cfDNA samples that need relabeling

[ao508]

Status:

• Sent a message on Feb 28th to IGO team (see #smile-igodata slack channel)

Waiting for confirmation that we can (correctly) get the cfDNA sample type from the CMO sample ID fields that they send as part of the sample manifest JSON. If so then we can publish these samples to the SMILE update workflow to allow the label generator to generate new labels for these cfDNA samples. If not then we'll need to reassess how to move forward with resolving these outstanding cases.

Work resolved:

• Ronak requested that the bait set information be updated for two requests. These are resolved and updated in the database.

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Extension of #1407.

This card covers the effort that might be required in submitting samples to the label generator to update their labels with cfDNA-specific sample type abbreviation.

At this point (2/19/25) we're waiting for confirmation from the PMs to see if they can provide a list of samples that are known to be cfDNA that we can check/pick out the samples that need their labels updated.

Query we can use to find samples affected:

MATCH (sm:SampleMetadata)
WHERE sm.cmoSampleName =~ "^C-([a-zA-Z0-9]+)-([TRMPGXFA])([0-9]{3})-([d|r])(.*$)"
  AND (sm.sampleType = "cfDNA" OR sm.sampleClass = "cfDNA")
RETURN DISTINCT sm.primaryId, sm.cmoSampleName, sm.sampleType, sm.sampleClass, sm.sampleOrigin

This query returns 52 samples in production that are cfDNA and do not have a sample type abbreviation specific to cfDNA samples.

Update Feb 26

• shared the sample data with Ronak, etc. for their reference. Notified that once the label generator change is deployed we will handle the updates for the affected samples.

Update Feb 27

• Scheduling a quick meeting with Ronak to discuss solutions.
• From Ronak:

Thank you, Angelica! I see samples in all these old requests as issues :

igoRequestId
14614_L
10342_D
12524_G
12524_F
13893_R

In addition to these, all the samples from ACCESS Version 2 have issues:

13715_Q
13893_T
14636_G
16772_B

[ao508]

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[ao508]

Update as of March 5th:

These requests need new labels and/or additional metadata updates

13893_T
14636_G
16772_B
13102_T -> This needs to have the IDT barcode changed as well
13715_Q -> Fix the meta information so all will need to be regenerated once that is done, I am not sure but this would need working with PM, here its Jene and Hilary 

A file shared with Ronak details which additional samples from other requests need new labels per the updated label generator logic for cfDNA samples.