Copy number analysis question

[Vemuri, Bhargav (vemuribv)]

Hello!

I'm looking to see if cBioPortal has between-group chromosome loss/gain analysis functionality. I know of two copy number tools already:

(1) In Group comparison, the Copy-Number tab shows differential CN alterations, like so:

As you can see, in the current analysis I'm doing, there seems to be a 3p loss/deletion (and this is already well established in the literature).

(2) In the single study Query, the CN Segments tab lets me visualize individual chromosomes/genome as a whole:

Here also, visually, the 3p loss is clear (along with 5q gain, also established in the literature).

Basically I'm wondering if there's any way to leverage these functionalities to quantitatively assess a hypothesis like "3p loss is observed preferentially in Group A compared to B". If something like that is possible with cBioPortal I would love to know more (or if there's an already existing tutorial/webinar on a similar analysis I will definitely check that out).

Thank you,

Bhargav Vemuri

[Tali Mazor]

Hi Bhargav,

There is not currently a feature explicitly for comparing arm level status between groups, but some studies, primarily those from TCGA, have arm-level status as clinical variables -- for example, here's a screenshot showing available data for TCGA LGG study:

https://www.cbioportal.org/study/summary?id=lgg_tcga_pan_can_atlas_2018

You can use these attributes to define groups for comparison, or you can define groups in another way and look for these in the 'Clinical' subtab of the group comparison feature.

-Tali

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