genomic profiles samples count is wrong for fusions

[tmazor]

GENIE is showing 100% of samples with fusion data, but I know that's not true.

In speaking with @Luke-Sikina this sounds like it may be a code problem and not a data problem. Which also means it may impact studies beyond GENIE.

@jjgao @ritikakundra is this something that's been discussed for GENIE previously?

[jjgao]

@kalletlak any insights?

@inodb fyi - I added this to our current sprint.

[kalletlak]

@jjgao @tmazor counts are dependent on samples having data in data files. For mutation(including fusion) profile - sample/case lists is also considered to check if the sample is profiled or not.

[jjgao]

@tmazor the problem is that we are still hijacking the mutations related code for fusions. Once we fully switch to SV table, it'll be solved. For the moment, @kalletlak will try to see if it is possible to utilize fusions case list (manually curated).

[tmazor]

Oh! That makes sense. Using the case lists sounds like a good interim solution until we do the SV switch. Thanks @jjgao @kalletlak

[tmazor]

I thought we had put a temporary fix in place, but public genie portal is showing 100% of samples with fusions again:

[onursumer]

@jjgao @tmazor The workaround does not work in this case because the sample lists genie_public_fusion and genie_private_fusion do not exits in the database. Therefore we calculate the frequency based on genie_public_sequenced and genie_private_sequenced. I think sequenced list include all mutations not just fusions.

This seems like the case for some other studies, but not sure if this is the case for all other studies.

[jjgao]

@ritikakundra is it possible to create case list to address this?

[ritikakundra]

@jjgao I can create one for GENIE and ask SAGE to add it in for the future. For other public and private studies it will take some time

[tmazor]

@ritikakundra @jjgao I'm still seeing this issue in the public v11 release. Is there any progress on getting those case lists for GENIE?

[ritikakundra]

@tmazor Yes, I need to reimport the study, should schedule it in a day or two.

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[tmazor]

This is still an issue in current GENIE v12 release

[ritikakundra]

@tmazor hmm I fixed it looks like reimport from Sage caused it to come back

[tmazor]

@ritikakundra hmmm ok - can you re-do for this latest version? and what is the fix? we'll need to do it for genie in our internal portal also.

[ritikakundra]

@tmazor ya doing it for all recent studies. We did ask Sage to add the caselists in, I think they have not yet added it in. Am meeting them on Thursday so I will reiterate it.