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20160811 Big Data for Health and Medicine

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20160811 Big Data for Health and Medicine

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Talk at the Midwest Big Data Hub: biomedical research in an increasingly digital world.

Talk at the Midwest Big Data Hub: biomedical research in an increasingly digital world.

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20160811 Big Data for Health and Medicine

  1. 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. 2. biomedical research in an increasingly digital world
  3. 3. biomedical research in an increasingly digital world production
  4. 4. biomedical research in an increasingly digital world distribution
  5. 5. biomedical research in an increasingly digital world aggregation
  6. 6. biomedical research in an increasingly digital world
  7. 7. biomedical research in an increasingly digital world
  8. 8. biomedical research in an increasingly digital world
  9. 9. biomedical research in an increasingly digital world
  10. 10. biomedical research in an increasingly digital world
  11. 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. 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. 13. sage bionetworks
  14. 14. sage bionetworks promote open systems, incentives, and norms to redefine how complex biological data is gathered, shared, and used our approach
  15. 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. 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. 17. public / private partnership between NIH, 10 biopharmaceutical companies and several non-profit organizations Accelerating Medicines Partnership
  18. 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. 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. 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. 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. 22. analysis of: 12 tumor types 6 molecular profiling platforms TCGA Pan-Cancer Consortium
  23. 23. 18NPG papers 68core projects 248researchers 28institutions 1070datasets 1723results TCGA Pan-Cancer Consortium
  24. 24. TCGA Pan-Cancer Consortium
  25. 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. 26. CRC Subtyping Consortium
  27. 27. A B C D E F 1 2 3 4 5 6 expert team data subtype CRC Subtyping Consortium
  28. 28. A B C D E F 1 2 3 4 5 6 ... expert team data subtype CRC Subtyping Consortium
  29. 29. CRC Subtyping Consortium
  30. 30. doi:10.1038/nm.3967 doi:10.7303/syn2623706 CRC Subtyping Consortium
  31. 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. 32. Healthmobile
  33. 33. Healthm
  34. 34. insular health trackingmove beyond
  35. 35. nearly 200 million smart phone users in US insular health trackingmove beyond
  36. 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
  37. 37. >75%
  38. 38. how to balance desire to share w/ importance of privacy?
  39. 39. 2013 september
  40. 40. 2015 march
  41. 41. the hype cycle
  42. 42. the hype cyclelaunching
  43. 43. participant-centered consent
  44. 44. changeable by participant
  45. 45. ~75k participants across all studies >70% opted to share broadly
  46. 46. 50 mPower
  47. 47. 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
  48. 48. motor initiation gait/balance hypophonia memory mPower activities
  49. 49. x y z userAcceleration gravity rotationRate attitude device motion readings at 100 hz gait / balance
  50. 50. gait / balance
  51. 51. Monty Python's The Flying Circus gait / balance
  52. 52. 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
  53. 53. 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
  54. 54. mHealth research communityParkinson
  55. 55. mHealth research communityParkinson
  56. 56. 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
  57. 57. mHealth research communityParkinson
  58. 58. mHealth research communityParkinson
  59. 59. mHealth research communityParkinson
  60. 60. mHealth research communityParkinson
  61. 61. promote an ecosystem where research is conducted for others to consume
  62. 62. 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.
  63. 63. 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
  64. 64. promote an ecosystem where research is conducted for others to consume … … research parasites … …
  65. 65. promote an ecosystem where research is conducted for others to consume
  66. 66. mHealth research community
  67. 67. mHealth research community Sage Bionetworks joins The Scripps Research Institute (TSRI) for PMI Cohort Program via Participant Technology Center (PTC) 06 July 2016
  68. 68. 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
  69. 69. riding the hype cycle together
  70. 70. brian m. bot ———————— principal scientist community manager brian.bot@sagebase.org @BrianMBot thank you sage bionetworks

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