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biomedical research in an increasingly digital world

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biomedical research in an increasingly digital world

  1. 1. brian m. bot | principal scientist | 2016 april 18 sage bionetworks pnw life science executive forum biomedical research in an increasingly digital world opportunities when problems are bigger than a single organization
  2. 2. sage bionetworks
  3. 3. sage bionetworks a non-profit organization which pilots a variety of components that are necessary to build a scientific research commons focused on a world where biomedical research will fundamentally change to be more open and collaborative supports communities of researchers working collaboratively across disciplines our approach
  4. 4. opportunities when problems are bigger than a single organization sage bionetworks
  5. 5. CRC Subtyping Consortium DREAM Challenges Progenitor Cell Biology Consortium TCGA Pan-Cancer Consortium CommonMind Consortium PsychENCODE Accelerating Medicines Partnership Resilience Project Influenza Vaccinations Dengue Fever Psychosis Spectrum Disorder mHealth Next Gen Scientific Publishing Mozilla Science Labs sage bionetworks
  6. 6. analysis of: 12 tumor types 6 molecular profiling platforms TCGA Pan-Cancer Consortium
  7. 7. 18NPG papers 68core projects 248researchers 28institutions 1070datasets 1723results TCGA Pan-Cancer Consortium
  8. 8. TCGA Pan-Cancer Consortium
  9. 9. CRC Subtyping Consortium DREAM Challenges Progenitor Cell Biology Consortium TCGA Pan-Cancer Consortium CommonMind Consortium PsychENCODE Accelerating Medicines Partnership Resilience Project Influenza Vaccinations Dengue Fever Psychosis Spectrum Disorder mHealth Next Gen Scientific Publishing Mozilla Science Labs sage bionetworks
  10. 10. CommonMind Consortium large public / private partnership phase I: prefrontal cortex ~300 SCZ, 300 control, 60 BD processing pipelines developed in collaboration between sage and mssm
  11. 11. CommonMind Consortium
  12. 12. CommonMind Consortium
  13. 13. CRC Subtyping Consortium DREAM Challenges Progenitor Cell Biology Consortium TCGA Pan-Cancer Consortium CommonMind Consortium PsychENCODE Accelerating Medicines Partnership Resilience Project Influenza Vaccinations Dengue Fever Psychosis Spectrum Disorder mHealth Next Gen Scientific Publishing Mozilla Science Labs sage bionetworks
  14. 14. CRC Subtyping Consortium
  15. 15. A B C D E F 1 2 3 4 5 6 expert team data subtype CRC Subtyping Consortium
  16. 16. A B C D E F 1 2 3 4 5 6 ... expert team data subtype CRC Subtyping Consortium
  17. 17. CRC Subtyping Consortium
  18. 18. collaborative analyses cloud-based file storage CRC Subtyping Consortium
  19. 19. code associated with results CRC Subtyping Consortium
  20. 20. doi:10.1038/nm.3967 doi:10.7303/syn2623706 CRC Subtyping Consortium
  21. 21. CRC Subtyping Consortium DREAM Challenges Progenitor Cell Biology Consortium TCGA Pan-Cancer Consortium CommonMind Consortium PsychENCODE Accelerating Medicines Partnership Resilience Project Influenza Vaccinations Dengue Fever Psychosis Spectrum Disorder mHealth Next Gen Scientific Publishing Mozilla Science Labs sage bionetworks
  22. 22. public / private partnership between NIH, 10 biopharmaceutical companies and several non-profit organizations Accelerating Medicines Partnership
  23. 23. ($ 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
  24. 24. mt sinai mayo / ufl / isb broad / rush emory integrated network analysis target discovery 300 case-control rnaseq, genotype, clinical 1000 case-control rnaseq, methylation, genotype, clinical 300 ad, tauopathy, control rnaseq, clinical 200 AD, MCI, control Proteomic, clinical data Accelerating Medicines Partnership
  25. 25. iPS neurons and astrocytes Mouse hippocamal slices Drosophila model Genetic analysis aB and Tau mouse models rAAV delivered models Proteomics Cultured neurons & astrocytes iPS compound screens Proteomics Cell Culture, Mouse Models Drosophila model mt sinai mayo / ufl / isb broad / rush emory target validation 2 3 5 12 Accelerating Medicines Partnership
  26. 26. 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
  27. 27. 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
  28. 28. CRC Subtyping Consortium DREAM Challenges Progenitor Cell Biology Consortium TCGA Pan-Cancer Consortium CommonMind Consortium PsychENCODE Accelerating Medicines Partnership Resilience Project Influenza Vaccinations Dengue Fever Psychosis Spectrum Disorder mHealth Next Gen Scientific Publishing Mozilla Science Labs sage bionetworks
  29. 29. DREAM Challenges
  30. 30. Columbia Professor Dimitris Anastassiou MPEG-2 compression of digital audio and video signals Modules of co-expressed genes shared across cancers Belief that these ‘attractors’ represent underlying biological mechanisms (bioinformatic ‘hallmarks of cancer’1) 1D. Hanahan, R. A. Weinberg. Hallmarks of cancer: The next generation. Cell 144, 646–674 (2011) DREAM Challenges
  31. 31. 17 April 2013 DREAM Challenges
  32. 32. CRC Subtyping Consortium DREAM Challenges Progenitor Cell Biology Consortium TCGA Pan-Cancer Consortium CommonMind Consortium PsychENCODE Accelerating Medicines Partnership Resilience Project Influenza Vaccinations Dengue Fever Psychosis Spectrum Disorder mHealth Next Gen Scientific Publishing Mozilla Science Labs sage bionetworks
  33. 33. 33 mHealth
  34. 34. 34 48,104 downloads from app store - first six months 16,585 participants consented 14,684 participants enrolled 9,520 agreed to ‘share broadly’ 1,087 self reported a professional diagnosis of Parkinson mPower
  35. 35. 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
  36. 36. Motor Initiation Gait/Balance Hypophonia Memory mPower activities
  37. 37. increasingly decentralized research ecosystem
  38. 38. democratization of research de-coupling of data collection and analysis cloud infrastructure gov’t agencies and public pushing for > sharing increasingly decentralized research ecosystem
  39. 39. brian m. bot ———————— principal scientist community manager brian.bot@sagebase.org @BrianMBot thank you sage bionetworks

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