OpenSpecimen 101 Training
Introduction
Welcome to OpenSpecimen 101!
The following course is designed to provide guidance on how to use and navigate features in OpenSpecimen, thereby assisting you with managing your specimen storage and processing within a lab for a clinical study.
By the end of this course, you should be able to understand not only the the basics of how OpenSpecimen can be configured, but also know how to choose your collection protocol, register participants, enter visit information and collect specimens, process specimen derivatives and aliquots, and manage specimen storage.
Enroll in the OpenSpecimen Canvas 101 course to learn the basics:
Overview of OpenSpecimen Application
The basic design of most projects involve registering participants. Each participant has one or more visits at which one or more samples are collected and processed at each of the visit events. It should be noted that occasionally a lab / study records only specimen data and OpenSpecimen is able to accommodate this as well.
Collection Protocols (CPs) represent the lab’s specific workflow, the expected visits and the specimens to be collected. CPs are unique to each study. For each of your studies, the BMIC staff will work you to configure a unique CP which allows the study team to set the number of events (Visits) along with the number of expected specimens to be collected at each visit, and document the processing associated with each sample.
OpenSpecimen supports this one-to-many concept as shown in the diagram below where the participant has one registration event, then one or more subsequent visits where clinical data can be captured at each visit. Additionally, one or more samples are collected and processed at each of the visit events
Figure 1 represents the types of information that can be captured at each level of the data. This predesigned template provides a method to link each sample back to the person from whom it was obtained and the clinical data associated with that person.
Samples can be collected at PLANNED or UNPLANNED visits. Continue reading to learn more!
Overview of Sample lineage : the relationships of processed samples
Primary samples that are collected directly from a participant are typically processed into other sample types which are either stored or aliquoted and stored. (expand below for explanation)
This is an example of a typical lifecycle of whole blood processed into serum or DNA and then aliquotted.
In OpenSpecimen, this hierarchical relationship is represented in a parent-child structure. Samples of any lineage can be parents of additional samples. So these relationships do not stop at the aliquot level.
If a specimen type changes from the parent to the child, then the child sample is ‘Derived’ from the parent.
If the specimen type does not change, the child specimen is considered an ‘Aliquot’.
For instance, it’s possible to make a primary cultured cell line from a frozen aliquot of PBMCs. This relationship is captured by creating a derivative from an aliquot.
OpenSpecimen uses colored dots as a visual indicator of status to show the status of a sample:
(green) = sample available
(red) = sample processed into another product and is no longer available (ie,closed)
(yellow) = pending
(grey) = missed or not collected
(pink) = pooled
(purple) = reserved
(blue) = distributed
Click on the topics below to get started!
Table of Contents
CTSI BMIC Help Center https://ctsi.utah.edu/cores-and-services/bmic