biomedical research in an increasingly digital world
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Sage Bionetworks is a non-profit organization that supports open and collaborative biomedical research across organizations through various consortiums and partnerships. Some of its initiatives include the TCGA Pan-Cancer Consortium involving analysis of 12 tumor types, the CommonMind Consortium involving collection and analysis of brain tissue samples for schizophrenia research, and the Accelerating Medicines Partnership, a public-private partnership focused on diseases such as Alzheimer's. Sage Bionetworks also supports data challenges and the development of collaborative research platforms.
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biomedical research in an increasingly digital world
- 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
- 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. opportunities when problems are bigger than a single organization sage bionetworks
- 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. analysis of: 12 tumor types 6 molecular profiling platforms TCGA Pan-Cancer Consortium
- 7. 18NPG papers 68core projects 248researchers 28institutions 1070datasets 1723results TCGA Pan-Cancer Consortium
- 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. 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
- 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
- 15. A B C D E F 1 2 3 4 5 6 expert team data subtype CRC Subtyping Consortium
- 16. A B C D E F 1 2 3 4 5 6 ... expert team data subtype CRC Subtyping Consortium
- 18. collaborative analyses cloud-based file storage CRC Subtyping Consortium
- 19. code associated with results CRC Subtyping Consortium
- 20. doi:10.1038/nm.3967 doi:10.7303/syn2623706 CRC Subtyping Consortium
- 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. public / private partnership between NIH, 10 biopharmaceutical companies and several non-profit organizations Accelerating Medicines Partnership
- 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. 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. 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. 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. 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. 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. DREAM Challenges
- 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. 17 April 2013 DREAM Challenges
- 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 mHealth
- 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. 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. Motor Initiation Gait/Balance Hypophonia Memory mPower activities
- 37. increasingly decentralized research ecosystem
- 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. brian m. bot ———————— principal scientist community manager brian.bot@sagebase.org @BrianMBot thank you sage bionetworks