UCSF Informatics Day 2014 - Keith R. Yamamoto, "Precision Medicine"

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Keith R. Yamamoto, PhD — Opening Remarks – Precision Medicine
Vice Chancellor for Research
Executive Vice Dean of the School of Medicine
Professor of Cellular and Molecular Pharmacology
UCSF

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  • Please read:a personal appeal fromWikipedia founder Jimmy Wales
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  • MULTI LAYERED AND INDIVIDUAL CENTRIC 
    Figure 1-2: The proposed, individual-centric Information Commons (right panel) is somewhat analogous to a layered Geographical Information System (left panel). In both cases, the bottom layer defines the organization of all the overlays. However, in a GIS, any vertical line through the layers connects related snippets of information since all the layers are organized by geographical position. In contrast, data in each of the higher layers of the Information Commons will overlay on the patient layer in complex ways (e.g., patients with similar microbiomes and symptoms may have very different genome sequences). Source: FPA 2011 (left panel)
    Many parameters, dynamic, flexible, integrated
    From researchers, clinicians, patients
  • UCSF Informatics Day 2014 - Keith R. Yamamoto, "Precision Medicine"

    1. 1. Precision Medicine:Precision Medicine: a revolution in research, health anda revolution in research, health and health care driven by informaticshealth care driven by informatics Keith YamamotoKeith Yamamoto keith.yamamoto@ucsf.edukeith.yamamoto@ucsf.edu UCSF Informatics DayUCSF Informatics Day June 10, 2014June 10, 2014
    2. 2. Biomedical & clininal research at an inflection pointBiomedical & clininal research at an inflection point datadata collection,collection, detaileddetailed description,description, “imprecise medicine”“imprecise medicine” mechanisticmechanistic understandingunderstanding ofof biological processes,biological processes, precisionprecision medicinemedicine How move through the inflection point?How move through the inflection point? • Merge sciences:Merge sciences: incorporate concepts and technologies ofincorporate concepts and technologies of physical sciences, engineering, computer science, informaticsphysical sciences, engineering, computer science, informatics • Build working continuum:Build working continuum: from fundamental discovery, tofrom fundamental discovery, to application, to addressing health and diseaseapplication, to addressing health and disease
    3. 3. Integrate practices and policies across three planesIntegrate practices and policies across three planes computation computation governmentgovernment industry industry ngo ngo academia academia clinicalclinical engineeringengineering chemistry chemistry physics physics Biomedical continuum:Biomedical continuum: Build seamless links betweenBuild seamless links between basic discovery, translation,basic discovery, translation, clinical care, patients, citizensclinical care, patients, citizens Transdisciplinary science:Transdisciplinary science: MergeMerge physics/chemistry/engineering/cphysics/chemistry/engineering/c omputationomputation theory, concepts, methods intotheory, concepts, methods into biomedical researchbiomedical research Stakeholder synergy:Stakeholder synergy: Cooperate acrossCooperate across .edu, .com, .gov and .org.edu, .com, .gov and .org Goal: Precision MedicineGoal: Precision Medicine
    4. 4. Imprecise Medicine: Where we are nowImprecise Medicine: Where we are now What is a disease gene? If I have one, why does it only changeWhat is a disease gene? If I have one, why does it only change thethe “risk”, sometimes by tiny amounts, that I will get the disease?“risk”, sometimes by tiny amounts, that I will get the disease? Why is disease diagnosis so far from an exact science?Why is disease diagnosis so far from an exact science? How could gathering more information about me, about otherHow could gathering more information about me, about other people, about mice, flies and yeast, make my health better?people, about mice, flies and yeast, make my health better? ““Normal” biology is complicated:Normal” biology is complicated: -- we don’t know mechanisms-- we don’t know mechanisms -- controlled by intersecting,-- controlled by intersecting, multistep signaling networksmultistep signaling networks -- highly context dependent, altered by many variables-- highly context dependent, altered by many variables Therefore,Therefore, diseasedisease,, as a deviation fromas a deviation from healthhealth, is similarly complex., is similarly complex. We need an integrated understanding of mechanisms.We need an integrated understanding of mechanisms.
    5. 5. Precision Medicine: Defined and ComparedPrecision Medicine: Defined and Compared Personalized medicine:Personalized medicine: Collect and analyze extensive information and data aboutCollect and analyze extensive information and data about patient, EHR to genome and beyond; physician uses thispatient, EHR to genome and beyond; physician uses this information and data to make more informed diagnosis andinformation and data to make more informed diagnosis and treatment plantreatment plan Current medical practice:Current medical practice: Use vital signs today relative to last visit (EHR?); assessUse vital signs today relative to last visit (EHR?); assess symptoms; physician uses expert background, experience andsymptoms; physician uses expert background, experience and judgment to diagnose, prescribejudgment to diagnose, prescribe Precision medicine:Precision medicine: Use massive data network that aggregates and analyzesUse massive data network that aggregates and analyzes information from huge patient cohorts, healthy populations,information from huge patient cohorts, healthy populations, experimental organisms– and reaches toward diseaseexperimental organisms– and reaches toward disease mechanisms, and precision diagnosis and treatment for eachmechanisms, and precision diagnosis and treatment for each individualindividual
    6. 6. Integrate rapidly expanding range and detail of biological,Integrate rapidly expanding range and detail of biological, clinical, behavioral and experiential information to:clinical, behavioral and experiential information to: • drive basic discovery with new syntheses and hypothesesdrive basic discovery with new syntheses and hypotheses • promote the development of a more accurate and precisepromote the development of a more accurate and precise classification of diseaseclassification of disease • advance speed and accuracy of diagnosis, therapy and cureadvance speed and accuracy of diagnosis, therapy and cure Building a research and health continuumBuilding a research and health continuum An enabling toolAn enabling tool Build anBuild an “Information Commons”“Information Commons” and “Knowledge Network” toand “Knowledge Network” to correlate and align disparatecorrelate and align disparate information, motivate researchinformation, motivate research team-building, convene allteam-building, convene all stakeholders, including patients,stakeholders, including patients, into a dynamic researchinto a dynamic research ecosystemecosystem TOWARD PRECISION MEDICINE   Board on Life SciencesBoard on Life Sciences   http://www.nap.edu/catalog.php?record_id=13284http://www.nap.edu/catalog.php?record_id=13284 Building a Knowledge Network for Biomedical Research and a New Taxonomy of Disease Precision MedicinePrecision Medicine
    7. 7. Geographical Information Systems and a biomedical information commons EHREHR Population studiesPopulation studies
    8. 8. New DiagnosesNew Diagnoses New Therapy ImplicationsNew Therapy Implications New Health OutcomesNew Health Outcomes New CorrelationsNew Correlations New HypothesesNew Hypotheses New Transdisciplinary LinksNew Transdisciplinary Links KnowledgeKnowledge NetworkNetwork BasicBasic DiscoveryDiscovery ClinicalClinical DiscoveryDiscovery ComputationalComputational Health ScienceHealth Science Digital HealthDigital Health OmicOmic MedicineMedicine InformationInformation CommonsCommons Patients &Patients & CitizensCitizens New knowledgeNew knowledge UCSF Precision MedicineUCSF Precision Medicine Platform &Platform & Outreach CoreOutreach Core
    9. 9. • Nucleate in neurological disease and cancer; rapid spread will encompass all areas • Build integrated, visualizable access to basic, translational, clinical, population data • Converge expertise and infrastructure resources of computer scientists, bioinformaticians, commercial partners, national lab, clinical and basic scientists UCSF Knowledge NetworkUCSF Knowledge Network
    10. 10. • Big dataBig data • Diverse data types:Diverse data types: e.g., -omics, imaging (e.g., cryoEM,e.g., -omics, imaging (e.g., cryoEM, brain activity, longitudinal MRI), EHR, population studies,brain activity, longitudinal MRI), EHR, population studies, environmental effectsenvironmental effects • Digital health:Digital health: wearable sensors, reporterswearable sensors, reporters • Data acquisition, aggregation, integration, analysisData acquisition, aggregation, integration, analysis • Continuous learningContinuous learning • Data storage, security, selective accessData storage, security, selective access • Data sorting and visualizationData sorting and visualization Computational/informatics challenges  Computational/informatics challenges  
    11. 11. •A research ecosystem that informs, integratesA research ecosystem that informs, integrates basic, clinical, population data, and includesbasic, clinical, population data, and includes allall stakeholder sectorsstakeholder sectors •Health and healthcare tailored to the individualHealth and healthcare tailored to the individual •Reduced healthcare costsReduced healthcare costs Precision medicine outcomesPrecision medicine outcomes Five of the world’s twenty leading academic biosciencesFive of the world’s twenty leading academic biosciences institutions are located here in California: UCSF, Berkeley,institutions are located here in California: UCSF, Berkeley, UCLA, Stanford and UC San Diego. Just as California ledUCLA, Stanford and UC San Diego. Just as California led the way with stem cell research, so too can we pioneerthe way with stem cell research, so too can we pioneer the new field of precision medicine which uses genomes,the new field of precision medicine which uses genomes, medical devices, computer sciences and other fields tomedical devices, computer sciences and other fields to treat individual patients instead of broad populations.treat individual patients instead of broad populations. California Gov Jerry BrownCalifornia Gov Jerry Brown 2014 State of the State Address2014 State of the State Address
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