Successfully reported this slideshow.
We use your LinkedIn profile and activity data to personalize ads and to show you more relevant ads. You can change your ad preferences anytime.
Upcoming SlideShare
Copy (2) of new open document presentation mental fitness use this one
Next

Share

MRC Stratified Medicine TranSMARTs

Mike Barnes, William Harvey Research Institute, QMUL on the MRC Stratified Medicine TranSMARTs

Related Books

Free with a 30 day trial from Scribd

See all
  • Be the first to like this

MRC Stratified Medicine TranSMARTs

  1. 1. MRC Stratified Medicine TranSMARTs Mike Barnes William Harvey Research Institute QMUL m.r.barnes@qmul.ac.uk 28/4/2015
  2. 2. Genomics: A Systems Approach Drug Endotypes Disease Endotypes Molecular Mechanisms TNFR1 Novel Mechanistic InsightsApoptosis Inflammation Omic (RNA, protein) Drug Response (Connectivity Map) TNF JNK1 NFKB CD20 Infliximab RituximabmabTocilizumabTNF signalling Cytokine signalling Genetic Synovium Blood
  3. 3. TranSMART: MRC Stratified Medicine RA-MAP MATURA Rheumatoid Arthritis Psoriasis Biologic response biomarkersDisease biomarkers
  4. 4. PSORTData Generation Pharma TranSMARTs MATURA TranSMART TranslationalMedicine Platform RA-Map TranSMART Portal Extraction Layer – Standardize extracted data formats Semantic normalisation Compliant,Auditable& Traceable CatalogofOntology& Terminology Data Checking & Validation Pseudo-anonymisation Platform Cohort Selection and Biostatistics Omics Analysis / Bioinformatics Biomarker Discovery NormalisedDataSharing PSORT TranSMART Clinical Cohort Phenotypic Data Demographics Clinical observations Clinical trail outcomes Adverse events Reference Data Literature Pathway data Gene metadata Drug data High content biomarker data Gene Expression Genotypes Metabolomics PK/PD markers Future TranSMARTs firewalledvirtualmachines MRC TranSMART data Infrastructure
  5. 5. TranSMART Data Content PSORT • Clinical, BADBIR, Clinical Trial • Transcriptomic (mRNA,miRNA), Genetics, metabolomic MATURA • Clinical, Clinical Trial • Genetics, Transcriptomics (mRNA, miRNA) RA-MAP • Clinical • Transcriptomics (mRNA, miRNA)
  6. 6. MRC Stratified Medicine: Security and Data Sharing Models “Controlled Data hub” • Data can be downloaded  Fully audit trail • Analysis at partner sites • Background data by CDA Pros • Available now • More agile analysis • Simpler admin • Analyst freedom locally Cons • Less secure “Analysis safe haven” • Data cannot be downloaded • All analysis on safe haven Pros • Secure Cons • Complex server admin • Less flexible analysis • VM access can be slow • Solution not available yet • Resource intensive (high cost) Open ClosedShared Principles • Standardised, versioned data • Access based on contribution “give more, get more” • Access control by data set
  7. 7. PSORT/RAMAP Controlled Data Hub TranSMART Data QC Secure Data Sharing Data Standardisation Data Integration Data Export Simple data analysis Analysis on Data Exports using local Compute resources • R statistical analysis etc • Machine Learning • GWAS • High-dimensional • High Performance computing pipelined analysis (plugins) R backend
  8. 8. MATURA “Analysis Safe Haven” Analysis on Data Exports using Elastic compute resources on VM • Standardised reference data sets • R statistical analysis etc • Machine Learning • GWAS • High-dimensional analysis • High Performance computing Data Exports MATURA CMB Approval Public Data Analysis VM
  9. 9. MRC Stratified Medicine: Infrastructure Evolution MRC eMEDLAB VM hosting •Central data centre •Open Stack Architecture •TranSMART hosting •Secure data access •Elastic compute for all analysis Sept2015Now •QMUL data centre •TranSMART hosting •Secure data access •Limited analysis
  10. 10. RA-MAP - TranSMART
  11. 11. Acknowledgements QMUL Richard Christie Simon Butcher Oliver Greenaway eTRIKS Anthony Rowe (J&J) Yike Guo Ioannis Pandis Wei Gu Denny Verbeeck Francisco Capdevila

Mike Barnes, William Harvey Research Institute, QMUL on the MRC Stratified Medicine TranSMARTs

Views

Total views

760

On Slideshare

0

From embeds

0

Number of embeds

15

Actions

Downloads

0

Shares

0

Comments

0

Likes

0

×