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Visit-level data fields are designed to record clinical details that can change over specific to that point in time. Each visit has its own unique characteristics, such as date, site at which the visit occurred, clinical diagnoses, and clinical status.

Planned longitudinal studies are usually pre-programmed with expected time points or visit descriptions and the expected samples to be collected based upon each study’s unique design. Each ‘Visit’ is pre-programmed with the expected primary specimens to be collected by the study coordinator and, in In some cases, the processed specimens derived from the primary samples . Therefore the visit descriptions and specimens will differ for every protocol.

Specimen and visit level data can be collected in a single step or in two steps. The single step process bypasses the visit page where detailed clinical data is recorded. The two-step process allows you to record clinical information about the patient at each visit prior to recording sample collection.

DELETE BELOW

Need a section on collecting unplanned specimens.

Need an unplanned specimen collection page, covered:

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Next section should be on collecting pre-planned derivatives and aliquots. This will vary depending on protocol. Might be part of original collection. So it’s tough to cover. But I think it belongs in its own page. Collecting pre-planned processing events (question)

Then creating unplanned deriv and aliqs.

That begs the question of if we need to have a separate page that describes Events and SRs.

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In order to grasp this, we first have to cover what derivatives and aliquots are, which is on the derivative/aliquot page that occurs after this step.

Need to revisit the below section: I don’t think it’s necessary now.

Specimen Data Entry

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CPs in which no Visit Level data is necessary, one can proceed directly to specimen collection from the Participant Registration page.

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Each CP can be configured for multiple visits. Each visit can be configured to have specific specimens that are to be expected. The expected specimens will be displayed in the ‘Specimens' box on the Visit Overview Page for each visit.

  1. For example, in the planned longitudinal study shown in this figure, there are 3 expected visits. T0D, T1D, and T30D.

  2. At T0D (pre-surgical), there are 2 expected specimens:

    1. Whole Blood (in ACD Vacutainer)

    2. Buccal Swab

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  3. For unplanned studies for which specimen type cannot be predicted, no specimen type is shown.

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From the Visit Overview Page, the expected specimens are shown in the Specimens table.

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  1. To collect one or more expected specimens, select the box next to the Description for the sample to be collected. Or select the top box (circled in red below) to select ‘all specimens’ and record all collections one one screen.

     

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  2. Once one or more samples are selected, additional options appear on the menu bar for the Specimens table.

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  3. Select the ‘+Collect’ from the bar to proceed to the Specimen collection page, where specimen-specific data will be recorded.

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The Specimen Collection page will display all of specimens that were chosen in the previous step.

 

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In this screen the Visit Site defaults to that entered for the Visit recorded in the previous step. If the Visit details were bypassed at the Participant Registration step, then you must enter the Visit Site here.

 

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The Collector and Receiver will default to the current user. If these are other than the user, they may be chosen from the dropdown list, but the person must exist in the OS user list.

 

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Collection Date and Received Date will default to the current date and time, but may be edited if different.

 

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If necessary, edit the sample quantity if it differs from expected.

 

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Details about sample Quality may be chosen, if desired. The dropdown list is on the right side of the screen.

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If the sample is to be stored, then the Container location can be chosen by clicking on this icon:

 

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This will open up the search for available containers. Click the search button to search for avialable locations.

 

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You must have a container built and assigned to your Site in order to store specimens. This will be addressed in a separate Knowledge Article.

Selecting ‘Submit’ will navigate to the Visit Overview page and show the Specimen Table with the collected specimens indicated with a purple dot and the Specimen Label assigned according to the CP Label details set up at CP configuration.

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are also pre-set. This saves time for the study team as fields are autofilled with expected values which can be overridden if necessary.

Documenting Visit Details

Each visit will have different characteristics (e.g, date of visit, new diagnosis, visit site, etc.). These are recorded on the visit page. It is possible to record vist data at the time of sample collection or record it later.

Expand
titleA closer look at capturing visit information

The standard fields associated with a visit include:

  1. Visit date

  2. Status: (Complete, Pending, Missed, Not Collected)

  3. Visit Site

  4. Clinical Diagnosis (multiple select): ICD 10 codes

  5. Clinical Status

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This process is recommended if collecting clinical data at the time of specimen collection. Note that any of the visit information can be edited at a later date.

  1. This Visit page can be accessed during the collection process using the Collect Visit feature. Choose ‘Visit’ from the ‘Collect’ button in the Pending Visit table on the Participant overview page.

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  3. This navigates to the Visit page.

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    1. Clinical Diagnoses can be entered in one of two ways. Multiple diagnoses may be chosen.

      1. Typing any part of the description of the clinical disease will display the matching choices in the dropdown.

      2. Typing the ICD 10 code will display the matching diagnosis. Note: OpenSpecimen uses ICD 10 diagnosis codes to record clinical disease descriptions which enables data querying and manipulation across studies.

      3. Example: typing ‘diabetes’ will display all subtypes of any ICD 10 containing ‘diabetes’.

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    2. Clinical Status can be used to record if a participant is a No Diagnosis / Control or to record their clinical status as related to the specific study. Each study will choose their own usage of these terms.

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      Cohort currently records only Case vs. Control. If your study has different designations for Cohort, these can be recorded with a custom field.

    4. Surgical Pathology Number may be entered, if available.

    5. Comments is a text field available for free typing.

  4. Visit data are saved by selecting:

    1. Create’ directs the user to the Visit overview page where details can be viewed and reviewed and edited if necessary; OR

    2. 'Proceed to Collection' directs the user to the Planned Specimen Collection page.

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  5. ‘Create’ navigates to the Visit Overview Page which displays the Visit details and the specimen table. All specimens will appear as ‘Pending’ (noted by the yellow dot next to the description).

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    If there are multiple visits, each visit will have its own Overview Page and its own forms attached if any are attached at the Visit Level.

    1. For each visit, the menu bar on the left shows 4 tabs and defaults to ‘Overview’:

       

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    2. If a Path Report is available as a .pdf, it may be uploaded from the Path Report tab.

    3. If Form-specific data is to be entered, any attached forms can be accessed from the Forms tab. (As as example, patient’s medications usually change over time and a different form can be completed at each visit for medications.)

    4. The Specimen tree tab functions as it does for Participants, by displaying the the specimen tree on the left side of the screen being viewed.

Editing Clinical data after specimen collection

It is common that clinical diagnoses or pathology is not obtained until after specimen collection occurs. If this is the case, the Clinical information can be added or updated at any time using ‘Edit’ on the Visit page.

  1. The Visit page can be accessed after collection by selecting the ‘Event Label’ in the ‘Occurred Visits’ table.

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  2. Choose ‘Edit’ for the Completed Visit.

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  3. Edit or update any fields as described above.

To skip the step of recording clinical data about the visit, navigate directly to the Specimen Collection.

  • By choosing 'Proceed to Collection' upon registering a participant, the Visit page will be skipped and you will be navigated directly to the planned specimen collection page for the visit chosen.

  • Navigate to the Participant overview for an existing participant. Choose ‘Specimens’ from the ‘Collect’ button on the Pending Visits table.

Collect Specimens From Pending Visits Table on Participant overview

Collect Specimens from Add Participant page

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