CCHMC`s Biobanking Software

Report
Biomaterial
Tracking &
Management
CCHMC’s Biobanking Software –
Biomaterial
Tracking &
Management
James Morgan
April 3, 2014
Presentation
Overview
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/
Biobanking
Definitions
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 CCHMC
Biobanking - CCHMC
• In BTM, CCHMC tracks ~ 40 biobank
freezers with ~ 500,000 samples stored
Need for biobanking
software
Biobanking Software
• Needs to:
– Track samples (usually barcoded) & their
locations in freezers
– Capture data associated with samples
• Type, Volume, D/T collection, Test results
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Connect samples to other samples
Associate samples to patients
Retain clinical data associated with patients
Connect patients to other individuals (family
members)
History of BTMCCHMC
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 BTMCCHMC
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
Description of BTM
BTM Purpose
• Facilitates unique identification and storage of
large numbers of samples and tracks each
sample’s movement throughout CCHMC.
Description of BTM Accession Samples
Description of BTM Accession Samples
Description of BTM Accession Samples Oncology
Description of BTM Accession Samples –
Annotation form
Description of BTM Storage Hierarchy
Description of BTM Accession Samples –
Storage Unit
Description of BTM Patient Data
Description of BTM Banks in production
environment
** Note – data privacy protected @ bank level
Description of BTM Banks in test environment
Description of BTM
CAP Certification
BTM (Cincinnati Biobank) Obtained CAP
(College of American Pathologists)
Certification July 2013
• ~ 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
CCHMC custom
BTM supplements
BTM Database Development:
• Bulk Uploads – Migration Set
CCHMC custom
BTM supplements
BTM Database Development:
• ETLs (Extract Transform & Load) from laboratory
equipment in the Cincinnati Biobank
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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:
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i2b2 data feed from BTM data warehouse – for de-identified cohort identification
CCHMC custom
BTM supplements
BTM Database Development:
•
Reports from BTM data warehouse
Process to Get Started
with BTM
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
– [email protected]
• Schedule a demo of BTM
Process to Get Started
with BTM
Steps for BTM Implementation:
https://btmhelp.cchmc.org/
Process to Get Started
with BTM
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
Process to Get Started
with BTM
BTM Team:
Sandip Patil, Apps. Spec. II
David Campbell, Sr. DBA
28 yr. exp. database design/dev. Disease research & I.T. exp.
PhD – biochemistry, MBA
BA – IS, MS in Info. Security
Michael Carr, Sr. Systems Dev.
13 yrs. exp. app. development
BA & MS – Psych.
James Morgan, BTM Mgr.
Todd Hoffert
Exp. organ/tissue transplant & I.T. 8 yrs. exp. database dev. (ETL & SSRS)
BA – Bus., MS – Tech.
BA – Bus.
BTM Conclusion
Questions

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