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