Frequently Asked Questions

Why hasn't my work appeared in Dimsum?

1. Dimsum is periodically updated with data from other systems. Check the page footer to see when the last refresh happened.

   
   Fetch time in page footer

2. The sample/library must have a requisition with a proper assay

   • The Edit Sample/Library page in MISO shows the requisition and assay(s) that an item is associated with.

3. Only items tied to a QC step appear in Dimsum.

   Dimsum QC Step	Subcategory	MISO Item
   Receipt		Requisitioned sample/library (any sample class)
   Extraction		Stock sample
   Library Preparation	TS*	First TS library or library aliquot in the hierarchy
   Library Preparation	Low-depth sequencing	Library
   Library Qualification	TS*	Last TS library aliquot in hierarchy; sometimes same item as library prep
   Library Qualification	Low-depth sequencing	Run-library with run purpose “Quality Control”
   Full-Depth Sequencing		Run-library with run purpose "Production”

   *and other assay tests that use library aliquots for qualification. Others may use a different library design code

4. Is there a case containing parent samples?

   • Child samples/libraries only show up if they are relevant to an assay test within the case. E.g. If the assay is WGS and you created a TS library, this will not be shown
   • The assay page in MISO shows the test parameters

   
   MISO assay tests

Why can’t I select the assay I want?

• Assay availability is configured at the project level (Edit Project > Assays table)
• If the requisition contains samples/libraries from multiple projects, all projects must have the assay
• Ensure that the requisitioned samples/libraries are in the project you intended
• You can check the Edit Requisition page to quickly see each item's project
• Libraries cannot be moved between projects - they belong to the same project as their parent sample

How do I remove samples/libraries from a case?

• A sample/library only belongs to a single requisition
• Children of requisitioned samples/libraries belong to the requisition of the parent
• Moving a child item to a different requisition removes it and any of its descendants from the original requisition

• Removing items from a requisition removes them from any cases for that requisition

  
  Example: Moving Aliquot 2 into its own requisition removes Aliquot 2 and Library 2 from the original requisition and its cases.

How do I include previous work in a new case?

Why?

• Reuse reference/normal
• Include the previous normal and tumour for follow-up cases such as pWGS

How?

Add the relevant samples/libraries as supplemental in the new requisition

• Leaves the items in their original requisition, but also includes them in the new one
• Supplemental items’ projects/pipelines are not associated with the case
• Supplemental items are not included in TAT calculation

• Supplemental items may have been QC’d under a different assay. Dimsum will indicate this

  
  The circle/checkmark icon indicates items passed under a different assay. The tooltip shows which assay.

Why are there extra tests in my case?

Usually this is caused by group IDs. Different group IDs cannot merge, so they create separate tests. Items that have NO group ID also cannot merge with other items that DO have a group ID.

Group ID is included in the Test column in Dimsum.

Why is my case associated with a particular project?

• Case projects come from requisitioned samples/libraries and any of their descendants that are included in the case
• Supplemental samples/libraries are not considered
• The Identity sample (donor) is not considered
  • Sometimes a donor is in an “accessioning project” separate from the “sequencing project”
• Note that a library belongs to the same project as its parent sample – libraries do not set their own project

You can hover over items in Dimsum to see their project

How do I limit my case to a single project?

Some cases are associated with multiple projects. This is usually caused by samples having been previously received into one project, then the samples themselves being used for sequencing in a different project. If the samples had previous data that could be used, then they could have been added as supplemental to the new requisition, as in Option 1 in the example below. Supplemental samples do not effect the case's projects. If the samples had to be derived and sequenced, they should have undergone the process described in Option 2 in the example below instead:

X1 is a tumour tissue sample – received in Project A for WTS

• Accessioned into Project A; Requisition 1 – WTS Assay
• Dual extraction done: X1TDNA and X1TRNA are the propagated samples
• X1TRNA aliquot transferred to library prep team

X2 is a buffy coat sample – received for Project B a year later for WGTS

• Accessioned into Project A, then changed to Project B (assumes knowledge that this is for a different project that already exists – often true but not always); Requisition 2 – WGTS Assay
• DNA extraction done: X2BCDNA is the propagated sample
• X2BCDNA aliquot transferred to library prep team
• X1TDNA aliquot (extraction from Requisition 1) transferred to library prep team

Option 1:

If the WTS data previously generated from X1TRNA is being used for the newly-requested WGTS assay, X1TRNA should be added as a supplemental sample to Requisition 2.

This option doesn't work well for X1TDNA since DNA isn't used in the WTS assay and there won't be any metrics for the sample or anything downstream of it.

Option 2:

If there is no previous data or the previous data will not be used, the samples should have new aliquots propagated into Project B. These should be added as requisitioned samples to Requisition 2. This may be done with X1TDNA and/or X1TRNA if appropriate. Note that these will be treated as receipt samples, and the extraction step will be marked N/A.

Using either option, the requisitioned samples in Requisition 2 and everything downstream of them are associated with Project B, so that will be the only project associated with the WGTS case.

Why is my case associated with a particular pipeline?

Case pipelines come from the case’s projects. See previous question regarding case project association.

Case pipelines

Why does my case have a particular deliverable?

Case deliverables are also defined by the case's projects. See previous question regarding case project association.

Why are there missing steps in a test?

1. Step appears grey with "N/A" text

   
   Extraction is skipped for these tests

   • Extraction will be marked N/A if stock/aliquot samples or libraries are requisitioned because we are not doing the extraction
   • Library preparation will be marked N/A if libraries are requisitioned because we are not doing the library preparation
   • Library qualification is skipped (and marked N/A) for some assay tests
   • Mainly intended for injection cases, where we receive sequencing data from a collaborator, and we are only doing analysis
   • When a case is stopped, all incomplete QC steps before Release Approval will be marked N/A

2. Step appears yellow/incomplete with no icons in it, while later steps show work in progress or completed

   
   Library Preparation step is missing

   • This is usually because a group ID was added later in the process
   • E.g. A new group ID is added to a library aliquot
     • This creates a separate test for the group ID
     • There are no samples/libraries with a matching group ID to include in that test, so extraction and library prep will be missing/incomplete
   • Consider whether this group ID should be in a separate case. If so, move the relevant samples/libraries to a different requisition

Why is a metric missing?

• Some metrics depend on a particular attribute. E.g. tissue material
• If this attribute is not set, there is no metric
• Some attribute values may not have a corresponding metric
• If the metric appears in Dimsum, but has no value, the value is not set in its usual place

• See QM-024 Quality Control and Calibration Procedures – Appendix A – QC Metrics, which details where all metrics come from

  
  Metric value missing

How do I close a case?

• A case is only closed when the release step QC is completed for each deliverable
• There can be failures at any step, but it may be possible to continue the case by repeating some work
• E.g. if library preparation fails, maybe another library prep can be attempted
• A case may be stopped (at the requisition level), but stopped cases still require release approval and release
• Any other incomplete gates are marked “N/A” when the case is stopped