Translational Informatics in the Pre-Competitive Era
The document discusses the concept of pre-competitive research in pharmaceutical R&D, emphasizing the need for collaborative frameworks and innovative informatics solutions, exemplified by the transmart platform. It highlights various ongoing projects and partnerships aimed at integrating clinical and biological data for translational research. The transmart initiative aims to facilitate data sharing and collaboration among pharmaceutical companies and academic institutions to enhance research efficiency and outcomes.
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Translational Informatics in the Pre-Competitive Era
- 1. Supported by Prominent internationalspeakers from h"p://workshop.eisbm.eu1
- 2. Translational Informatics inthe Pre- Competitive Era Anthony Rowe PhD Principal Research Scientist Research and Development IT – External Innovation EISBM Workshop – 13 June 2012
- 3. Disclaimer • Presentations areintended for educational purposes only and do not replace independent professional judgment. • Statements of fact and opinions expressed are those of the participants individually and, unless expressly stated to the contrary, are not the opinion or position of the Janssen Pharmaceutical Companies or its affiliates. 29/02/2012 2
- 4. Agenda • Pre-competitive Research •Translational Informatics • The TranSMART Project • Examples of ongoing studies
- 5. What do wemean by the precompetitive era?
- 6. Backdrop: Pharma R&DProductivity Gap R&D IT External Innovation 6/13/2012 5
- 7. Janssen’s Vision R&D IT External Innovation 6
- 8. The models ofdrug discovery are evolving Proprietary content Public provider content provider Big Life CRO Patient Science organization Company Pharma Regulatory authorities Academic group Service provider Software vendor R&D IT External Innovation 6/13/2012 7
- 9. Leading to precompetitivecollaborative research Proprietary content Big Life Public provider Science content Company provider P Big Life CRO Patient Science P organization Company Regulatory P authorities Academic group Big Life Science Service provider Company Software vendor R&D IT External Innovation 6/13/2012 8
- 10. R&D IT ExternalInnovation 9
- 12. Some example IMIProjects Project Research Area U-BIOPRED Severe Asthma PharmaCog Alzheimer's E-TOX Toxicology OncoTrack Colon Cancer EHR4CR Electronic Health Records BT Cure Rheumatoid Arthritis Predict-TB Tuberculosis EMIF Medical Informatics ETRIKS Knowledge Management R&D IT External Innovation 6/13/2012 11
- 13. Translational Informatics inpre- competitive research R&D IT External Innovation 12
- 14. Goal 1: Enabletranslational informatics Bio-banks Cohorts Biomarkers Bed Bench Bed Care Stratified Companion EHR Medicine Diagnostics Pathways Evidence Based Personalised Medicine Medicine In-vivo/In- Clinical Omic NGS Imaging vitro PK/PD Registry Centre 1 Centre 2 Centre 3 Centre 4 Centre 5 Centre n 29/02/2012 13
- 15. Goal 2: Enablecollaboration in network of partners Proprietary content Big Life Public provider Science content Company provider P Big Life CRO Patient Science P organization Company Regulatory P authorities Academic group Big Life Science Service provider Company Software vendor R&D IT External Innovation 6/13/2012 14
- 16. We need technologyto support Virtual Biotech Networks...
- 17. What collaboration toolsdo we use • Project Collaboration • Data Collaboration – Base Camp ... – Group Camp – Grant Snap – Project Place – Drop Box – Skype – Webex – Go To Meeting – Internal Platforms – Wikis – Millarium – Sales Force.com • Note: heavy use of cloud technologies
- 18. Our contribution: TranSMARTfrom Johnson & Johnson Szalma et al. Journal of Translational Medicine 2010, 8:68 R&D IT External Innovation 6/13/2012 17
- 19. Informatics Challenges Common Challenges tranSMART approach Clinical Data organised and A central system to manage managed separately across knowledge for the research different groups organisation Research Data fragmented Integrate Clinical and Omics in and not linked to the clinical a single repository to support data translational research No single place to find out A search tool to explore what research has already internal and external publish taken place research Routine exploratory analyses A suite of tools to support take a long time for common exploratory biostatistics questions R&D IT External Innovation 18
- 20. The TranSMART Platform– 60,000 Ft Query and Analysis Tools Patient Biological Data Data • A data management solution to systematically combine clinical and biological data for translational research • A suite of analytical and informatics tools to use this data in translational questions 29/02/2012 19
- 21. The TranSMART Platform •Use Cases – what is the correlation between animal models and human data – what is the best biomarker strategy for a given compound – what is the best indication for a given compound – how can a disease stratified based on clinical data – is there support for a target of interest based on clinical data • Data – Clinical data, clinical and pre-clinical gene expression, protein profiling (ELISA, RBM), SNP, PD markers, metabolomics, proteomics • In-house – immunology (large and small mol), oncology, cardiovascular, psychiatry • Public and commercial – Curated text & Text indexing – Master data, ontologies, vocabularies and metadata – Federated sources • User Interfaces – Search Gene, pathway, disease, compound, trial, and combinations – Hypothesis testing - Cohort selection and comparison/analysis – Hypothesis generation - Gene signatures – Analytics workflows 20 29/02/2012
- 22. Open Source: TheTranSMART Project • An initiative to make open source Janssen’s translational research platform TranSMART • Available today www.transmartproject.org under GPL v3 license • A growing community of academic and industrial involvement – Especially in IMI funded projects 29/02/2012 21
- 23. tranSMART for precompetitiveresearch IMI OncoTrack IMI BTCure Predect IMI IMI Safe-T Stembancc UBIOPRED IMI IMI Predict EMIF TB J&J Internal IMI eTRIKS Abirisk Use One Mind RA – MAP Consortium NIH MRC Consortium Sage Bio ASTEROID Networks 6 Other Pharma R&D IT External Innovation 22
- 24. Example Projects • IMIUBIOPRED • IMI OncoTrack • Sage Bionetworks • One Mind • eTRIKS
- 25. IMI U-BIOPRED: Biomarkersfor Severe Asthma • Key Facts • Identification of novel biomarkers of severe asthma • 40 Partners (20 Academic, 10 SME, 10 EFPIA) • Novel Cohort and Biobank of Severe Asthma Patients (n=750) • Profiling of Genomics, Proteomics, Lipidomic, Breathomic • Matching with in-vivo and in-vitro models R&D IT External Innovation 6/13/2012 24
- 26. Knowledge Production Process Process: Patient Omics Samples Knowledge Delivery Data Data Procedure: Data Analysis Protocol SOP (SRM) KM Structure Plan Data Management: TransMart Governance eCRF LIMS Files Others? 25
- 27. UBIOPRED Data Sources Number of Data Class Assay/Data Source Sample Types Samples Clinical ECRF (medical history, N/A 725 adult, 525 lung function, drug use) longitudinal 300 paediatric Clinical Patient Reported Up to 100 Outcomes Clinical Patient Diaries - Up to 100 Transcriptomics Human Genome U133 Blood Up to 600 Plus 2.0 Array Proteomics NanoMate ESI Sputum, Serum 1500 Proteomics MS(E) Sputum, Serum 150 Lipidomics Sputum, 1500 NanoMate-ESI Plasma Lipidomics lipidomic screen - LC/QTOF Urine 1000 Lipidomics lipidomic screen - LC/QTOF Sputum 1000 Breathomics eNose Breath Up to 1000 Breathomics GC-MS Breath Up to 100 Metagenomics TBC Nasel swabs TBC CT Morphology readouts Chest CT TBC Histology Cell counts readouts Broncoscopy Up to 288 R&D IT External Innovation 26
- 28. Recruitment Analysis –Built in less than 5 minutes R&D IT External Innovation 27
- 29. R&D IT ExternalInnovation 28
- 30. R&D IT ExternalInnovation 29
- 31. Analytical Registry –Organisational Knowledge Management Manage Document N A L Y T I CA Data Sets & SOPS A L Investigators TranSMART Data Mart and Search Engine for Study Data R Y Manage Collaborate EG R I ST Around Cohort Design Ideas Selections
- 34. UBIOPRED Current Status:13 June 2012 • Undertaking an interim analysis of our first 60 patients – Bench Test the UBIOPRED system – Look for early signals in well validated platforms • Clinical, Sputum, Urinine & Serum Lipidomics – Preliminary lipid data analysis performed by Xian Yang – Methods will be posted on the analytical registry • Clinical data being review for quality – Looking for outliers, batch effects – TranSMART projects starting soon • UBIOPRED Scientific Board will reviewed in 2 weeks time IMI Day 2012
- 35. OncoTrack Consortium • Key Facts • Methods for systematic next generation oncology biomarker development (Focus on Colon Cancer) • 19 Partners (7 Academic, 4 SME, 8 EFPIA) • Sequencing the genome, transcriptome and methylome of each tumor (primary tumor and metastasis) • Sequencing includes tumor derived material (CTCs, free circulating DNA, CSCs, xenografts) • Driving NGS work in tranSMART project 34
- 36. Sage Bionetworks Collaboration •Providing comparator arm of a J&J clinical trial for CTCAP • Provided tranSMART for KM • Universal “opt-in” and “Portable Informed Consent” Janssen R&D Information Technology 11/1/2011 35
- 37. tranSMART for OneMind For Research Janssen R&D Information Technology 1/27/2012 36
- 38. eTRIKS: Summary • Problem:No open KM infrastructure to support pre-competitive (& competitive) cross-institute TR. No public knowledge base of curated TR data. • Proposal: • Consortia to develop & deliver an open TR KM infrastructure & Service • Built around J&J’s tranSMART open platform • Curation of content (live and historic TR trials) • Support of existing IMI initiatives • UBIOPRED, OncoTrack, Safe-T, etc... • TR KM standards, enabling TR data sharing • Promotion of TR analytics innovation. • Mirror of US tranSMART consortia (tba) • Benefits: • Consortia Model & Costs: • Improved TR project operating efficiencies • $31m / 5 year • Stable legacy: IMI TR data security • 10 Pharma (AZ/J+J Lead) • Access to curated historical content enabling • ~5 AMC/SMEs with experience in TR both: KM service delivery • Analytics/Methodology innovation • Review impact in year 2: with follow • Novel x-study translational discovery on funding - possible IMI ‘Big Idea’ • Enables x-institute TR data sharing • Curation funded by supported IMI • Strengthened TR Ix community projects 37
- 39. TranSMART in theBigger Landscape Commercial Technology Industry (e.g.) Recombinant Open Source eTRIKS Project Galaxy Projects US Public Private Consortia EU Public Private Consortia Standards Groups(e.g.) Horizon 2020 CDISC Biopharma Industry (e.g.) Open Information Day – 17 June 2011 - Brussels
- 40. Summary • Pre-competitive researchis creating new virtual organisations • Precompetitive research requires innovative IT Solutions that break down new organisational barriers • Open Source TranSmart is a part of that puzzle
- 41. Questions? Join us at: www.transmartproject.org R&D IT External Innovation 6/13/2012 40