Recurrent CNV analysis

Question

[enho]

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.

Answer 1

[Kevin Blighe]

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:

• TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages adapted by me, here: A: How to extract the list of genes from TCGA CNV data )

Kevin