MRC eMedLabl Stratified medicine theme overview
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Transcript of MRC eMedLabl Stratified medicine theme overview
The eMedLab
Stratified Medicine theme
Michael Barnes
(on Behalf of the eMedLab Exec and Tech Governance Group)
UCL, Crick, QMUL, LSHTM, Sanger, EBI, KCL
19 10 2016
www.emedlab.ac.uk
• 13 internationally competitive stratified medicine discovery engines
• Build on NIHR and DA clinical research funding
• Total investment c. £60m
• 3 charity co-funders (CRUK, ARUK, BHF)
• 32 academic and 51 commercial partners
MRC Stratified Medicine Consortia
COPDMAP
RAMAP-I
MASTERMIND
GAUCHERITE
STOP-HCV
MATURA-I
UKPBC
STRATA
PSORT
MASTERPLANS
RASP-UK
AIM HY
S-CORT Auto-Immune
Respiratory
Cancer
Infections
Mental Health
Cardiovascular
Diabetes
Congenital
RAMAP-II
MATURA-II
Cancer Research UK Stratified Medicine Programme – Key Metrics
Stratified Medicine in a Nutshell
Omic (RNA, protein)
Drug Response (Connectivity Map)
Genetic Epigenetic
Disease tissue
Blood
FACS
TNF IL6
BAFF
CD20 • Endotype1 • Endotype2 • Endotype3
Disease Endotype
Adalimumab
Rituximab
• Anti-TNF • Anti-IL6 • Anti-CD20
Drug Endotype IL6
TNF
BAFF
CD20
Belimumab Tocilizumab
• Anti-TNF • Anti-IL6 • Anti-CD20
Response Biomakers
Multi -Omics
What does success look like?
+
eMedLab
is a hub 7 partners
Diverse data types
electronic health records
genomic
images
Diverse expertises
clinician scientists
analytics
basic science
£9M Hardware Investment
6048 cores 5.5PB storage Fast connections
Stratified Medicine Theme
• 6 projects
• 5 diseases
• Common drugs
• Common mechanisms
eMedLab VM architecture: MATURA
• TranSMART and Command Line Analysis combined – Hosts TranSMART and command line queue system
– Users access TranSMART by external web
– Command line Access by VPN
• Elastic computing on eMedLab – VM nodes are raised by Elastic Cluster and terminated when idle
– Slurm queing system
Head
Queue
Node 1 Node 2 Node n
12 cores 64GB RAM
32 cores 320GB RAM
32 cores 320GB RAM
32 cores 320GB RAM
Elastic Compute VM nodes MATURA Head Server
VPN login
eMedLab
Embassy
Data sharing
Standards
Meta-analysis
Secure
A Secure Collaboration Environment
CHART Juvenile
Idiopathic Arthritis
TARGET Giant cell Arteritis
SLE
RA
RA
Psoriasis
VM VM
VM VM
VM VM
Theme Academy
Meeting Aims
• Share some great science
• Brainstorm stratified medicine informatics challenges
• Propose solutions
• Feedback to MRC Stratified Medicine Strategy
• Have fun
AGENDA Introduction to eMedLab – Nick Luscombe
A Clinician’s Perspective on Stratified Medicine Challenges – Amy Foulkes
PSORT : Defining And Studying Biologic Reponse– David Watson
Cancer Stratified-Medicine Case Study – Bissan Al-Lazikani
A Pharma perspective on Stratified Medicine Challenges– Anthony Rowe
RA-Map: A Systems Biological Approach To Disease Stratification – Chris Johns
Keynote: Interactive visualization of multi-omics data-- Simon Anders, FIMM
Patient stratification using large-scale patient-level data – Nophar Geifman
Panel Discussion – Computational challenges for Stratified Medicine
Tea & Coffee