The assay progress report is designed to capture the specimen collection and assay processing lifecycle. It displays the current status of which specimens have been collected and processed in your study. For each assay in your study, the report displays some status value for each participant/timepoint: whether the specimen has been collected or not, whether assay results are available or not, and whether any adverse events have occured, such as unusable or unexpected assay results . For example the status report below shows that most specimens have been successfully processed resulting in valid assay data, but one participant (PT-102) has an incomplete specimen processing history.

Data Requirements

Assay progress reports are only available in a study folder. The following data sources are used to render the assay progress report:

Data SourceRequired?DescriptionSource Schema and Table(s)
ParticipantsRequiredThe study must have participant data present.study.Participant
VisitsRequiredStudy visits must be defined. Both date-based or visit-based studies are supported.study.Visit
Assay ScheduleRequiredAssay schedules must be defined, as described in the topic Manage Assay Schedule.study.AssaySpecimen
study.AssaySpecimenVisit
Assay resultsRequiredSome table must be present to hold assay results. This can be a dataset or an assay design that has been copied to the study.User defined assay results.
Specimen status queryOptional (see below for details)Specimen status information is drawn from a query. Any query, such as a query based on a list, can serve this function as long as it has the required fields.User defined query.

The Specimen status query must expose the following fields:

  • ParticipantId (of type String)
  • VisitId (of type Integer)
  • SequenceNum (of type Double)
  • Status (of type String)
Allowed values for the Status field are list below. Allowed values are case-sensitive.
  • expected
  • collected
  • not-collected
  • not-received
  • available
  • not-available
  • unusable
Note that the Specimen status query is not strictly necessary to render a report. If the query is omitted, a simple report can be rendered based on the assay results in the study: if assay results are present for a given Participant/Visit, then the report will display the status "available" (); otherwise "expected" () will be displayed, as shown below.

Create the Assay Progress Report

Once the data sources are in place, you can add a progress report for any of your assays.

  • Click the Clinical and Assay Data tab.
  • On the Data Views web part, click the drowndown triangle () and select Add Report > Assay Progress Report
  • On the Create Assay Progress Repoort screen, for each assay you wish to include in the report, click the pencil icon ().
  • This brings up Status Information Query pop up dialog. Use the dropdowns to point to the query which contains the specimen status information and click Submit. (Note if no status query is pointed to, then the Specimen Repository will be used to display a simplified report by default, see above for details.)
  • The make the report visible to Readers or above, select the checkmark Share this report with all users?. Leaving this checkmark unselected makes it visible only to you and other Administrators.
  • To finish the progress report, click Save
  • The progress report is added to the Data View web part. To view the report click it in the Data Views web part, or add it to a study tab using the Report web part.

Export

The Export button is activated when a single assay is selected for display. Clicking Export downloads all of the assay data for the selected assay.

Discussion

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