign QSpec SASPECT QuasiProto VIBE-MS ScanSifter MAZIE ProteoWizard massQC NIST DirecTag HMMatch Myrimatch TagRecon IDPicker iProphet PepArML Scaffold PTM Assignment PepCyber Monstermod TRANCHE - DATA SHARING (caBIG silver compliance review) caGRID

  5. R01: Data Analysis and Sharing(verification-stage technologies) Existing Proteomic Pipelines Software developed at CPTC RAW files from LC-MS/MS MRM data analysis MRM experiment design Discovery-stage technologies • Total of 26 computational tools developed • (for discovery- & verification-stage technologies) • Community Data Sharing • (TRANCHE - caBIG silver compliance review) Discovery software ESP Skyline MaRiMba Myrmidon TRANCHE - DATA SHARING (caBIG silver compliance review) caGRID

  6. R21, R33: Technology Development(examples) Mass Spec Technology Biochip Technology • Evaluation of phosphopeptides to SH2-binding domains • Prototype • Public database of designing phosphopeptides to human SH2-binding domains • Sensitivity: >10-fold • Throughput: >10-fold • Dynamic range: improvement w/ 50% reduction in CV values Dr. Richard Smith, Pacific Northwest National Laboratory Dr. Xiaolian Gao, University of Houston

  7. IAA & Contract: Reagents & Resources NCI mAb Characterization Program • Reference Materials • Yeast lysate (SRM 3953) • Peptide mixture (SRM 3592) • Standards Kits • Discovery LC-MS/MS • Verification MRM • Labeled cancer-specific proteins – 120 proteins (and expression vectors) • 2.5 year • Highly-characterized mAbs(10 assay process) • SOP driven • 3 mAbs per antigen • >77 mAbs available • hybridomas • MTAs in dev. • 1 year • Resources • CPTAC data sets; SOPs; Software tools; Best practice/FDA documents

  8. CPTC: Program-Wide Highlights • Data release • Strategic alliance with scientific organizations • Leveraged activities

  9. Data Release May 2009 • International Summit on Proteomics Data Release and Sharing Policy (Aug. 2008) • Key Participants: NCI, NHGRI, NCBI, DOE, Wellcome Trust, European Commission, Genome Canada, major journals • Foundation upon which guidelines can be developed on sharing proteomics research data • Latest updates: • Toronto Data Release workshop (May 2009) • Journal of Molecular & Cellular Proteomics editorial board meeting (June 2009) • Scientific American magazine (June 2009) • J. Proteome Res. follow-up (July 2009) Amsterdam Principles Recommendations from the 2008 International Summit on Proteomics Data Release and Sharing Policy: The Amsterdam Principles Rodriguez, H., J. Proteome Res., Articles ASAP (As Soon As Publishable)

  10. Strategic Alliance with Scientific Organizations American Association for Cancer Research 2009: Educational workshop at annual meeting 2010: Symposium session in planning American Association for Clinical Chemistry American Society for Mass Spectrometry 2008: - Plenary talks 2009: - Clinical article - Plenary talk - Joint workshop 2010: - CLN special issue (edited by Anderson, Carr, Hortin) - Workshops - MOU 2008: Methods workshop 2009: Plenary session Korean Functional Proteomics Center Human Proteome Organization 2007, 2008: - Plenary session 2009: - Software adoption (CPAS) - MRM adoption - MOU • 2006, 2007, 2008, 2009 • CPTAC workshops

  11. Leveraged Activities • Foundations supporting CPTAC investigators • Entertainment Industry Foundation (Pfizer, TGen), Canary Foundation, Stand Up To Cancer • NIH institutional centers taping CPTAC centers (NHLBI) • OBBR – biospecimen research network • Commercialization of products • New Institute: Center For Analytical Instrumentation Development (CIAD) • Multiple SBIR topics (bundling reagents)

  12. CPTC – Connecting the Global Proteomics Community ProteomeBinders (United Kingdom) University of Victoria Proteomics Center (Canada) Wellcome Trust & European Bioinformatics Institute (United Kingdom) Genome Canada (Canada) Human Protein Atlas (Sweden) Ontario Cancer Biomarker Network (Canada) Functional Proteomics Center (South Korea) The IMAGE Consortium (Germany) NCI/NIH* Atomic Energy Commission, Division of Life Sciences (France) “…. significant challenges to the translation of proteomic discoveries into clinical applications. The best way forward is through highly collaborative and integrated consortia of expert proteomic groups such as those formed through the NCI’s CPTAC program.” Gabriel N. Hortobagyi, M.D., Professor of Medicine; Nellie B. Connally Chair in Breast Cancer ; Chairman, Department of Breast Medical Oncology , The University of Texas M D. Anderson Cancer Center Monash University (Australia)

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