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Clinical-Genomics / cg

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Add tissue check before uploading to loqus #3159

Closed jemten closed 6 months ago

jemten commented 7 months ago

Description

After discussiong with @moahaegglund it seems like cg only uses customer id to decide which loqus database to upload the vcf to. Sometimes tumour samples are sent through cust002 and it would be preferable to not have that sample uploaded to the germline database.

Suggested solution

Add a check to see if the sample is a tumour sample before uploading to loqusDB.

This can be closed when

Describe what needs to be done for this issue to be closed

Blocked by

If there are any blocking issues/prs/things in this or other repos. Please link to them.

henrikstranneheim commented 7 months ago

We also have this for MIP-DNA uploads:


        if case.tumour_samples:
            LOG.error(f"Case {case.internal_id} has tumour samples. Cancelling upload.")
            raise LoqusdbUploadCaseError
jemten commented 7 months ago

Ah, that looks like the check we wanted. Right @moahaegglund?

ivadym commented 7 months ago

Ah, that looks like the check we wanted. Right @moahaegglund?

But do we have any cases that shouldn’t have been uploaded to Loqusdb? If that's the case, you can send me those, and I can look more into what's going on

moahaegglund commented 7 months ago

Good that we have this check, we missed in the code when we looked the other day. A question to this is if it would be good to also include a check on the sample source from LIMS and only allow certain sources to be uploaded to loqusDB? I do not know how frequent this is but we have just had a sample that's been reanalysed in balsamic instead of mip-dna as it was in the first analysis a couple of years ago. We marked it as tumor now, it's an exome and sample source is tissue (FFPE).

henrikstranneheim commented 7 months ago

I wonder if FFEP would be a problem? @dnil @ivadym @jemten

Really important to keep the cancer samples out. Do we need to improve any documentation? @moahaegglund @karlnyr

dnil commented 7 months ago

Yes, I agree on blocking FFPE. It is different enough from our usual blood samples, and will often be from tissues with expected non-constitutional mutation load. It seems they are not always flagged as tumor when intended for MIP analysis. They certainly also not just from solid tumors: e.g. overgrowth syndromes etc.

We can also open a new customer for KGG for somatic work, and repeat the wish to expect constitutional samples from cust002.

ivadym commented 7 months ago

I think it also makes sense to bock them for Balsamic, but I'll bring it to a cancer refinement

ivadym commented 6 months ago

We've decided to block them for Cancer uploads too.

After merging https://github.com/Clinical-Genomics/cg/pull/3215, any cases with a sample source in LIMS containing ffpe/FFPE won't be uploaded to Loqusdb.