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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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CCHMC’s Biobanking Software –

Biomaterial

Tracking &

Management

James Morgan

April 3, 2014

BiomaterialTracking &Management


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

    • Connect samples to other samples

    • Associate samples to patients

    • Retain clinical data associated with patients

    • Connect patients to other individuals (family members)


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)


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


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

    • 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


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. 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.


BTM Conclusion

Questions


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