Premium Resource - Specimen functionality is a legacy feature available with Premium Editions of LabKey Server. For new installations, we recommend using Sample Manager instead. Learn more or contact LabKey.

Specimen Quality Control provides row-level flagging of data for quality control during specimen import. Conflicting information during import of specimen data will automatically trigger a flag, the conflicting column will be left blank, and the row will have color highlighting on specimen grids for all users.

In addition to this automated flagging, administrators can enable Manual QC flagging/unflagging and let other users with appropriate permissions manually set or unset QC flags. Once a vial's QC state has been set manually, it will no longer be updated automatically during the import process.

Guidelines for Flagging

Conflicting information on specimen data will trigger a flag, the conflicting column will be left blank, and the row will have color highlighting. Example flag situations:

  • An imported specimen's globalUniqueID is associated with more than one primary type, as could occur if a clinic and repository entered different information pre- and post-shipment.
  • A single sample is simultaneously at multiple locations, which can occur in normal operations when an information feed from a single location is delayed, but in other cases may indicate an erroneous or reused globalUniqueID on a vial or other aliquot.
  • Conflicting Draw Timestamps are detected. See below for more about this case.
Primary specimens that meet user-specified protocol-specific criteria can also be flagged. Examples of QC problems that could be detected with this method include:
  • A saliva specimen present in a protocol that only collects blood (indicating a possibly incorrect protocol or primary type).
  • Primary specimen aliquoted into an unexpectedly large number of vials, based on protocol expectations for specimen volume (indicating a possibly incorrect participantID, visit, or type for the specimen).
Note that the tools refer to "vial" for a specimen aliquot, but in the case of tissue blocks or other divisions, the specimen sample may not actually be a vial.

Enable Manual QC Flagging

An administrator can enable or disable manual QC flagging; when enabled, specimen coordinators are also authorized to set manual QC flags.

  • Click the Manage tab.
  • Under Specimen Repository Settings, click Manage Display and Behavior.
  • Set the Manual QC flagging/unflagging dropdown to Enabled.
  • Click Save.

Work With Specimen QC Flags

Enable Specimen QC

To enable Specimen QC, go to a specimen grid and click Enable Comments/QC.

The button you clicked will become a dropdown menu titled Comments And QC. To disable, select Exit Comments and QC mode from this menu.

Change Quality Control Flags

  • After you have enabled specimen QC in a grid, you can select one or more rows using the check boxes on the left. QC flags can be bulk-applied to several rows.
  • Select Comments And QC > Set Vial Comment or QC State for Selected.
  • Under Quality Control Flags select one of the options:
    • Do not change quality control state
    • Add quality control flag
    • Remove quality control flag (shown only if any selected rows already have flags)
  • Under Comments, if any of the specimens you have selected already have existing comments, you will have the option to replace them, append new comments to them, or leave existing comments unchanged.
  • Add new comments if you wish.
  • Click Save Changes.
  • Return to the grid to see red highlighting on flagged vials:

Review Flagged Vials

To filter to the set of rows with QC flags, scroll to find the Quality Control Flag column and filter on true. You can also save a custom grid with this filter if you want to make it easy to quickly retrieve flagged vials.

Flagging Draw Timestamp Discrepancies

The Draw Timestamp for a specimen vial is expected to remain constant over time. However, as specimens are moved among labs sometimes the time portion is lost. Also, occasionally time corrections are made to the repository but it is difficult to change all events associated with a specimen. Whenever the Draw Timestamp differs among events the specimen is flagged with a QC flag and the Draw Timestamp is not shown.

To provide more information about possible discrepancies, upon import to the SpecimenEvent table, the DrawTimestamp field value is used to generate new DrawDate and DrawTime fields in the Vial and Specimen tables (the SpecimenEvent table retains the existing DrawTimestamp field only). QC Flagging will apply individually to the DrawDate and DrawTime fields on the Vial table, allowing the administrator to still import the row but be able to determine whether the discrepancy is significant.

Related Topics

For more information about quality control settings for study datasets, see Dataset QC States: Admin Guide.


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