Appendixes



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The Genomic Revolution: Implications for Treatment and Control of Infectious Disease - Working Group Summaries Appendixes

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The Genomic Revolution: Implications for Treatment and Control of Infectious Disease - Working Group Summaries This page intentionally left blank.

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The Genomic Revolution: Implications for Treatment and Control of Infectious Disease - Working Group Summaries The 3rd Annual National Academies Keck Futures Initiative Conference The Genomic Revolution: Implications for Treatment and Control of Infectious Disease Arnold and Mabel Beckman Center, Irvine, California November 10-13, 2005 AGENDA Wednesday, November 9 (Hyatt Regency Newport Beach) 6:00–10:00 p.m. Welcome Reception / Registration – Garden Room 1 & Garden Thursday, November 10 (Arnold and Mabel Beckman Center of the National Academies) 7:45 and 8:15 a.m. Bus pick-up from the Hyatt Regency Newport Beach to the Beckman Center 8:00 a.m. Registration (Outside Auditorium) 8:00–9:00 a.m. Breakfast (Dining Room) 9:00–9:30 a.m. Welcome and Opening Remarks (Auditorium) Wm. A. Wulf, President, National Academy of Engineering Harvey V. Fineberg, President, Institute of Medicine Richard N. Foster, Board Member, W.M. Keck Foundation Robert Waterston, Chair, Genomics Steering Committee

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The Genomic Revolution: Implications for Treatment and Control of Infectious Disease - Working Group Summaries 9:30–10:30 a.m. Overview “Tutorial” Sessions   Genomics, Structural Biology, and Rational Vaccine Design Gary J. Nabel Director of the Vaccine Research Center National Institute of Allergy and Infectious Diseases National Institutes of Health   Diversity of Human Microbial Pathogens and Commensals / Host-Pathogen Interaction (Part I) David Relman Associate Professor of Microbiology & Immunology and of Medicine Stanford University Chief, Infectious Diseases Section Veterans Administration Palo Alto Health Care System   Question and Answer section for these two presentations will take place at 11:30 10:30–11:00 a.m. Break (Atrium) 11:00 a.m. – 12:15 p.m. Overview “Tutorial” Sessions / Q&A   Diversity of Human Microbial Pathogens and Commensals / Host-Pathogen Interaction (Part II) David Relman   11:30–12:15 Q&A – Gary Nabel, David Relman, and Claire Fraser 12:15–1:30 p.m. Lunch (Dining Room)

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The Genomic Revolution: Implications for Treatment and Control of Infectious Disease - Working Group Summaries 1:30–3:00 p.m. Overview “Tutorial” Sessions / Q&A   Team Science Mary E. Lidstrom Vice Provost of Research Professor in Chemical Engineering and Microbiology Frank Jungers Chair of Engineering University of Washington   Team Science: The Microscale Life Sciences Center (MLSC) Deirdre Meldrum Director, NIH CEGS Microscale Life Sciences Center and the UW Genomation Laboratory Professor of Electrical Engineering University of Washington   2:30–3:00 Q&A 3:00–3:30 p.m. Task to Working Group 3:30–4:00 p.m. Break (Atrium / Palm Court 2 / Bay View 2) 4:00–6:00 p.m. Working Group Session 1 (Locations throughout Beckman Center)   2. Technology to improve rapid response. Bay View II – 2nd floor   3. Develop an inexpensive diagnostic test. Laguna – 2nd floor   5. Spend $100 million to prevent the next pandemic flu. Emerald Bay – 2nd floor   6. Can genomics facilitate vaccine development? Irvine Cove – 2nd floor   9. Develop a device to detect and identify pathogens. Board Room – 1st floor

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The Genomic Revolution: Implications for Treatment and Control of Infectious Disease - Working Group Summaries   10. Shared pathways of attack for prevention. Harbour – 2nd floor   11-1. Role of public health in integrating genomics. Balboa – 1st floor   11-2. Role of public health in integrating genomics. Newport – 1st floor   12. Sequence an individual’s genome for under $1,000. Crystal Cove – 1st floor   14-1. Natural variation in disease resistance. Lido – 2nd floor   14-2. Natural variation in disease resistance. Back Bay – 2nd floor 6:00–7:00 p.m. Reception / Networking 7:00–9:00 p.m. Dinner and Communication Awards Presentation (Atrium) 9:00 p.m. Buses depart Beckman Center for Hyatt Regency Newport Beach 9:00–11:00 p.m. Informal Discussions / Hospitality Room Hyatt Regency Newport Beach – Garden Room 1 and Garden Friday, November 11 (Beckman Center) 7:15 and 7:45 a.m. Bus pick-up from the Hyatt Regency Newport Beach to the Beckman Center 7:30–8:30 a.m. Breakfast (Dining Room) 8:30–10:45 a.m. Overview “Tutorial” Sessions / Q&A (Auditorium)

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The Genomic Revolution: Implications for Treatment and Control of Infectious Disease - Working Group Summaries   Some Roles of Computation in Molecular Biology Michael Waterman University Professor Professor of Biological Sciences, Mathematics, and Computer Science University of Southern California   Human Genetic Variation Leonid Kruglyak Professor of Ecology and Evolutionary Biology and the Lewis-Sigler Institute for Integrative Genomics Princeton University   Dual Meaning of Dual Use Robert Cook-Deegan Director, Center for Genome Ethics, Law, and Policy Institute for Genome Sciences and Policy Duke University   10:00–10:45 Q&A 10:45–11:15 a.m. Break (Atrium) / Friday Poster Set-up 11:15 a.m. – 12:45 p.m. Overview “Tutorial” Sessions / Q&A   Issues from Developing Countries: What are their needs? What are their unique delivery and implementation issues (access, cost, power requirements, transportability, etc.)? Austin Demby Senior Staff Fellow Global AIDS Program Centers for Disease Control and Prevention

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The Genomic Revolution: Implications for Treatment and Control of Infectious Disease - Working Group Summaries   Genetic Analysis of Innate Immune Sensing Bruce Beutler Professor Department of Immunology Scripps Research Institute   12:15–12:45 Q&A 12:45–2:00 p.m. Lunch (Friday session posters available for previewing) 2:00–3:45 p.m. Working Group Session 2 (Same meeting places as session 1) (3:00–3:45—Coffee and refreshments will be available in the Atrium, Palm Court 2, and Bay View 2) 3:45–5:00 p.m. Working Group Report Outs (Each group gives a 5 minute debrief) (Aud.) 5:00–6:30 p.m. Friday Poster Session   5:00–5:45 p.m. Odd numbered posters are attended   5:45–6:30 p.m. Even numbered posters are attended   (Refreshments will be served Atrium) 6:30 p.m. Buses depart Beckman Center for Hyatt Regency Newport Beach 7:00–9:00 p.m. Buffet Dinner – Hyatt Regency Newport Beach – Terrace Room 9:00–11:00 p.m. Informal Discussions / Hospitality Room Hyatt Regency Newport Beach – Garden Room 1 and Garden

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The Genomic Revolution: Implications for Treatment and Control of Infectious Disease - Working Group Summaries Saturday, November 12 (Beckman Center) 7:45 and 8:15 a.m. Bus pick-up from the Hyatt Regency Newport Beach to the Beckman Center 8:00–9:00 a.m. Breakfast (Dining Room) 9:00–10:30 a.m. Overview “Tutorial” Sessions / Q&A (Auditorium)   Human Genome Sequencing at $5,000 a Pop Robert H. Waterston Head, Department of Genome Sciences William H. Gates III Chair of Biomedical Sciences University of Washington School of Medicine   Microsystems Todd Thorsen Assistant Professor of Mechanical Engineering Massachusetts Institute of Technology   10:00–10:30 Q&A 10:30–11:00 a.m. Break (Atrium) / Saturday Poster Set-up 11:00 a.m. – 1:00 p.m. Working Group Session 3 (Same meeting places as session 1) 1:00–2:00 p.m. Lunch (Saturday session posters available for previewing) 2:00–3:30 p.m. Saturday Poster Session   2:00–2:45 p.m. Odd numbered posters are attended   2:45–3:30 p.m. Even numbered posters are attended   (3:00–4:00—Coffee and refreshments will be available in the Huntington Room, Palm Court 2, and Bay View 2)

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The Genomic Revolution: Implications for Treatment and Control of Infectious Disease - Working Group Summaries 3:30–5:30 p.m. Working Group Session 4 (Same meeting places as session 1) 5:30–6:30 p.m. Networking / Reception 6:30 - 8:00 p.m. Dinner (Atrium) 8:00 p.m. Buses depart Beckman Center for Hyatt Regency Newport Beach 9:00–11:00 p.m. Informal Discussions / Hospitality Room Hyatt Regency Newport Beach – Garden Room 1 and Garden Sunday, November 13 (Beckman Center) 7:15 and 7:45 a.m. Bus pick-up from the Hyatt Regency Newport Beach to the Beckman Center 7:30–8:30 a.m. Breakfast (Dining Room) 8:30–10:15 a.m. Working Group Report-Outs (Auditorium) (15 minutes per group) 10:15–10:45 a.m. Break (Atrium) 10:45 a.m. – 12:00 p.m. Working Group Report-Outs – continued (Auditorium) 12:00–1:00 p.m. Lunch 12:00 and 1:00 p.m. Buses depart for Hyatt Regency Newport Beach and John Wayne Airport

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The Genomic Revolution: Implications for Treatment and Control of Infectious Disease - Working Group Summaries THE GENOMIC REVOLUTION: IMPLICATIONS FOR TREATMENT AND CONTROL OF INFECTIOUS DISEASE WORKING GROUP TOPICS TECHNOLOGY Design a point-of-care diagnostics for rapid detection of viral and bacterial pathogens. (not running) Identify what technological advances in the fields of science and engineering need to be developed (either new technology or novel integration of existing technologies) to improve rapid response to new or emerging diseases? For example, can carefully reengineered viruses or bacteria become the next generation of therapeutic agents? How can computational biology better integrate the vast amounts of genomic knowledge to assist these efforts? Develop an inexpensive (and cost-effective) diagnostic test (infection, genotype) that could be deployed in countries with little scientific research infrastructure. How can nanotechnology and new rapid diagnostic methods for other targets be adapted to diagnose malaria species, drug-resistance mutations, and vaccine-resistance polymorphisms in malaria-endemic countries? Can genetically modified organisms be used to control disease? (not running) VACCINES / GENOMIC ANALYSIS AND SYNTHESIS How would you spend $100 million over the next five years to prevent the next pandemic flu? What would be the research strategy to utilize fully the genomic sequences of the hosts and pathogens to accelerate the development of therapeutics and vaccines for its prevention and control? How can genomics facilitate vaccine development? Would efficient methods of synthesis of genomes help? Can genomics help to improve the assessment of efficacy of vaccines? What are the safety concerns?

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The Genomic Revolution: Implications for Treatment and Control of Infectious Disease - Working Group Summaries How can genomic analysis of immune evasion strategies facilitate vaccination against HIV? (not running) How can genomic analysis of immune evasion strategies facilitate vaccination against malaria? (not running) DIAGNOSIS Develop a device to rapidly and sensitively detect and identify pathogens in an environment/population, spread either naturally or through deliberate acts. Can genomics help differentiate between natural and deliberate disease outbreak and provide evidence for attribution? Do we know what defines—both genotypically and phenotypically—a pathogen vs. a nonpathogenic invader? If not, how can we determine this? Are there shared pathways of attack that might provide new avenues of prevention? How can we find them? Once identified, what methods can be developed to stop them? Explore the emerging role of public health in integrating genomics in surveillance, outbreak investigations, and control and prevention of infectious diseases. (two sections will be running due to high interest in this topic) NATURAL VARIATION What will it take to sequence an individual person’s genome for under $1,000 in ten years? Can evolutionary models of the emergence of resistance in a pathogen combined with combinatorial treatment schemes be used to develop a strategy to hold the pathogen in check? (not running) How can we use natural variation in disease resistance to understand host-pathogen interactions and devise new therapies? (two sections will be running due to high interest in this topic)