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Informatics in Breast Cancer ResearchI-SPY 2 TRIAL & TRANSCEND
Sarah Davis, MSUniversity of California, San FranciscoDecember 6, 2011
I-SPY 2 TRIAL
Five Critical Components
• Neoadjuvant Setting
• Molecular and Imaging Biomarker Guidance
• Multiple Drugs Tested Simultaneously
• Adaptive Trial Design
• Common Platform for Sharing Data
The I-SPY 2 TRIAL Changes the Paradigm
I-SPY 2 TRIAL
• Screen phase 2 agents in combination with standard chemotherapy in neoadjuvant setting– Endpoint is pCR– Intermediate endpoint is MRI Volume
• Accelerate process of identifying drugs that are effective for specific breast cancer subtypes– Integration of biomarkers
• Reduce the cost, time, and number of patients needed to get effective drugs to market– “threshold” is 85% predicted likelihood of success in a 300-patient
phase 3 trial for drug-biomarker pair
Design goals of I-SPY 2
I-SPY 2 TRIAL
S
U
R
G
E
R
Y
* HER2 positive participants will also receive Trastuzumab. An investigational agent may be used instead of Trastuzumab.
Tissue
Paclitaxel* +Investigational Agent C AC
MRIBiopsy
Blood Draw
MRIBlood Draw
MRIBlood Draw
Paclitaxel* +Investigational Agent D AC
Paclitaxel* +Investigational Agent E AC
Paclitaxel* +Investigational Agent B AC
Paclitaxel* +Investigational Agent A AC
Paclitaxel*
AC
ON
STUDY
MRIBiopsy
Blood DrawMUGA/ECHO
CT/PET
Screening
RANDOMIZE
Consent #2Treatment Consent
Consent #1
I-SPY 2 Adaptive Trial Design
I-SPY 2 TRIAL
S
U
R
G
E
R
Y
Tissue
Paclitaxel* +Investigational Agent C AC
MRIBiopsy
Blood Draw
MRIBlood Draw
MRIBlood Draw
* HER2 positive participants will also receive Trastuzumab. An investigational agent may be used instead of Trastuzumab.
Paclitaxel* +Investigational Agent D AC
Paclitaxel* +Investigational Agent E AC
Paclitaxel* +Investigational Agent B AC
Paclitaxel* +Investigational Agent A AC
Paclitaxel*
AC
ON
STUDY
MRIBiopsy
Blood DrawMUGA/ECHO
CT/PET
Screening
RANDOMIZE
Consent #2Treatment Consent
Consent #1
I-SPY 2 Adaptive Trial Design (con’t)
I-SPY 2 TRIAL
S
U
R
G
E
R
Y
Tissue
Paclitaxel* +Investigational Agent C AC
MRIBiopsy
Blood Draw
MRIBlood Draw
MRIBlood Draw
* HER2 positive participants will also receive Trastuzumab. An investigational agent may be used instead of Trastuzumab.
Paclitaxel* +Investigational Agent D AC
Paclitaxel* +Investigational Agent E AC
Paclitaxel* +Investigational Agent B AC
Paclitaxel* +Investigational Agent A AC
Paclitaxel*
AC
ON
STUDY
MRIBiopsy
Blood DrawMUGA/ECHO
CT/PET
Screening
RANDOMIZE
Consent #2Treatment Consent
Consent #1
Paclitaxel* +Investigational Agent FG AC
I-SPY 2 Adaptive Trial Design (con’t 2)
I-SPY 2 TRIALI-SPY 2 Adaptive Trial Schema:Screening & Randomization
Patient presents with newly diagnosed
≥ 2.5cm invasive tumor consents to be Screened
Core biopsy to assess eligibility
Eligibility determined by: Ability to tolerate MRI Ability to generate 44k
Agilent microarray Other clinical variables Patient not on study
Not considered good candidate for chemotherapy
Patient On StudyRandomized to treatment arm based on: ER, PR status HER2 Status MammaPrint
scoreIs patient:• MammaPrint
Low Risk• ER + and
HER2 -
Yes
NoEligibility Assessment Process
I-SPY 2 TRIAL
How biomarkers are used in I-SPY 2
Qualifying Biomarkers
RPMA Pathway Markers Drug Sensitivity Predictor RCB Predictor (Affy Array) ....
Used to Validate Response to Therapy, done in CLIA Lab
Exploratory Biomarkers
Reflects Next Generation Technology (keeping pace)
DNA Methylation Exon Sequencing RNA Sequencing miRNA Circulating Tumor Cells Pharmacogenomics MRI SER Segmentation ....
StratificationBiomarkers
Used for Stratification, Response to Therapy
(may require IDE)
ER, PR, HER2 (Community)MammaPrint (Agilent array)TargetPrint (Agilent array)MRI Volume (Sentinelle)
I-SPY 2 TRIAL
Biospecimen Processing in I-SPY 2
Biospecimen Collected
Biospecimens Processed Tissue sectioned, tumor cellularity assessed Tissue processed (per SOP) Samples aliquoted, stored (per SOP)
Ship to I-SPY Lab
Assays Performed, Results Obtained(Stratification, Qualifying, Exploratory)
Ship to Research Labs (per Protocol)
caIntegratorTolven eCHR(Case Report Form)
Assays Results Reported
Stratifying Qualifying, Exploratory
I-SPY 2 TRIAL
Informatics Needs of I-SPY 2
• Manage information across multiple sites• Data gathering must be closely monitored as the trial
depends on rapid eligibility determination and therapeutic intervention - do not want to delay therapy
• Randomization as a web service (automated - but with review)
• Combining evaluation of drugs and biomarkers together– Biomarker data is of various types (arrays, imaging volume,
numeric scales, etc..)
• Scientists need access to data early and in an integrated fashion (one stop shopping)
I-SPY 2 TRIAL
What is TRANSCEND?
TRANslational Informatics System to Coordinate Emerging Biomarkers,
Novel Agents, and Clinical Data
An IT Bundle to Support Adaptive Trials with Novel Agents and Emerging Biomarkers
I-SPY 2 TRIAL
TRANSCEND Objectives
• Develop an information management infrastructure to support adaptive clinical trials like I-SPY 2
• Provide real-time data verification for more efficient analysis of trial data
• Provide a demonstration of caBIG infrastructure in use in a large multi-center trial
• Demonstrate integration of a clinical system (electronic health record system) with a clinical research infrastructure
I-SPY 2 TRIAL
Physician Reported Data
• A large fraction of clinically produced data in EHRs is ‘narrative’ text and not computable
• EHRs typically focus on ‘primary use’ of data, so narrative text is fine for this – provisioning clinical processes and care
• “Secondary Use”– Eg: Prospective/Retrospective research, Quality Improvement,
Comparative effectiveness– Typically requires analytics, which require structured, high-
quality, “controlled” data
I-SPY 2 TRIALWhat is new or different about TRANSCEND?
• Using a clinical information system rather than Clinical Trials Management System to collect patient data through CRFs
• Everything is web accessible without the need of downloadable plug-ins
• Randomization is adaptive, functions via web service• Integration of caTISSUE with a clinical information system
in the context of a trial• Using caINTEGRATOR v2.0 as a scientist portal to study
data– caARRAY for storing data that is accessible via caINTEGRATOR
I-SPY 2 TRIAL
Tolven eCHR
Data Coordinating
Center
Study SitesCase Report
Forms
Agendia
Integration Hub
(caXchange)
caTissue Suite caIntegrator
caAers caArray
Research Labs
MD Anderson
Randomization Engine
Automated interface
Manual interface
TRANSCEND - Systems Overview
I-SPY 2 TRIAL
TRANSCEND Interoperability
Standards for Data Exchange• Open-source HL-7 RIM (eCHR)• Semantic Interoperability modeled on BRIDG 2.1
– Use of caDSR Common Data Elements
Systems for Data Exchange• caExchange• iHUB-Mirth Connect (Enterprise Service Bus)
I-SPY 2 TRIALImplementation and Use of TRANSCEND in an Adaptive Clinical Trial
• Web-based and very easy to use for the end-user– Study Coordinators, Monitors, and Investigators
• Auto-population of data across systems reduces manual data entry errors– Specimen IDs in caTissue
• Real time data collection & review reduces delays in getting trial data to Data Review Committees and Trial Investigators
I-SPY 2 TRIAL
• Electronic copy of source documentation with each CRF
• Easy to complete case report forms with smart logic
TRANSCEND – eCHR Data Collection
I-SPY 2 TRIAL
• Real-time data review and verification
• Instant submission of CRF with source documentation to Data Coordination Center
TRANSCEND – eCHR Data Verification
I-SPY 2 TRIAL
TRANSCEND – eCHR Data Collection (con’t) • Email alerts to when a CRF is
ready for review & verification
• Email alerts when a CRF is rejected by the DCC
I-SPY 2 TRIAL
TRANSCEND – eCHR Data Collection
I-SPY 2 TRIAL
What Were the Challenges for End-Users?
• Change in Clinical Research Culture– Real time data collection & verification
Study Coordinators:• Cannot wait weeks to complete a case report form• Need case report forms to be verified before patient can proceed in
trial• Make source data available electronically and de-identified
Trial Monitors:• Cannot wait weeks/months to review case report forms for data
entry accuracy• Challenges normal way of business – drastically reduce time spent
on-site at each study site
• Identified gaps in standards of verifying data– Trial Monitors are also playing the role of Data Auditor
I-SPY 2 TRIAL
What Were the Challenges Technically?
• Overall– Move towards ‘enterprise bus’ as an integration rather than API-
based point-to-point integration – Install systems early to deal with logistical issues far in advance
of needing the systems
• caExchange– Required custom Java programming– Transaction rollback not an option
• However iHub has this capability
• caTissue– Transaction rollback not an option
• Requires manual removal of an entry
I-SPY 2 TRIAL
Future Direction with 2TRANSCEND
Integrate additional platforms• Web-based Patient Communication and Care Plan
– Aids in decision making about participating in a clinical trial as well as enabling study staff to communicate with patient’s regarding study appointments
• Web interface allowing patients to directly input:– Adherence to treatment regimens– Adverse events (PRO-CTCAE)– Follow-up information
• Adopt Annotation Imaging Mark-up (AIM) tool to enable researches ability to centrally review and analyze images
I-SPY 2 TRIALHow to Achieve TRANSCEND Functionality with Other Systems
TRANSCEND-like interoperability with other systems in support of clinical trials & biobanking
•OpenClinica•Local Institutional CTMSs •Cooperative Group Trial Management Systems •? Others ??
I-SPY 2 TRIAL
• Dr. Laura Esserman – I-SPY TRIAL, TRANSCEND PI (UCSF)• Dr. Michael Hogarth - TRANSCEND Technical Director (UC Davis)• Meg Young – TRANSCEND Project Manager (UCSF)• Sarah Davis – I-SPY 2 TRIAL Manager (UCSF)
– Joyce Lee, Julia Lyandres (software testing, quality control)
• Sorena Nadaf – Informatics Design (UCSF)• Dr. Angela DeMichele – Clinical Oncology (UPenn)• Don Berry & Kyle Wathen – Randomization Engine (MDACC)• John Churin – Software Lead Engineer (Tolven)• Ashwin Koleth – Software Development (Cyrus-XP)• John Koisch – Architecture (NCI)• Kathy Hajopoulos – Project Oversight (UCSF)• Nancy Roche – Project Oversight (SAIC)
TRANSCEND TEAM
TRANSCEND development funded by the National Cancer Institute (NCI), Subcontract # 28XS197
I-SPY 2 TRIAL
• Dr. Laura Esserman – I-SPY TRIAL, 2TRANSCEND PI (UCSF)• Dr. Michael Hogarth - 2TRANSCEND Technical Director (UC Davis)• Sarah Davis– 2TRANSCEND Project Manager (UCSF)• Meredith Buxton – I-SPY 2 Program Director (UCSF)• Dr. Angela DeMichele – Clinical Oncology (UPenn)• Don Berry & Kyle Wathen – Randomization Engine (MDACC)• John Churin – Software Lead Engineer (Tolven)• Ashwin Koleth – Software Development (Cyrus-XP)• Eve Shalley – Project Manager (NCI)• Santosh Joshi & CBIIT caCIS Team (NCI)• Ian Fore & CBIIT caTissue Team (NCI)• Paul Baumgarnter & CBIIT caAERS Team (NCI)• Juli Klemm & CBIIT caArray Team (NCI)• Shine Jacob & CBIIT caIntegrator Team (NCI)• Robert Shirley & CBIIT Architechture Team (NCI)
2TRANSCEND TEAM
2TRANSCEND development funded by the National Cancer Institute (NCI), Agreement No. 12ST1002
I-SPY 2 TRIAL
TRANSCEND
Breakout B – End-User Session
• Detailed Workflow from End-Users Perspective
• Questions & Feedback from Community
I-SPY 2 TRIAL
Tolven eCHR
Data Coordinating
Center
Study SitesCase Report
Forms
Agendia
Integration Hub
(caXchange)
caTissue Suite caIntegrator
caAers caArray
Research Labs
MD Anderson
Randomization Engine
Automated interface
Manual interface
TRANSCEND - Systems Overview
I-SPY 2 TRIAL
TRANSCEND & caTissue - WorkflowTolven eCHR
Data Coordinating
Center
Study SitesCase Report
Forms
Agendia
Integration Hub
(caXchange)
caTissue Suite
Automated interface
Manual interface
I-SPY 2 TRIAL
TRANSCEND & caTissue – Workflow (con’t)
Study Coordinator (CRA)
- In Clinic - In Tolven
Collect Sample
CRF Completed
(specimen ID created)
Specimen Created with ID,
etc.
Specimen Processed,
details recorded
Lab Staff
- In caTissue
I-SPY 2 TRIALTRANSCEND & caTissue – Workflow (con’t 2)Study Coordinator (CRA)
- In Clinic - In Tolven
Collect Sample
CRF Completed
(specimen ID created)
Specimen Created with ID,
etc.
Specimen Processed,
details recorded
Lab Staff
- In caTissue
I-SPY 2 TRIALTRANSCEND & caTissue – Workflow (con’t 3)
Collect Sample
CRF Completed
(specimen ID created)
Specimen Created with ID,
etc.
Specimen Processed,
details recorded
Study Coordinator (CRA)
- In Clinic - In Tolven
Lab Staff
- In caTissue
I-SPY 2 TRIALTRANSCEND & caTissue – Workflow (con’t 4)
I-SPY 2 TRIALTRANSCEND & caTissue – Workflow (con’t 5)
I-SPY 2 TRIALImplementation of caTissue in the Lab
• Set up of Lab workflows and caTissue– Setting up actual freezer and mapping– Printing of Labels from caTissue– Setting up child-specimen in caTissue
• Lessons learned– Engage Lab users in how caTissue works/capabilities
• Helps with setting up workflows/collection protocols
I-SPY 2 TRIAL
Questions & Feedback
• Can other Institutions/Groups extend interoperability of caTissue as used in TRANSCEND?
• What other systems would you integrate with caTissue?
I-SPY 2 TRIAL
Questions & Feedback (con’t)
• Differences in biobanking for adaptive clinical trials vs. traditional?
• What standards are used in clinical research?– Does this pose any challenges?
I-SPY 2 TRIAL
Questions & Feedback (con’t 2)
• How to engage participation from End-Users in design/set-up?
I-SPY 2 TRIAL
Questions & Feedback (con’t 3)
• How would you go about setting up IT systems to support your projects/workflow?– What would be the architecture?– Who would be the user of each system?