Labs can be collected for either manual entry or via bulk import. Either way, the lab values entered on subject CRFs can be checked automatically by the system and subsequently flagged as out of range for further evaluation by a Clinician. A pre-specified determined measurement unit can also be auto-populated by the system.
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The remainder of this article will walk through setting up Lab Ranges in the system and how they are then applied. (click on each to open help on the topic)
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Enable Lab Range Functionality
To enable Lab Range functionality, check the study setting shown below from the Study Configurations page:
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Next, the appropriate user roles will need the right permissions. Since labs are tied to sites, and a site can be part of multiple studies, access to lab configuration is a host-level function. For this reason, access is a host-level permission:
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Create a form or set of forms to collect lab data
Many clinical studies collect labs of some sort - or variety. This article will cover all the aspects of a lab form that need to be set appropriately if you need the system to check lab normals. Conveniently, there is a public form library available to use a lab form example that is already set up appropriately as outlined in the steps below.
Identify the form as a Lab Form in the form properties, and ensure the visit transaction date is the date the labs were collected. This date will be what the system evaluates if the lab ranges are only applicable in a specified time period (as seen during lab range mapping).
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Use a dropdown field for the site to identify which lab was used, but do not create any choices within it. The lab sites are related to the study sites later on during setup in the Site Document Manager. The lab sites specified there will be what ends up populating these choices for the user entering data.
Once a dropdown field is in place, select the special property titled "Local Lab" as shown below.
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Lastly, use a fixed normalized table to collect the lab tests required. Fixed tables will pre-populate the first column based on the choices (lab tests) used in the dropdown field.
The table field types and names should individually match what is shown below, but depending on the information you want to populate on the table, not all of these fields are required
Additional columns/fields can be used as well but will not be part of the lab range checks.
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The choices included in the first column (dropdown field) need to match whatever the names of the labs are that will be used in the range source file (used in
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the next step).
In other words, if a lab test is named in the choices, it also needs to be present in the lab ranges file, even if it will not be checked.
The Radio group for checking the normal range shown above (field name: LABNORMNY) needs to have the choices No and Yes in that order, where No has a database value of 1 and Yes has a database value of 2.
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Configure the lab sites and range mapping
The Lab Range Manager is used to set up lab sites and their corresponding ranges based on the various dependencies that may exist in the study.
It can be found under the Website Host menu:
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Once open, use the form highlighted below to populate the table above it with the various lab sites that will apply across the entire study. Lab sites will be associated with study sites in the next step. There is no limit to the number of lab sites you can create.
Labs are essentially entities similar to sites that can be utilized across various studies within the same host account. If making changes to existing labs, be sure those labs are not part of another study on the account. If they are, making a change to it would affect both studies.
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Now its time to create the various lab ranges for each lab site by selecting the link highlighted below:
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This is where you will map each column from the source file to the system.
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The source file must be CSV format |
First, add the number of columns that exist in the source file in sequential order. The only rules of inclusion are that the lab name must be the first column, and two of the columns should be effective start and stop dates.
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It is important to include ALL columns of the source file - even if they will not be used. In such cases, the column type will simply be labeled as "Filler (Ignore)". |
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After adding the number of rows needed, it's time to map each row to a column in the source file.
To do this, select the Edit link on each row, provide a name (does not need to match the source file), and select what its function is based on the list of options shown below. At a minimum, the required items will be:
Lab Test Name
Protocol min and max
Lab Unit Code
Effective date range
Currently, the Lab min/max options are not functional in the system. Please use only the Protocol min/max to map the lab ranges.
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Notice in the list of options under Column Type, any external variables/lab range stratifications are at the bottom of the list. If you need one that is not listed, create an external variable first.
The images below show both an example source file and how each of the items from the column type applies to each one.
If a test is present in the lookup table, it must have values for any external variables included. In other words, if gender is a variable, it must not be left blank in the lookup table. Additionally, if a subject is entered in the study without gender indicated, the system will not run the checks.
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The column names you enter for each item do not need to match the column name in the source file. The order is how the system determines the columns.
Any range dependencies, like the gender and age shown above, must be set as external variables in the study.
Notice the Age is two columns in the source file, but only accounted for in row 3 of the mapping. This is because for any number/value dependencies like age or weight or BMI, for example, the system assumes it must be a range where the low range column is first and the high range column is second.
The gender can use "M" or "F" for Male and Female respectively. The system assumes "B" is for Both, but Both do not need to be an actual choice in the study.
Any columns that need to be skipped in the source file should be set as "Fillers".
The most important items to be sure are mapped are:
Lab Test Name - Must match the lab test names used in the study CRF. If a lab test is in the CRF but not on this file, it will cause a saving error for users doing data entry. If checks will not be done on a certain lab test, it's okay to still include them in the file but do not enter any values for the min/max.
Protocol Min Value
Protocol Max Value
Lab Unit Code
All dependencies (e.g. Age, Race, Weight, etc) or the effective start/end dates of the ranges are optional. Currently, the Lab min/max values are not functional but will be coming soon for added capability.
When all items are mapped, select the link on the right side of the page that is highlighted in the image above.
Next, return to the Lab Manager page to import the source file. If the mapping saved correctly, there will be an option to Import File:
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Now upload the CSV file and ensure it is read successfully. The table will display on the page if the file is read successfully.
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After one lab site is setup with mapping, if all other lab sites follow the same source file format, the mapping can easily be copied to the next site:
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Labs exist at the host/account level. This means if labs are set up in one study, anything done with them on a separate study will affect any other study. The reason for this is that labs are tied to sites, and sites exist at the host level before they are attributed to studies which they are part of. Next, read about how to associate the study sites with appropriate lab sites. |
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Identify which lab sites are associated with each site in the study
Lab sites need to be associated with study sites because the study sites might use a specific lab or specific group of labs. The associated labs will then be available for the site users to choose from on the lab forms.
Labs sites and study sites are associated with and set up in the Site Document Manager The corresponding permission must also be enabled as discussed in https://crucialdatasolutions.atlassian.net/wiki/pages/resumedraft.action?draftId=55312481.
In the image below, you can see there are five study sites. The first three study sites have 1 or 2 lab sites associated. In this example, we need to associate the fourth study site with a couple of different labs. To do so, select the link highlighted in the image.
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This will open a page listing the lab sites that were created in the Lab Range Manager application during lab range setup.
Select the lab sites that might be used by the current study site and save the changes.
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Now, when the site users are entering lab data on a lab form, they will only have those lab site options to choose from. This is how the system will then know which data ranges to use for each of the lab collections. The image below shows an example of this.
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Next read about how https://crucialdatasolutions.atlassian.net/wiki/spaces/TKSP/pages/250806429/Entering+Lab+Data works on lab forms.
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Enter Data to Test Ranges
This section discusses the data points on a lab assessment form that need to be addressed if the system is checking range results on the form.
The example form below shows a series of labs being collected within a predefined table:
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The numbered items in the image above are the three data points needed by the system to evaluate lab ranges appropriately. Read about each one below.
Lab site selection - Select which local lab is applicable for the data being submitted. The system uses this to evaluate the corresponding ranges. The options to select from are defined by the Study Administrator.
Date - This is not only important for the study data, but also for the system to look at the effective date on any of the lab ranges.
Lab Result - In the table of labs above, the result is the only piece of data the system will need from the user. The Unit column and the Out of Normal Range column both get auto-populated by the system after the record is saved. Note, the units and range check will be instantly saved to the database when the user saves the record. However, the two auto-populated items may not be seen on the eCRF until the page is refreshed or the form is reloaded after saving.
After entering the variables described above, save the form to trigger the system to run the checks. The Units for each lab will automatically populate along with the Out of Range indication.
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If the Lab ranges are not checked, it is likely due to missing variables collected on another form needed for the range checks. A common example is Age and Gender collected on the Demographics form. Since lab ranges often depend on the subject’s age and gender, those are needed before the range checking can occur. |
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