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