Index of Biospecimens

1. Duke Index of Biospecimens to Enable Sharing of Biospecimen Collections Index of Biospecimens Aenoch J. Lynn and Helena J. EllisDuke Biobank and Duke Translational Medicine Institute, Duke University, Durham, NC Institution Homepage URL Organization Collection Protocol Name Start Date End Date Specimen Availability Available to non-Duke Organizations * Available to Commercial Organizations * Available to non-US Organizations * Collaboration Required * Abstract The Duke Biobank created the Index of Biospecimens (the Index) to promote the sharing of sample collections. The Index holds metadata on collections, participants, samples; aggregate counts on participants and samples; and attributes indicating additional types of data that may be available and how the samples may be shared. Individual participant data are not held in the Index. Access to the Index is restricted through Shibboleth authentication. Problem Addressed Collecting samples is one of the most expensive steps in clinical and translational research. The Index of Biospecimens is a catalog of sample collections available for sharing within Duke. The Index allows researchers in need of samples for research to browse through a catalog of available collections and to contact PIs of collections of interest. User Interface Methods Acknowledgements Duke University School of Medicine Duke Cancer Institute DTMI Biomedical Informatics Core NIH/NCRR grant UL1 RR024128 Special ThanksBen Powers, IMS Kevin Meagher, IMS Henry (Hal) Beresford, DOCR Justin Levens, DOCR Search Interface Search Results • Duke Index of Biospecimens • Web tool to facilitate the secondary use of samples • Based on NCI’s Specimen Resource Locator and Common Biorepository Model (CBM) • Duke-specific extensions were added to meet Duke’s requirements • The CBM: • Was designed for national sharing of samples • Is a repository of sample collection metadata • Was developed by a national collation of academic and industry leaders • Data Governance for the Index • Duke researcher with a valid NetID may use the Index • Specimens must have been collected under an IRB protocol • PI of the collection maintains control • All requests to use samples goes through PI • PI responsible for honoring participant consents • Collections are not moved from their storage location • Data in the Index may be removed at any time Contact Person Name Email Address Phone Address Group Annotation Availability Patient Demographics Available * Exposure History Available * Histopathologic Data Available * Non-Omics Lab Data Available * Longitudinal Specimens Available * Matched Specimens Available * Family History Available * Study Treatment Data Available * Follow-up Permissible * Outcome Information Available * • Getting Data Into the Index • CBM data model too complex for most data managers • Partnered with Duke Office of Clinical Research (DOCR) to assist with data manipulation • Help larger groups with programmers load their own data into the Index • Email Biospecimen Expediter for help Making Connections – Has Collection Successful diabetes researcher with over 15 years of clinical research experience has a sample collection with: • 300 participants • 140 male, 145 female, 10 unknown, 5 not reported • White, Black, Asian, native American • 1200 samples • Collected whole blood • Type 1 Diabetes Mellitus diagnosis • 300 blood, 300 serum, 600 DNA • All samples stored at -80°C • Additional demographics, Lab data, Family history, Participant medical history Collection Details • Application Code • The Index of Biospecimens is based on the NCI’s Specimen Resource Locator, version 2.0 • Source code for the SRL is available through NCI • Customizations performed by Information Management Services (IMS), Calverton, MD • Modified source code available through the Duke Biobank or IMS Index Class Model (based on the CBM) Participant Collection Gender * Ethnicity * Participant Count Race * † Reference PubMedID Diagnosis * • Making Connections – Wants Samples • Search web interface for collection metadata • Identify collections of interest • Contact PI of collection to request access to samples Duke Annotation Omics Lab Data Available * Medical History Available * Consent for Secondary Use * Data Shared Outside of Duke Short Protocol Description PI Preferences for Method of Contact Hide Group Affiliation ? ! ? ? † = New addition = Duke-specific table * = Queryable Field Specimen Collection Anatomical Source * Specimen Type * Participant Count Research Study Preservation * Existing Collection Secondary use of existing collections Existing Collection New Collection Existing Collections Primary collections are expensive Search collection metadata Existing Collection Index of Biospecimens Existing Collection Existing Collection • Subject recruitment • Subject consenting • Sample collection • Sample processing (919) 668-8026 biobanker@duke.edu Existing Collection • Searching existing collections • Sample processing Existing Collection Patient Age Group * (At Time Of Collection) Existing Collection Contact Aenoch Lynn aenoch.lynn@duke.edu +1-919-668-8026 Helena Ellis Duke Biobank Director helena.ellis@duke.edu +1-919-668-7831 Existing Collection Existing Collection Reuse of existing collections saves money and resources • Aggregate data on subjects and samples • Gender • Race/Ethnicity • Age at Collection • Diagnosis • Anatomical Source • Specimen Type • Preservation • Availability • Annotations Existing Collection Existing Collection Researchers in need of research samples had no easy way of discovering if existing collections are available at Duke Researcher gets contact information for existing collections that match search criteria