Precision Medicine: Precision Medicine: a revolution in research, health and a revolution in research, health and health care driven by informatics health care driven by informatics

Keith YamamotoKeith Yamamotokeith.yamamoto@ucsf.edukeith.yamamoto@ucsf.edu

UCSF Informatics DayUCSF Informatics DayJune 10, 2014June 10, 2014

Biomedical & clininal research at an inflection pointBiomedical & clininal research at an inflection point

datadata collection, collection, detailed detailed description, description, “imprecise medicine”“imprecise medicine”

mechanistic mechanistic understandingunderstanding of of biological processes, biological processes, precision precision medicinemedicine

How move through the inflection point? How move through the inflection point?

• Merge sciences: Merge sciences: incorporate concepts and technologies of incorporate concepts and technologies of physical sciences, engineering, computer science, informatics physical sciences, engineering, computer science, informatics

• Build working continuum: Build working continuum: from fundamental discovery, to from fundamental discovery, to application, to addressing health and diseaseapplication, to addressing health and disease

Integrate practices and policies across three planesIntegrate practices and policies across three planes

computationcomputation

governmentgovernment

industry

industry

ngongo

academiaacademia

clinicalclinical engineeringengineeringchemistrychemistry

physicsphysicsBiomedical continuum:Biomedical continuum:Build seamless links between Build seamless links between basic discovery, translation, basic discovery, translation, clinical care, patients, citizensclinical care, patients, citizens

Transdisciplinary science:Transdisciplinary science:Merge Merge physics/chemistry/engineering/cphysics/chemistry/engineering/computationomputationtheory, concepts, methods into theory, concepts, methods into biomedical researchbiomedical research

Stakeholder synergy:Stakeholder synergy:Cooperate across Cooperate across .edu, .com, .gov and .org.edu, .com, .gov and .org

Goal: Precision MedicineGoal: Precision Medicine

Imprecise Medicine: Where we are nowImprecise Medicine: Where we are now

What is a disease gene? If I have one, why does it only change What is a disease gene? If I have one, why does it only change the the “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 other How 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 from as a deviation from healthhealth, is similarly complex. , is similarly complex. We need an integrated understanding of mechanisms.We need an integrated understanding of mechanisms.

Precision Medicine: Defined and ComparedPrecision Medicine: Defined and Compared

Personalized medicine:Personalized medicine:Collect and analyze extensive information and data about Collect and analyze extensive information and data about patient, EHR to genome and beyond; physician uses this patient, EHR to genome and beyond; physician uses this information and data to make more informed diagnosis and information and data to make more informed diagnosis and treatment plan treatment plan

Current medical practice:Current medical practice:Use vital signs today relative to last visit (EHR?); assess Use vital signs today relative to last visit (EHR?); assess symptoms; physician uses expert background, experience and symptoms; physician uses expert background, experience and judgment to diagnose, prescribejudgment to diagnose, prescribe

Precision medicine:Precision medicine:Use massive data network that aggregates and analyzes Use 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 disease experimental organisms– and reaches toward disease mechanisms, and precision diagnosis and treatment for each mechanisms, and precision diagnosis and treatment for each individualindividual

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 precise promote the development of a more accurate and precise

classification of disease classification 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 an Build an “Information Commons” “Information Commons” and “Knowledge Network” to and “Knowledge Network” to correlate and align disparate correlate and align disparate information, motivate research information, motivate research team-building, convene all team-building, convene all stakeholders, including patients, stakeholders, including patients, into a dynamic research into 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

Geographical Information Systems anda biomedical information commons

EHREHR

Population studiesPopulation studies

New DiagnosesNew DiagnosesNew Therapy ImplicationsNew Therapy Implications

New Health OutcomesNew Health Outcomes

New CorrelationsNew CorrelationsNew HypothesesNew Hypotheses

New Transdisciplinary LinksNew Transdisciplinary Links

Knowledge Knowledge NetworkNetwork

Basic Basic DiscoveryDiscovery

Clinical Clinical DiscoveryDiscovery

Computational Computational Health ScienceHealth Science Digital HealthDigital Health

Omic Omic MedicineMedicine

Information Information CommonsCommons

Patients & Patients & CitizensCitizens

New knowledge New knowledge

UCSF Precision MedicineUCSF Precision Medicine

Platform & Platform & Outreach CoreOutreach Core

• 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

• 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  

•A research ecosystem that informs, integrates A research ecosystem that informs, integrates basic, clinical, population data, and includes basic, clinical, population data, and includes

all all 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 biosciences Five 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 led UCLA, Stanford and UC San Diego. Just as California led the way with stem cell research, so too can we pioneer the 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 to medical 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