Amplification over deletion/Deletion over amplification?

Question

[vctrm67]

I am running GISTIC on some modified ASCAT copy number profiles. Part of the algorithm is a deconstruction/reconstruction of the copy number profile to find statistically likely underlying somatic copy number alterations. The output is a structure Q that is described as:

The Qs structure added to D has four fields for different kinds of events:
 'amp' contains pure amplification (over amplification) events, 'del' pure
deletion events, 'aod' amplifications over deletions, and 'doa' deletions
over amplifications.

What are amplifications over deletions, what are deletions over amplifications, and how do they differ from pure amplification/deletion? The documentation doesn't describe it at all and I can't find it online.

Answer 1

[Kevin Blighe]

In the context of ASCAT and tumour biology, this can occur in a tumour sample whereby an allele undergoes loss of heterozygosity (deletion of one allele) but then is later amplified. Similarly, another position could undergo amplification but then later deletion of one or more alleles over this position.

It is possible to model these scenarios and assign a p-value for the NULL hypothesis that they are not present, which is what I assume the developers of ASCAT already do.

Kevin

[vctrm67]

I see; do you know how about in the context of GISTIC? That is where I see these labels.

[Kevin Blighe]

Can you please show more information about where you are seeing this output? For example, which command produced it and in which output file did you see it?. Thanks!