From the Office of Biorepositories and Biospecimen Research
Part of the Mission and Goals Statement
… the limited availability of carefully collected and controlled, high-quality human biospecimens annotated with essential clinical data and properly consented for broad investigational use … is repeatedly identified by the scientific community as a leading obstacle to progress in post-genomics cancer research …
National Cancer Institute (NCI)
Office of Biorepositories and Biospecimen Research (OBBR) http://biospecimens.cancer.gov/about/overview.asp
Accessed April 4, 2014

For Researchers
• Combine different biobanks
– Hollings Cancer Center
– MUSC Brain Bank
– SCTR biobank
• Link different data sets on one screen

For Biorepository Personnel
• Add additional knowledge relating to their samples without having to go to many different systems.

Admin Slide
• Filter by ICD-9 codes – diagnostic descriptions
• Filter by demographics
– Age
– Sex
– Race
• Ability to de-identify data or eliminate entirely
• Maintain an audit trail of samples reviewed
• Add to shopping cart or wish list
• Simple to use

Combines data from multiple data sources
• Campus wide use of TissueMetrix using Oracle
• Clinical Data Warehouse using Sybase IQ
• Cancer Registry’s IMPAC system using MS SQL
• Cerner CoPathPlus streaming HL7 messages
• PenRad for mammography informatics
• Lucene.Net indexing ICD-9 codes
• Excel spreadsheets

Geek Slide
• Portal uses DNN as foundation
• Authentication using LDAP
• ICD-9 searches are created using Lucene.net
• User Interface uses HTML5, JavaScript, jQuery
• Web Services are written in JSON
• MS SQL is used for middle tier
• 128 bit Encrypted values change every 3 minutes

YES
Does it have a Web
Service?
NO
YES
START
Identify
System.
Can we
Transform Data
Internally?
NO
Staging
Area
Transform as needed
Application
Web Service
Balancing Act

TissueMetrix using Oracle
• Export data nightly to MS SQL database Data
Warehouse
• Data is transformed and cleansed so it has consistent meaning.
• May involve restructuring, redefining, filtering, combining, recalculating and summarizing data fields

Disease Sites
Anal
Bladder
Breast
Cases
TissueMetrix data
Tumor
Primary
Plasma Buffy Coat
20 5 9 10
700 256 451 277
250 190 365 292
Plasma
19
233
345

Clinical Data Warehouse using Sybase IQ
• Web Service to access data
• Pass in an MRN and Date Range get back ICD-9
Codes
• Working on:
– Getting back Lab results
– Getting back Treatments
– Other areas

Commercial Program using MS SQL
• Web Service to access data
• Pass in an MRN and get back
– Tumor Information
– Histology
– Grade
– Treatment
– Other areas

Cerner CoPathPlus streaming HL7 messages
• HermeTech HL7 listener
• De-identifying Message and build the document based upon the role of the user.
• Pass the data down in JSON to be displayed as standard HTML

Path
Reports
Web Service
TissueMetrix
TBD
Sources
Radiology
Cancer
Registry
CDW

• 128 bit Encrypted value changes every 3 minutes and is included in the Header of every browser request
• MRN is passed encrypted with key that changes every 3 minutes
• Values are checked on the Web Server to be within accepted values before sending to the
Database Server

• Provides researchers with a simplified view of specimens in inventory
• Users do not require direct access to the database
• Provides for electronic messaging when further interest in specimens is identified
• Identifies availability of specimens for grant proposals

Anita L. Harrison, MPA
Associate Director of Administration
Hollings Cancer Center
Medical University of South Carolina
William Morgenweck morgenww@musc.edu
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