TCGA CNV Files Segment Mean

Question

[neenu.abraham8]

How can we calculate copy number variation(gain/loss/amplification/deletion)based on segment mean value or segment median given in TCGA CNV file? Also suggest a reference to such calculation

[Jimbou]

A similar question and some answers How To Process The Cnv Level 3 Data From Tcga

In general a zero value corresponding to CN2. You have to define a threshold for a deletion and duplication. This group used -0.2 and 0.2, respectively. http://mcr.aacrjournals.org/content/12/4/485.long

[neenu.abraham8]

Thanks for your information....

Answer 1

[Kevin Blighe]

I have given a full pipeline here, i.e., for taking the CN segment mean data and identifying recurrent gains and losses: C: How to extract the list of genes from TCGA CNV data

To then annotate the identified regions, take a look here: A: How to extract the list of genes from TCGA CNV data

Kevin