20160811 Big Data for Health and Medicine

brian m. bot | principal scientist |

2016 aug 11

sage bionetworks

big data for health and medicine

biomedical research in an increasingly digital world

| @BrianMBot

university of nebraska at omaha



production


distribution


aggregation






6%

21%

8%

11%

54%cannotreproduce

can reproduce in principle

can reproduce w/discrepancies

can reproduce from processed data w/discrepancies

can reproduce partially

the status quo tolerates poor communication of findings

Ioannidis A. et al. Nature Genetics 2009

“Scientists often study the past as obsessively as historians because few

other professions depend so acutely on it. Every experiment is a conversation with

a prior experiment, every new theory a refutation of the old”

-Siddhartha Mukherjee, The Emperor of All Maladies

sage bionetworks

sage bionetworks

promote open systems, incentives, and norms to redefine how complex biological data is

gathered, shared, and used

our approach

sage bionetworks

engage diverse communities of researchersaround biological and analytical problems

too complex for a single institution

our focus

empower citizens to track their own healthand contribute deep phenotypic data to

research topics important to them

CRC Subtyping Consortium

DREAM ChallengesProgenitor Cell Biology Consortium

TCGA Pan-Cancer Consortium

CommonMind Consortium

PsychENCODE

Accelerating Medicines Partnership

Resilience Project

M2OVE-AD Consortium

Dengue FeverLINCS project

Oncology Molecular ClassifiersNext Gen Scientific Publishing

Mozilla Science Labs

sage bionetworks

public / private partnership between NIH, 10 biopharmaceutical companies

and several non-profit organizations


http://www.nytimes.com/2014/02/05/health/nih-joins-drug-makers-and-nonprofits-on-stubborn-diseases.html

($ Millions) Total Project Total NIH Total

IndustryAlzheimer’s

Disease 129.5 67.6 61.9

Type 2 Diabetes 58.4 30.4 28

Rheumatoid Arthritis 41.6 20.9 20.7

TOTAL 229.5 118.9 110.6


Target Discovery

Target Discovery

Target Discovery

Target Discovery

Target Validation

Target Validation

Target Validation

Target Validation

Shared Information for

Target Identification

coordinate sharing of early-phasetarget identification insights


AMP-AD Collaborative

Workspace

Quarterly Depositions

Broad/RUSH

Mt. Sinai

U Fl/ISB/Mayo

Emory

Sage

Other Partners

Individual Partner Workspaces AMP-AD Data Portal

Consortium Space

Public space

AMP-AD Synapse Project Structure






PsychENCODE


Resilience Project




sage bionetworks

M2OVE-AD Consortium

analysis of: 12 tumor types 6 molecular profiling platforms


18NPG papers

68core projects248

researchers

28institutions

1070datasets1723

results







PsychENCODE


Resilience Project




sage bionetworks

M2OVE-AD Consortium


A

B

C

D

E

F

1

2

3

4

5

6

expert team data subtype


A

B

C

D

E

F

1

2

3

4

5

6

...

expert team data subtype



doi:10.1038/nm.3967 doi:10.7303/syn2623706


sage bionetworks

engage diverse communities of researchersaround biological and analytical problems

too complex for a single institution

our focus

empower citizens to track their own healthand contribute deep phenotypic data to

research topics important to them

Healthmobile

Healthm

insular health trackingmove beyond

nearly 200 million smart phone users in US



Stephen Lam / Getty

Tech giants moving into health may widen inequalities and harm research, unless people can access and share their data, warn John T. Wilbanks and Eric J. Topol.

(but be careful)

20 july 2016

>75%

how to balance desire to share w/ importance of privacy?

2013 september

2015 march

the hype cycle

the hype cyclelaunching

participant-centered consent

changeable by participant

~75k participants across all studies

>70% opted to share broadly

50

mPower

passive measures

gps - displacement

vectors

gps - displacement

vectors- -

structured activities

tapping activity

walking/standing activity

voice activity memory game

surveys MDS-UPDRS PDQ8

MDS-UPDRS PDQ8

MDS-UPDRS PDQ8

MDS-UPDRS PDQ8

four symptoms of PD

motor initiation gait/balance hypophonia memory

motor initiation gait/balance hypophonia memory

mPower activities

x

yz

userAcceleration

gravity

rotationRate

attitude

device motion readings at 100 hz

gait / balance

gait / balance

Monty Python's The Flying Circus

gait / balance

mPower six month data release

9,520 unique participants

8,320 completed at least one task

198,639 total activities and surveys completed

1,087 self reported parkinson diagnosis

mPower six month data release

task name type of task and schedule

unique participants unique tasks

demographics survey - once 6,805 6,805

MDS-UPDRS survey - monthly 2,024 2,305

PDQ8 survey - monthly 1,334 1,641

memory activity - t.i.d. 968 8,569

tapping activity - t.i.d. 8,003 78,887

voice activity - t.i.d. 5,826 65,022

walking activity - t.i.d. 3,101 35,410

mHealth research communityParkinson


Parkinson’s Disease Foundation Eli Lilly AstraZeneca Apple Verily Intel Infocepts Posit Science

MIT The Ohio State University University of Otago University of Texas Health Science Center Istanbul Sehir University University of Iowa University of Virginia University of Toronto Johns Hopkins University Vanderbilt University University of Rochester McGill University Xi'an Jiaotong University University of Washington Harvard University






promote an ecosystem whereresearch is conductedfor others to consume


…A second concern held by some is that a

new class of research person will emerge — people who had nothing to do with the

design and execution of the study but use another group’s data for their own ends,

possibly stealing from the research productivity planned by the data gatherers, or even use the data to try to disprove what

the original investigators had posited.


……

There is concern among some front-line researchers that the system will

be taken over by what some researchers have characterized as

“research parasites”research parasites


……

research parasites……


mHealth research community


Sage Bionetworks joins The Scripps Research Institute (TSRI) for PMI Cohort Program via Participant Technology Center (PTC)

06 July 2016


Sage Bionetworks joins The Scripps Research Institute (TSRI) for PMI Cohort Program via Participant Technology Center (PTC)

In collaboration with Scripps Participant Technologies Center (PTC):

• Sage Bionetworks will be responsible for the patient consent and data governance, as well as the community outreach and participant engagement efforts of the PTC

• Sage Bionetworks will also be engaged in the scientific and engineering work to develop new methodologies for measuring symptoms of health and disease, including developing symptom measurements for phone, wearable, and other sensors

riding the hype cycle

together

brian m. bot———————— principal scientist community manager

[email protected] @BrianMBot

thank you

sage bionetworks

mailto:[email protected]