CCHMC’s Biobanking Software – James Morgan April 3, 2014 B iomaterial T racking & M anagement B iomaterial T racking & M anagement

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 – Presentation Overview

What is biobanking? Storing biological (blood, urine, skin, etc.) samples (usually human) for clinical or research purposes –Usually in liquid nitrogen freezers -80 O /-194 O C –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. 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

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 bank level

Description of BTM - Banks in test environment

BTM (Cincinnati Biobank) Obtained CAP (College of American Pathologists) Certification July 2013 Description of BTM CAP 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: Bulk Uploads – Migration Set CCHMC custom BTM supplements

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

BTM Database Development: Reports from BTM data warehouse CCHMC custom BTM supplements

Process to get started with BTM Contact BTM Team via website or address: – 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

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. DBA 28 yr. exp. database design/dev. BA – IS, MS in Info. Security Sandip Patil, Apps. Spec. II Disease research & I.T. exp. PhD – biochemistry, MBA Michael Carr, Sr. Systems Dev. 13 yrs. exp. app. development BA & 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.

Questions BTM Conclusion