This document summarizes Brian Bot's presentation on biomedical research in an increasingly digital world. It discusses how biomedical data is increasingly being produced, aggregated, and shared digitally. Only a small percentage of studies can be fully reproduced due to issues with data availability and documentation. However, organizations like Sage Bionetworks are working to promote open sharing of complex biological data through diverse collaborations and by empowering citizens to contribute their own health data to research. One example is the mPower study on Parkinson's disease which has involved thousands of participants sharing passive and active data through mobile apps.

1. 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

2. biomedical research in an increasingly digital world

3. biomedical research in an increasingly digital world
production

4. biomedical research in an increasingly digital world
distribution

5. biomedical research in an increasingly digital world
aggregation

6. biomedical research in an increasingly digital world

7. biomedical research in an increasingly digital world

8. biomedical research in an increasingly digital world

9. biomedical research in an increasingly digital world

10. biomedical research in an increasingly digital world

11. 6%
21%
8%
11%
54%
cannot
reproduce
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

12. “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

13. sage bionetworks

14. sage bionetworks
promote open systems, incentives, and norms
to redefine how complex biological data is
gathered, shared, and used
our approach

15. sage bionetworks
engage diverse communities of researchers
around biological and analytical problems
too complex for a single institution
our focus
empower citizens to track their own health
and contribute deep phenotypic data to
research topics important to them

16. CRC Subtyping Consortium
DREAM Challenges
Progenitor Cell Biology Consortium
TCGA Pan-Cancer Consortium
CommonMind Consortium
PsychENCODE
Accelerating Medicines Partnership
Resilience Project
M2OVE-AD Consortium
Dengue Fever
LINCS project
Oncology Molecular Classifiers
Next Gen Scientific Publishing
Mozilla Science Labs
sage bionetworks

17. public / private partnership between NIH,
10 biopharmaceutical companies
and several non-profit organizations
Accelerating Medicines Partnership

18. ($ Millions)
Total
Project
Total NIH
Total
Industry
Alzheimer’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
Accelerating Medicines Partnership

19. 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-phase
target identification insights
Accelerating Medicines Partnership

20. 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
Accelerating Medicines Partnership

21. CRC Subtyping Consortium
DREAM Challenges
Progenitor Cell Biology Consortium
TCGA Pan-Cancer Consortium
CommonMind Consortium
PsychENCODE
Accelerating Medicines Partnership
Resilience Project
Dengue Fever
LINCS project
Oncology Molecular Classifiers
Next Gen Scientific Publishing
Mozilla Science Labs
sage bionetworks
M2OVE-AD Consortium

22. analysis of:
12 tumor types
6 molecular profiling platforms
TCGA Pan-Cancer Consortium

23. 18NPG papers
68core projects
248researchers
28institutions
1070datasets
1723results
TCGA Pan-Cancer Consortium

24. TCGA Pan-Cancer Consortium

25. CRC Subtyping Consortium
DREAM Challenges
Progenitor Cell Biology Consortium
TCGA Pan-Cancer Consortium
CommonMind Consortium
PsychENCODE
Accelerating Medicines Partnership
Resilience Project
Dengue Fever
LINCS project
Oncology Molecular Classifiers
Next Gen Scientific Publishing
Mozilla Science Labs
sage bionetworks
M2OVE-AD Consortium

26. CRC Subtyping Consortium

27. A
B
C
D
E
F
1
2
3
4
5
6
expert team data subtype
CRC Subtyping Consortium

28. A
B
C
D
E
F
1
2
3
4
5
6
...
expert team data subtype
CRC Subtyping Consortium

29. CRC Subtyping Consortium

30. doi:10.1038/nm.3967 doi:10.7303/syn2623706
CRC Subtyping Consortium

31. sage bionetworks
engage diverse communities of researchers
around biological and analytical problems
too complex for a single institution
our focus
empower citizens to track their own health
and contribute deep phenotypic data to
research topics important to them

32. Healthmobile

33. Healthm

34. insular health trackingmove beyond

35. nearly 200 million smart phone users in US
insular health trackingmove beyond

36. insular health trackingmove beyond
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

38. >75%

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

41. 2013 september

42. 2015 march

44. the hype cycle

45. the hype cyclelaunching

47. participant-centered consent

48. changeable by participant

49. ~75k participants across all studies
>70% opted to share broadly

50. 50
mPower

51. 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

52. motor
initiation
gait/balance hypophonia memory
mPower activities

53. x
y
z
userAcceleration
gravity
rotationRate
attitude
device motion readings at 100 hz
gait / balance

54. gait / balance

55. Monty Python's The Flying Circus
gait / balance

59. 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

60. 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

61. mHealth research communityParkinson

62. mHealth research communityParkinson

63. 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
mHealth research communityParkinson

64. mHealth research communityParkinson

65. mHealth research communityParkinson

66. mHealth research communityParkinson

67. mHealth research communityParkinson

68. promote an ecosystem where
research is conducted
for others to consume

69. promote an ecosystem where
research is conducted
for 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.

70. promote an ecosystem where
research is conducted
for others to consume
…
…
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

71. promote an ecosystem where
research is conducted
for others to consume
…
…
research parasites
…
…

72. promote an ecosystem where
research is conducted
for others to consume

73. mHealth research community

74. mHealth research community
Sage Bionetworks joins The Scripps Research Institute (TSRI) for
PMI Cohort Program via Participant Technology Center (PTC)
06 July 2016

75. mHealth research community
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

76. riding the
hype cycle
together

77. brian m. bot
————————
principal scientist
community manager
brian.bot@sagebase.org
@BrianMBot
thank you
sage bionetworks