Scout: My Cancer genome link does not work

[heronikdin]

Hi!
MCG link button does not work, I get this message all the time:

Can you please help or do you know what the issue is?

Regards, Hero

[northwestwitch]

Hi @heronikdin. Do you have a specific variant with links not working? I've tested this ones:
https://scout.scilifelab.se/cust087/unitedaphid/27b33e25b3b4931bce6f7f54455504fd
https://scout.scilifelab.se/cust087/awakekoala/63832ccc0e66b89a75126aa551161d40

and they seem to work

[heronikdin]

Hi @northwestwitch
Ok, thats good to know, so basically if the vriant is not there I will get an error message and if it is there it will surely come up? Just making sure, becasue many variant I have looked up does not come up.

Regards, HEro

[northwestwitch]

I'm not sure, I never used My Cancer Genome. Have you tried searching those with the link that doesn't work using the search form: https://www.mycancergenome.org/content/biomarkers/ ?

[dnil]

Thanks for the report @heronikdin! There may absolutely be some mismatch with the variant nomenclature - you know how picky things can be with different variant types, transcripts, transcript versions, hgvs normalisation etc - so a couple of non-working examples will be brilliant!

[heronikdin]

ok, let me get back to you on that. I will use the link you send @northwestwitch and compare.

Thanks!

[northwestwitch]

This one doesn't work: https://scout.scilifelab.se/cust087/F0037910/c84da1539be5e01a3abb674d3cfb8ecc

[dnil]

Nor this for instance: https://scout.scilifelab.se/cust087/awakekoala/97a89ff3796a065a2327fca002f72480

A quick search at MCG finds none of them. Coincidentally, we are currently listening in on a seminar about TP53 mutation, and it was not on that list either.. 😉

[dnil]

We can make these more adaptive as soon as annotation of them are integrated into Balsamic. In theory, even without pre-annotation, we could also poll MCG for existence of the variant before adding the link out, but that would slow the system down a bit.

[northwestwitch]

Sounds like a good plan @dnil (checking in the VCF annotation). This is not the only link that doesn't work if the data is not present on the external server and if we start to check them all before loading the page it will be significantly slower I think.. So I suggest we go with the Balsamic annotation (is it already on the balsamic task list?)