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

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

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:• 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 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

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

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.

Questions

BTM Conclusion