Question: Recurrent CNV analysis
gravatar for noshadho
16 months ago by
noshadho10 wrote:

Hello everyone,

I am working on WGS data, and I am interested to do some copy number analysis. Particularly, I am looking to see what regions of genome has been applified (or deleted) recurrently in a specific cancer cohort. I know there is a tool for this called GISTIC 2.0, but it has been developed sometime around 2011.

I was wondering, has there been any new tools after GISTIC 2.0 that would do the same? Do they have better Sensitivity/Specificity?

Thank you.

ADD COMMENTlink modified 16 months ago by Kevin Blighe69k • written 16 months ago by noshadho10
gravatar for Kevin Blighe
16 months ago by
Kevin Blighe69k
Republic of Ireland
Kevin Blighe69k wrote:

There are many tools to detect CNV (to be proper, in a somatic context, we should call them somatic copy number alterations (CNA)). To gauge the sensitivity/specificity of all of these would be a difficult task, but it would essentially require a comparison to a reference 'gold standard' dataset that contains known copy number variants and structural variants.

There is nothing 'wrong' with GISTIC 2.0. If you want a full pipeline for detecting recurrent somatic CNAs in the TCGA datasets, then take a look here:


ADD COMMENTlink written 16 months ago by Kevin Blighe69k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1499 users visited in the last hour