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CCHMC’s Biobanking Software –

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CCHMC’s Biobanking Software –. B iomaterial T racking & M anagement. James Morgan April 3, 2014. B iomaterial T racking & M anagement. Presentation Overview. Topics to be addressed:. Biobanking definitions Need for biobanking software History of BTM-CCHMC Description of BTM

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  1. CCHMC’s Biobanking Software – Biomaterial Tracking & Management James Morgan April 3, 2014 BiomaterialTracking &Management

  2. 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/

  3. 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

  4. 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

  5. Biobanking Definitions - CCHMC Biobanking - CCHMC • In BTM, CCHMC tracks ~ 40 biobank freezers with ~ 500,000 samples stored

  6. 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 • Connect samples to other samples • Associate samples to patients • Retain clinical data associated with patients • Connect patients to other individuals (family members)

  7. History of BTM-CCHMC 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)

  8. 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

  9. Description of BTM BTM Purpose • Facilitates unique identification and storage of large numbers of samples and tracks each sample’s movement throughout CCHMC.

  10. Description of BTM - Accession Samples

  11. Description of BTM - Accession Samples

  12. Description of BTM - Accession Samples - Oncology

  13. Description of BTM - Accession Samples – Annotation form

  14. Description of BTM - Storage Hierarchy

  15. Description of BTM - Accession Samples – Storage Unit

  16. Description of BTM - Patient Data

  17. Description of BTM - Banks in production environment ** Note – data privacy protected @ bank level

  18. Description of BTM - Banks in test environment

  19. 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

  20. 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

  21. CCHMC custom BTM supplements BTM Database Development: • Bulk Uploads – Migration Set

  22. 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

  23. CCHMC custom BTM supplements BTM Database Development: • i2b2 data feed from BTM data warehouse – for de-identified cohort identification

  24. CCHMC custom BTM supplements BTM Database Development: • Reports from BTM data warehouse

  25. 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 • help-btm@bmi.cchmc.org • Schedule a demo of BTM

  26. Process to Get Started with BTM Steps for BTM Implementation: https://btmhelp.cchmc.org/

  27. 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

  28. Process to Get Started with BTM

  29. Process to Get Started with BTM BTM Team: • Sandip Patil, Apps. Spec. IIDisease research & I.T. exp. • PhD – biochemistry, MBA • Michael Carr, Sr. Systems Dev.13 yrs. exp. app. development • BA & MS – Psych. • David Campbell, Sr. DBA28 yr. exp. database design/dev. • BA – IS, MS in Info. Security • Todd Hoffert 8 yrs. exp. database dev. (ETL & SSRS) • BA – Bus. • James Morgan, BTM Mgr.Exp. organ/tissue transplant & I.T. • BA – Bus., MS – Tech.

  30. BTM Conclusion Questions