OpenSpecimen - Overview

Initial Considerations

OpenSpecimen is a Laboratory Management software program designed specifically for labs to track specimen storage and processing based upon clinical study design.

 The OpenSpecimen General Design

 The standard workflow of collecting specimens:

1. There are two types of protocols that are supported by OpenSpecimen:

   1. Specimen-centric: for studies in which no patient data is collected or tracked with the sample (biobanking) 

   2. Participant-centric: for studies in which participant demographic and disease-specific data is collected, stored, and linked to specimen data.

      1. Planned: Longitudinal studies can be designed to specify details regarding specimen collection for predefined time points.

      2. Unplanned: No defined visits or specimen requirements are set allowing the user to record the collection of any specimen type at any time.

2. Listed below are key features associated with each Collection Protocol:

 What OpenSpecimen Offers

1. Opportunity for labs to comply with FDA and CLIA regulations for securing specimens

2. Assign roles to users that will restrict access to PHI and access to specific Protocols

3. Associate Individual consent statements with each patient

   1. Query users by specific consent events

   2. Attach signed consent pdfs

4. Upload and extract text from Pathology Reports

5. Design specimen requirements per visit instructing coordinators regarding collection criteria

6. Query samples or participants based on any criteria recorded in your Collection Protocol

7. Create a customized dashboard with your metrics of interest

8. Create custom forms to record study-specific information

9. Create derivatives and aliquots (may be defined in CP)

10. Automatically generate and print labels according to a predefined schema

11. Automatic assignment of storage locations to parent specimen, derivatives, and aliquots

12. Restrict sample storage by Sample Type and/or Collection Protocol

13. Record Processing Events, for example:

    1. Freeze (recording freeze media used)

    2. Fixation (record fixative used)

    3. DNA/RNA extraction, etc.

14. Reserve specimens for specific projects or collaborators

15. Automatically mark specimens as ‘closed’ when exhausted

16. Distribute and receive specimens for outsourcing or collaborations

 What OpenSpecimen Does Not Provide or Offer

1. A clinical laboratory information management system (LIMS)

2. Direct interface with Epic (this option is supported by OS, but the University of Utah does not yet support this option).

   1. If you are interested in interface for your lab, the laboratory director should complete a Help Desk ticket

3. Ability to use your legacy sample numbering system as the primary participant ID or specimen IDs.

4. Automatic translation and upload of legacy data

   1. Supports manual upload of bulk data in .csv format

   2. User must map legacy data fields to fields in OpenSpecimen

Unique Considerations

1. If projects are assigned different IRB numbers, use one Collection Protocol per IRB.

   1. Add the same participant to multiple CPs with the click of a button

   2. Restricts study-specific data to the appropriate protocol

   3. Distribute specimens to the specimen-centric Tissue Bank Protocol for storage without compromising PHI

   4. Tissue Banks that store PHI and other patient data will use a Participant-centric protocol.

2. You must be open to change regarding modifications to the sample process flow and specimen labeling schema used by your laboratory.

   • Import of legacy data can be performed maintaining the current sample labeling, but implementing new specimen labeling will likely be necessary.

3. If custom data fields are required by the Collection Protocol, custom forms can be designed, but this process involves a learning curve to use the advanced features. The BMIC is here to help with that.

4. A networked label printer is required for label printing.