Bridging Clinical and Research Data through Informatics

Transcription

1 Bridging Clinical and Research Data through Informatics Bas de Veer MS University of Washington

2 ITHS Introduction One of 62 CTSA sites nationally Approximately 160 faculty and staff More than 6,000 researchers from nearly 200 institutions across the five-state WWAMI region

3 REDCap Setup at ITHS Multi-Instance Solution (Linux based) Main Production (6.0.1) Development/Test (6.1.0) Data Coordination Center (LTS ) LDAP Authentication By The University of Washington 0.6 FTE User Support/0.25 FTE System Administrator Projects / Active Users Monthly Classes (Intro & Advanced) Various Consulting Services

4 Bio-Medical Informatics Consult Team Data Migration Access/Excel to REDCap Case Report Form Development Custom Dynamic SQL Links Study Design Informatics Support EMR Report Building EMR Custom Queries

5 University of Washington Clinical Data Repository a.k.a. Amalga

6 UW Medicine Amalga Amalga Today: 3.8M patients, 22M visits, 220M+ lab results, 150M+ diagnoses & procedures over 17 years >60 data sources populating Amalga in realtime, hourly, or nightly Amalga Continues to Grow 20 Terabytes of data now 4M new messages/day 37 more sources planned Prioritization by Clinical Data Repository Oversight Committee (CDROC) 6

7 Amalga Clinical Data Repository

8 What is Amalga? A Data Aggregation Platform With an Orchestrated Ingestion Process Filing Services accept incoming files and messages from external systems Message Queues load the data into queues of data of the same type Parsers process the messages from the queues into database tables Integrated master patient index and identity management Integration Analysts perform these tasks on the Amalga team

9 What is Amalga? A Data Management/Reporting Platform Structured Query Language and the SQL Server Database Data manipulation: selecting, filtering, sorting, grouping SQL Server Integration Services Packaging data management tasks into jobs, moving data in/out of Amalga SQL Server Reporting Services Web delivery of production reports Amalga team Application Consultants plus Affiliate Developers perform these tasks Entire Amalga effort supported by a technical team of system and database administrators

10 New Type of Consult Service Previous Deliverable From Data Pull: Excel File Dense Insecure (IRB Nightmare!!) Snapshot of Data New Deliverable: Populate a REDCap Project Easy & Secure Access for Multiple Users Integration With Custom Research Data Automatic Updates (Optional)

11 REDCap Amalga Bridge Based of Chris Nefcy s REDCap Wrapper & REDCap API Christine Fong Adapted Those Into a C# Library Use the Library to Setup a SSIS* Task API Token URL of the REDCap Instance Type of Action Pull Data Dictionary Pull Data From REDCap Push Data Into REDCap One Time Or On a Schedule *SQL Server Integration Services

12 Case Study: LARC Project Title: Long Acting Reversible Contraception (LARC) Principal Investigator: Sarah Prager Desired Outcomes: Retrospective Study; Abstract EMR data from women over a three year period to determine efficiency and complications of Intra Uterine Devices (IUD s).

13 REDCap Amalga Bridge

14 Case Study: GICPP Project Title: SCCA Gastrointestinal Cancer Prevention (GICPP) Clinic: Electronic database of patients Principal Investigator: Andrea Burnett-Hartman ITHS KL2 scholar at FHCRC Mentors: John Inodomi and Bill Grady Desired Outcomes: Summarize GICPP patient information providers can use to improve patient care Provide a database to query for potential research studies

15 GICPP Patient Electronic Database Demographics DOB Race Gender Smoking status UW Medicine visits First visit Last visit Number of inpatient/outpatient Number of PCP visits Subsequent GICPP visits Cancer History Family history of cancer Personal history of cancer Incident cancer Initial GICPP visit Age Weight Reason for referral Provider Visit codes Medical Procedures and Diagnoses resulting from Procedures Colonoscopy Urine cytology Hysterectomy Colectomy Bladder cystectomy Genetic testing Medications Medications at GICPP visit Aspirin Statins Metformin

16 Amalga >100 database tables generated >10 Amalga tables queried multiple source systems HL7 patient registration MIND diagnoses and procedures ORCA notes Epic patient encounters ORCA and Epic medication orders 16 stored procedures created

17 Deliverable - REDCap 659 GICPP patients Data displayed in secure web-based form Data imported from Amalga Customized input controls Data organized into separate sections or forms

18 Users can add comments Hide fields when no data to display

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21 Lessons Learned Clinical Notes Natural Language Processing Two Distinct sets of Expertise are needed Study Design/REDCap Design Amalga Query Design Abstraction Projects have a Break-Even Point Depends on Complexity & Number of Records REDCap as Deliverable is preferable: Security Backups Biostatistics Frequent API Calls can have an impact on a normal REDCap installation Great Additional Source of Revenue

22 Acknowledgements Chris Nefcy Christine Fong, MS Tony Black, MA Sally Lee, PhD Principle Investigators: Sarah Prager, MD Andrea Burnett-Hartman, MD