GISTIC results. Too many deleted genes?

Question

[rin]

Hi all

I am kind of sceptical about some results I got from GISTIC 2.0.

Using the following parameters I got a huge number of deleted genes while just a few amplified. More specifically, 587 amplified vs. 3461 deleted.

Input parameters used: Amplification Threshold = 0.1 Deletion Threshold = 0.1 Cap Values = 1.5 Broad Length Cutoff = 0.7 Remove X-Chromosome = 0 Confidence Level = 0.99 Join Segment Size = 4 Arm Level Peel Off = 1 Maximum Sample Segments = 2000 Gene GISTIC = 1

Are such results considered "normal"? Most of the publications I could find were not mentioning so many altered genes.

Thank you in advance. R.

[Kevin Blighe]

What is the source of your data? I mean, a tumour biopsy, obviously? Have you tried other programs like HMMcopy or FREEC?

[rin]

Hi Kevin!

I am using Masked segmented data from TCGA. And no this is the only tool I have used, so far.

Answer 1

[Kevin Blighe]

For others landing on this page, please contact the GISTIC team directly:

• A: GISTIC input parameters.
• A: GISTIC 2.0 all threshold file versus genome browser

Kevin