tranSMART Overview
University of MichiganJohns Hopkins UniversityCollaboration
Brian D. Athey UM
Kenneth J. Pienta JHU
Kev...
Presentation Outline
• Motivating & Conceptual Background
• tranSMART at Johns Hopkins University

– Overall Scope
– Scope...
UMHS Data Architecture Unifying the Three Missions:
Education, Research, & Patient Care

Brian Athey
& ECRIT
1/11/11

Admi...
UMHS Data Architecture Unifying the Three Missions:
Education, Research, & Patient Care
Education
Admissions

Clinical Sch...
Supporting Academic Health Centers is beyond ‘just Epic’ :
Translational Biomedical Knowledge Creation & tranSMART

 Gend...
Conceptual Vision: Building a Knowledge Network
“Towards Precision
Medicine”, Institute
of Medicine (IOM);
2011, NAS.org.
The Science in the Middle: Linking models and driving problems to
measurement core facilities, enabled by tranSMART

Lee H...
tranSMART | JHU | Scaling to Johns Hopkins Medicine
Platform Development Collaboration
Pienta /
Athey
Collaboration

•
•
•...
Bioinformatics/tranSMART

Trans-Brady Datamart/tranSMART

Clinical studies
Preclinical therapeutics
Preclinical Studies
Mo...
Bioinformatics/tranSMART

Trans-Brady Datamart/tranSMART

Clinical studies
‘omics

Metabolism

anti-CXCR4

3D

Cytoskeleto...
tranSMART | JHU | The Brady
• Datasets to be harmonized and loaded into tranSMART
(patients & samples including bioreposit...
Presentation Outline
• tranSMART – Brief History / Current Use/Demo
• tranSMART at Johns Hopkins University

– Scope of Pi...
tranSMART | JHU | Pienta-Athey Lab Project
• Platform Development of 3D Microscopic
Imaging Technologies, Analytical Pipel...
Fundamental Microscopy Data Types
• Nuclear Morphometry
• Nuclear size
• Nuclear circularity and shape parameters
• DNA co...
TMPRSS-ERG Fluorescence Micrograph
• Bracken, H,
et al,
Association
of SPINK1
Expression
and
TMPRSS2:E
RG Fusion
with
Prog...
Dataset Explorer – Images (prototype) 2
Athey Imaging Pipeline Service to tranSMART
Platform
Experiment
Cells, Prep, Features, Channels
Microscope Setup/Image
Ful...
tranSMART | JHU | Leveraging Global Initiatives
• NIH National Center for Integrative Biomedical
Informatics (NCIBI); Mich...
NIH National Center for Integrative Biomedical
Informatics (NCIBI) integration with tranSMART
Tools

Data
NCIBI in tranSMART
Gene2MeSH

Metab2MeSH

The user can find Medical Subject
Headings (MeSH terms) enriched for a
particula...
NCIBI in tranSMART
Metscape

The user can visualize the interactions of
genes, enzymes, reactions and
compounds in human m...
Demo Screenshots
Terry Weymouth
Tuesday, Nov 5, 2013
Demo Site Login
Dataset Explorer - Overview
Dataset Explorer – Summary Statistics
Dataset Explorer – Images (prototype) 1
Dataset Explorer – Hierarchical Clustering 1
Dataset Explorer – Hierarchical Clustering 2
Gene List Panel
NCIBI - Pubmed
NCIBI – Concept Explorer (ConceptGen)
NCIBI - Pubmed
NCIBI – Compound Network (MetScape)
NCIBI – Gene2Mesh
NCIBI – Metab2Mesh
Spotfire @ Michigan w/tranSMART
tranSMART Architecture – where Spotfire fits
Option 1 – as a Core Application with Information Links to the underlying Dat...
tranSMART Architecture – where Spotfire fits
Option 2 – as a Scientific Analysis Tool with capability to consume output fr...
Spotfire: Translational Data – Novel GEA analysis
Kruskal-Wallis test
of all significantly
differentially
expressed probes...
Spotfire: Translational Data – Merge NGS and GEA
tranSMART | UM | Scaling to U-Michigan Medicine
Platform Development Collaborations
Athey/
Burant
Collaboration

•
•
•
•

...
Thank you/Questions/Discussion

Quiz: Which one is which?
Upcoming SlideShare
Loading in …5
×

tranSMART Community Meeting 5-7 Nov 13 - Session 3: Characterization of the cell phenotypes involved in metastasis

1,339 views

Published on

tranSMART Community Meeting 5-7 Nov 13 - Session 3: Characterization of the cell phenotypes involved in metastasis
Characterization of the cell phenotypes involved in metastasis: Using tranSMART to enable high-throughput heterogeneous data integration and analysis
Brian Athey, University of Michigan

Published in: Health & Medicine, Technology
0 Comments
0 Likes
Statistics
Notes
  • Be the first to comment

  • Be the first to like this

No Downloads
Views
Total views
1,339
On SlideShare
0
From Embeds
0
Number of Embeds
254
Actions
Shares
0
Downloads
31
Comments
0
Likes
0
Embeds 0
No embeds

No notes for slide

tranSMART Community Meeting 5-7 Nov 13 - Session 3: Characterization of the cell phenotypes involved in metastasis

  1. 1. tranSMART Overview University of MichiganJohns Hopkins UniversityCollaboration Brian D. Athey UM Kenneth J. Pienta JHU Kevin A. Smith UM Terry E. Weymouth UM 6 November 2013 Sanofi tranSMART Paris Meeting
  2. 2. Presentation Outline • Motivating & Conceptual Background • tranSMART at Johns Hopkins University – Overall Scope – Scope of Pienta-Athey Lab Collaborative Demonstration Project • Digital Microscopy Service, NCIBI tools and data, EMT-MET Transformation • Future: Establishing and harmonizing databases across The Brady Institute • Future: Evaluating PE or IDBS Electronic Laboratory Notebook (ELN) integration; Institutional level • tranSMART at Michigan – PerkinElmer (PE) Spotfire Collaboration – Current and Future
  3. 3. UMHS Data Architecture Unifying the Three Missions: Education, Research, & Patient Care Brian Athey & ECRIT 1/11/11 Admissions Research Pre, Post- Award Education IT Security IT SERCUIRTY Ctools/Saki 3 Visiting Student Application Service(VSAS) M-Pathways Research Proteomics Core Metabolomics Facilities/ ‘Omics’ eThority (billing) Tissue Biorepositories Collexis ULAM Research Administration Data Warehouse RedCAP Populations Research Individuals Research & BioDBX Data Quality Velos Management Diseases Metrics Systems Data Marts Demographics OpenClinica Others … Registries Research Data Warehouse CareLink/ Eclipsys Clinical Quality Analysis Metrics Database Reporting (CAD) & Peer Others Review Pharmacy Radiology Scheduling HIM/ Documentation Others… CDR Epic Clarity HSDW i2b2 Emergency Med. Patient Care Revenue Cycle Systems Pathology Legacy+/Epic EHR Enterprise Federated Data Warehouse CAD Historical SPORES Ambulatory Data Biomedical Engineering HIPAA/IRB Services (Honest Broker, DE-ID Consent Management, …) Common Identifier Services (Patient, Provider, Information Bus Service-Oriented Research, Specimens, External Mappings) Vocabulary & Terminology Mapping Services (ICD-9/10 SNOMED, IMO, caDSR, ...) ITIT Security Security Campus Systems Curriculum Eval. System Bioinformatics Research Click Administration Commerce Systems (IRB) Clinical Scheduling & Grading System Education Knowledge Repository Next-Gen Sequencing Portals / Providers, Payors, P. Health Databases / HIEs / NHIN Comprehensive Clinical Assessment Exam Messaging Bus, ETL & External Collaboration Services (SOA, caGRID, SHRINE, ...) Health Sciences Library Resources NIH-Specific & External Data Resources (PubMed, GenBank, KEGG, GO, etc.) High Performance Cloud Computing & Data Storage Bioinformatics and Systems Biology Workbenches • Reporting • Visualization • Analysis & • Data Mining Data Sharing with External Collaborators International Industry: Pharma/ caBIG I2b2/ CTSAs Biotech TCGA SHRINE
  4. 4. UMHS Data Architecture Unifying the Three Missions: Education, Research, & Patient Care Education Admissions Clinical Scheduling Metabolomics BioDBX Individuals Tissue Biorepositories Diseases M-Pathways eThority (billing) Velos Others… Collexis ULAM CTools/Sakai 3 IT Security IT SERCUIRTY Campus Systems Curriculum Evaluation System Education Knowledge Repository Research Administration Data Warehouse CIDSS Analytics & Reporting Tools Populations Pharmacy Ambulatory Emergency Med. Pathology Revenue Cycle Demographics Registries Others … Research Data Warehouse CAD i2b2 Others Radiology Scheduling Centricity Documentation OpenClinica SPORES CareLink/ Eclipsys Others… CDR HSDW Historical Data HIM Epic Clarity Biomedical Engineering HIPAA/IRB Services (Honest Broker, De-ID Consent Management, …) Common Identifier Services (Patient, Provider, Research, Specimens, External Mappings) Vocabulary & Terminology Mapping Services (ICD-9/10 SNOMED, IMO, caDSR, ...) ITIT Security Security Click Commerce (IRB) Proteomics RedCAP Patient Care Systems Legacy + Epic Epic EHR Portals / Providers, Payors, P. Health Databases / HIEs / NHIN Comprehensive Clinical Assessment Exam Research Research Core AdministrationFacilities/‘Omics’ Quality Systems Metrics Research & Research Quality Metrics Reporting Data Next-Gen & Management Data Marts Sequencing Research Pre, Peer Systems Post- Award Bioinformatics Review Brian Athey & ECRIT 1/11/11 Messaging Bus, ETL & External Collaboration Services (SOA, caGRID, SHRINE, ...) Health Sciences Library Resources NIH-Specific & External Data Resources (PubMed, GenBank, KEGG, GO, etc.) High Performance Cloud Computing & Data Storage Bioinformatics and Systems Biology Workbenches • Reporting • Visualization • Analysis & • Data Mining Data Sharing with External Collaborators International Industry: Pharma/ caBIG I2b2/ CTSAs Biotech TCGA SHRINE
  5. 5. Supporting Academic Health Centers is beyond ‘just Epic’ : Translational Biomedical Knowledge Creation & tranSMART  Gender  Ethnicity  Age  Weight  Diagnosis  Medical History  Biological Models  Technologies  Algorithms Research  Lab Tests  Genes  Proteins  Literature  Databases  Terminologies  Ontologies
  6. 6. Conceptual Vision: Building a Knowledge Network “Towards Precision Medicine”, Institute of Medicine (IOM); 2011, NAS.org.
  7. 7. The Science in the Middle: Linking models and driving problems to measurement core facilities, enabled by tranSMART Lee Hood IOM February 27, 2012
  8. 8. tranSMART | JHU | Scaling to Johns Hopkins Medicine Platform Development Collaboration Pienta / Athey Collaboration • • • • • • 3-D Imaging Cell Lines 3-D Tissue Imaging Genomics, Epigenomics Proteomics Metabolomics Data and Metadata concerning studies Brady Urological Institute Other Johns Hopkins Units • Bio-specimen Repositories • Next Generation Sequencing Core • Morphology Core • Specified links to CRM and EHR resources • Oncology Dept. • Cancer Center • Others • Broader enablement of Personalized Medicine
  9. 9. Bioinformatics/tranSMART Trans-Brady Datamart/tranSMART Clinical studies Preclinical therapeutics Preclinical Studies Modeling Mathematical Modeling Theory Pienta lab: The etiology of cancer cell dormancy in the cancer ecosystem
  10. 10. Bioinformatics/tranSMART Trans-Brady Datamart/tranSMART Clinical studies ‘omics Metabolism anti-CXCR4 3D Cytoskeleton In vivo Dispersion studies 2DCell morphology CD44 RBM3 OVO-ZEB RCI EMT-MET Modeling Dormancy Pienta lab: The etiology of cancer cell dormancy Stem?
  11. 11. tranSMART | JHU | The Brady • Datasets to be harmonized and loaded into tranSMART (patients & samples including biorepositories) – – – – – – – – Primary prostatectomy (>10,000) Active surveillance (>1000) Familial genetics (>1000) Radiation Oncology (>5000) Advanced prostate cancer (>100) Kidney cancer (>100) Bladder cancer (>100) Pediatric bladder extrophy (>500)
  12. 12. Presentation Outline • tranSMART – Brief History / Current Use/Demo • tranSMART at Johns Hopkins University – Scope of Pienta-Athey Lab Collaborative Demonstration Project (EPI-EMT Transformation in PCa) – National Center for Integrative Biomedical Informatics (NCIBI) Tools, PerkinElmer (PE) Spotfire – Establishing and Harmonizing databases across The Brady Institute – Currently: Evaluating PE or IDBS Electronic Laboratory Notebook (ELN) – Future: Scaling more broadly to Johns Hopkins Medicine • tranSMART at University of Michigan
  13. 13. tranSMART | JHU | Pienta-Athey Lab Project • Platform Development of 3D Microscopic Imaging Technologies, Analytical Pipelines, and Data and Information Reporting Services – Integrative characterization of the cell phenotypes involved in metastasis – Re-engineering image processing pipeline • Accommodate fluorescence Interphase FISH • Tissue imaging replacing Feulgen with DAPI or other appropriate DNA staining
  14. 14. Fundamental Microscopy Data Types • Nuclear Morphometry • Nuclear size • Nuclear circularity and shape parameters • DNA content via integrated fluorescent signal • Chromosome Territories • Position, shape, volume • Sub-territory bodies (loci, collections of loci, chromosomal segments e.g. TDs) • Position, shape, volume • Immunofluorescence of , e.g., epigenetic histone marks • Localization to CTs, sub-territory bodies, morphometric nuclear regions
  15. 15. TMPRSS-ERG Fluorescence Micrograph • Bracken, H, et al, Association of SPINK1 Expression and TMPRSS2:E RG Fusion with Prognosis in EndocrineTreated Prostate Cancer. Clin. Cancer Res., 2010
  16. 16. Dataset Explorer – Images (prototype) 2
  17. 17. Athey Imaging Pipeline Service to tranSMART Platform Experiment Cells, Prep, Features, Channels Microscope Setup/Image Full Image Metadata & DB 1K x 1K x Z x C Grid Images QC C0 Nucleus Bounding Box Spectral Unmixing … 1K x 1K x Z x C Grid Images Nucleus BB Raw Raw C… Cn Raw C1 Raw C0 Voxels and Clusters For each BB Voxel list file: x,y,z,v0, … vn Image file: for each color Stats: Min, Max, Stdev Threshold: intensity and size For each BB color cluster Voxel list file: x,y,z,v Voxels: count, centroid Threshold: intensity and size Electronic Lab Notebook Outputs to tranSMART Tissue/Nuclear Morphometry Chromosome Territories Locus-specific Immuno-fluor Metadata for above
  18. 18. tranSMART | JHU | Leveraging Global Initiatives • NIH National Center for Integrative Biomedical Informatics (NCIBI); Michigan-based – Bioinformatics, Systems Biology Network Analysis, Reference Data
  19. 19. NIH National Center for Integrative Biomedical Informatics (NCIBI) integration with tranSMART Tools Data
  20. 20. NCIBI in tranSMART Gene2MeSH Metab2MeSH The user can find Medical Subject Headings (MeSH terms) enriched for a particular gene with links to the supporting PubMed publications. The user can find Medical Subject Headings (MeSH terms) enriched for a particular compound with links to the supporting PubMed publications.
  21. 21. NCIBI in tranSMART Metscape The user can visualize the interactions of genes, enzymes, reactions and compounds in human metabolomics pathways. ConceptGen The user can find biomedical concepts (pathways, MeSH terms, GO terms) enriched for a list of genes or associations between concepts based on overlapping gene sets.
  22. 22. Demo Screenshots Terry Weymouth Tuesday, Nov 5, 2013
  23. 23. Demo Site Login
  24. 24. Dataset Explorer - Overview
  25. 25. Dataset Explorer – Summary Statistics
  26. 26. Dataset Explorer – Images (prototype) 1
  27. 27. Dataset Explorer – Hierarchical Clustering 1
  28. 28. Dataset Explorer – Hierarchical Clustering 2
  29. 29. Gene List Panel
  30. 30. NCIBI - Pubmed
  31. 31. NCIBI – Concept Explorer (ConceptGen)
  32. 32. NCIBI - Pubmed
  33. 33. NCIBI – Compound Network (MetScape)
  34. 34. NCIBI – Gene2Mesh
  35. 35. NCIBI – Metab2Mesh
  36. 36. Spotfire @ Michigan w/tranSMART
  37. 37. tranSMART Architecture – where Spotfire fits Option 1 – as a Core Application with Information Links to the underlying Data Stores Source: Stuart D, Harju J, Shi W, Hanauer D, Aronzon D, Liu J, Sharma R, Manion F, Xia H, Hutter C, Gruber S. tranSMART Supports a Post-GWAS Data Coordinating Center. American Medical Informatics Association Annual Symposium, Chicago IL, November 4-7, 2012.
  38. 38. tranSMART Architecture – where Spotfire fits Option 2 – as a Scientific Analysis Tool with capability to consume output from the Core Applications Source: Stuart D, Harju J, Shi W, Hanauer D, Aronzon D, Liu J, Sharma R, Manion F, Xia H, Hutter C, Gruber S. tranSMART Supports a Post-GWAS Data Coordinating Center. American Medical Informatics Association Annual Symposium, Chicago IL, November 4-7, 2012.
  39. 39. Spotfire: Translational Data – Novel GEA analysis Kruskal-Wallis test of all significantly differentially expressed probes vs. all clincal response criteria Overlay binned gene expression levels on time-ontrial plot Embedded links out to Entrez, Uniprot, etc.
  40. 40. Spotfire: Translational Data – Merge NGS and GEA
  41. 41. tranSMART | UM | Scaling to U-Michigan Medicine Platform Development Collaborations Athey/ Burant Collaboration • • • • MRC2 NIH Regional Metabolomics Center Genomics, Epigenomics • Proteomics Metabolomics • Data and Metadata • concerning phenotypic studies in investigational • weight management clinic • Others NIH National Metabolomics DCC @ SDSC Bio-specimen Repositories Next Generation Sequencing Core Nutrition Core Specified links to CRM and EHR resources • • • • Nephology • Broader enablement of Personalized Medicine Cancer Center Research IT Others schools and colleges
  42. 42. Thank you/Questions/Discussion Quiz: Which one is which?

×