biomedical research in an increasingly digital world

brian m. bot | principal scientist |

2016 april 18

sage bionetworks

pnw life science executive forum

biomedical research in an increasingly digital worldopportunities when problems are bigger than

a single organization

sage bionetworks

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 researchwill fundamentally change to be more open and collaborative

supports communities of researchers working collaboratively across disciplines

our approach

opportunities when problems are bigger than a single organization

sage bionetworks

CRC Subtyping Consortium

DREAM ChallengesProgenitor Cell Biology Consortium

TCGA Pan-Cancer Consortium

CommonMind Consortium

PsychENCODE

Accelerating Medicines Partnership

Resilience Project

Influenza Vaccinations

Dengue FeverPsychosis Spectrum Disorder

mHealthNext Gen Scientific Publishing

Mozilla Science Labs

sage bionetworks

analysis of: 12 tumor types 6 molecular profiling platforms


18NPG papers

68core projects248

researchers

28institutions

1070datasets1723

results






PsychENCODE


Resilience Project





sage bionetworks


large public / private partnership

phase I: prefrontal cortex

~300 SCZ, 300 control, 60 BD

processing pipelines developed in collaborationbetween sage and mssm





PsychENCODE


Resilience Project





sage bionetworks

A

B

C

D

E

F

1

2

3

4

5

6

expert team data subtype


A

B

C

D

E

F

1

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...

expert team data subtype


collaborative analyses

cloud-based file storage


code associatedwith results


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






PsychENCODE


Resilience Project





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


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


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


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

DREAM Challenges

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

17 April 2013

DREAM Challenges





PsychENCODE


Resilience Project





sage bionetworks

33

mHealth

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

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

increasingly decentralized research ecosystem

democratization of research

de-coupling of data collection and analysis

cloud infrastructure

gov’t agencies and public pushing for > sharing

increasingly decentralized research ecosystem

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

[email protected] @BrianMBot

thank you

sage bionetworks

mailto:[email protected]