Introduction
Welcome to OpenSpecimen 101!
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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.
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Overview of OpenSpecimen Application
The basic design of any project involves 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
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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! |
Planned Sample Overview
Visits are set to capture the known time points at which specimen collections will occur.
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The CP for this example ‘Demo study” has been configured to collect samples at three known visits.
 Each visit has characteristics that can be preset. For example, this visit will always occur at the University Hospital and, in order to be enrolled in this study, the requirement is that a participant has a New Diagnosis of kidney disease with Type 1 diabetes. Presetting this saves the coordinator from having to record this information for each patient.  Each visit has defined primary samples that will be collected. Each sample has its own characteristics (like volume and collection container). These can be preset per protocol to save data entry time for the study team. Of course these pre-set values can be updated if volume collected is different! In this Baseline visit, the primary samples to be collected are whole blood in four different containers (EDTA, Sodium Heparin, PAXgene, and Serum separator) and 10 mL of urine.  Primary samples that have expected processing events are pre-programmed for ease of data collection. Clicking the arrow to the left of any sample will expand the specimen tree associated with that sample.  This protocol calls for 24 mL of whole blood collected in sodium heparin tubes to be processed into 6 2mL aliquots of plasma and 3 aliquots of PBMCs at 1 x 107 cells per aliquot. |
Unplanned Sample Overview
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Some biobanking protocols allow for collection of a variety of specimens which cannot be predicted ahead of time. OpenSpecimen allows for the collection of any specimen type under an event. Because these specimens are not preplanned, details about the sample are not already recorded in OpenSpecimen. All information about the specimen needs to be recorded for each sample at the time of collection. See guide <insert link>.  |
Single Visit Studies or Recollection Events Overview:
Some studies have only a single time point at which one or more known samples are collected and occasionally a recollection is necessary.
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Any visit (and associated specimens) can be collected more than once. The characteristics of that visit will remain the same as the original, but it will be assigned a new date and a new visit name. Consider a Baseline visit that was collected and a sample was damaged in transport. The baseline visit might have to be collected a second time prior to treatment. These two events can be captured using two Baseline visits. Example: at the Baseline visit, the serum separator tube of blood was hemolyzed and needs to be recollected. The damaged specimen can be labeled as such and a second Baseline visit can be collected to record the new serum separator tube.  Occurred visit table following collection of second blood tube considered to be a Baseline visit sample.  |
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)
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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.
 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:
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