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
UCSF Informatics Day 2014 - Keith R. Yamamoto, "Precision Medicine"
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. 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. 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. 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. 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. 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
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. • 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. • 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. •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
Hinweis der Redaktion
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