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