CCHMC’s Biobanking Software –
James Morgan
April 3, 2014
Biomaterial Tracking & Management
Biomaterial
Tracking &
Management
Topics to be addressed:• Biobanking definitions• Need for biobanking software• History of BTM-CCHMC• Description of BTM• CCHMC custom BTM supplements
– Bulk uploads, ETLs– i2b2 feed (de-identified for cohort identification)
• Process to get started with BTM– https://btmhelp.cchmc.org/
Presentation Overview
What is biobanking?• Storing biological (blood, urine, skin, etc.)
samples (usually human) for clinical or research purposes
– Usually in liquid nitrogen freezers -80O/-194OC
– Samples will be viable for research for ?? Years
• First step in genomics/personalized medicine
Biobanking Definitions
What is the purpose of biobanking?• To allow researchers to examine DNA and
attempt to determine how faults in DNA cause diseases.
• Once research programs can work out the cause of different diseases and conditions, they can use this knowledge to begin to develop treatments or cures that can improve or save the lives of those affected.
http://www.biomedinvo4all.com/en/research-themes/medical-data-and-biobanks/medical-data-and-biobanks-basics#1
Biobanking Definitions
Biobanking - CCHMC• In BTM, CCHMC tracks ~ 40 biobank
freezers with ~ 500,000 samples stored
Biobanking Definitions - CCHMC
Biobanking Software• Needs to:
– Track samples (usually barcoded) & their locations in freezers
– Capture data associated with samples • Type, Volume, D/T collection, Test results
– Connect samples to other samples– Associate samples to patients– Retain clinical data associated with patients– Connect patients to other individuals (family
members)
Need for biobanking software
BTM-CCHMC
• ~ 7 years ago CCHMC made the decision to outsource biobanking software versus build it in-house
• Software and support team were/are funded through Division of Pathology & Center for Autoimmune Genomics and Etiology (CAGE)
History of BTM-CCHMC
Daedalus Software, Inc. (DSI) &Biomaterial Tracking & Management (BTM)
• Selected as CCHMC’s biobanking software solution– DSI retains the software code (Java-based)– CCHMC hosts both the application and underlying
database (SQL)– CCHMC performs custom database development– CCHMC works closely with DSI to guide/influence
future versions of BTM• ~ 3 upgrades/year• ~ 1 user group meeting/upgrade
History of BTM-CCHMC
BTM Purpose• Facilitates unique identification and storage of
large numbers of samples and tracks each sample’s movement throughout CCHMC.
Description of BTM
BTM (Cincinnati Biobank) Obtained CAP (College of American Pathologists) Certification July 2013
Description of BTMCAP Certification
• ~ 40 policies, procedures & work instructions were created in Compliance 360 to obtain certification
CCHMC custom BTM supplements
CCHMC Custom BTM Database Development
• Development performed in SQL– SQL Server Integration Services (SSIS) & SQL Server
Reporting Services (SSRS)– Bulk uploads – requirements = migration set
• Lab equipment ETLs (Extract, Transform & Load)• i2b2 data feed (from BTM data warehouse)
– De-identified for cohort identification
• Reports (from BTM data warehouse)
**Note – these are custom projects, not turnkey solutions
BTM Database Development:• ETLs (Extract Transform & Load) from laboratory
equipment in the Cincinnati Biobank– Small volume DNA/RNA extraction equipment – Large volume DNA extraction equipment– DNA, RNA and protein analysis – Quality Control
CCHMC custom BTM supplements
BTM Database Development:• i2b2 data feed from BTM data warehouse – for de-identified cohort identification
CCHMC custom BTM supplements
Process to get started with BTM
• Contact BTM Team via website or email address:– https://btmhelp.cchmc.org/
• Everything submitted via website is logged as a helpdesk ticket in RT
• Schedule a demo of BTM
Process to Get Started with BTM
Steps for BTM Implementation:
Process to Get Started with BTM
https://btmhelp.cchmc.org/
Steps for BTM Implementation:• Permission/request from Principal Investigator
– Form on website– Option for Principal Investigator to appoint designee
• Users setup in Test Environment – Test workflow– Setup storage– Test configuration changes
• Request to create BTM bank in PROD
Process to Get Started with BTM
BTM Team:
Process to Get Started with BTM
David Campbell, Sr. DBA28 yr. exp. database design/dev.BA – IS, MS in Info. Security
Sandip Patil, Apps. Spec. IIDisease research & I.T. exp.PhD – biochemistry, MBA
Michael Carr, Sr. Systems Dev.13 yrs. exp. app. developmentBA & MS – Psych.
James Morgan, BTM Mgr.Exp. organ/tissue transplant & I.T.BA – Bus., MS – Tech.
Todd Hoffert 8 yrs. exp. database dev. (ETL & SSRS)BA – Bus.