Question: GISTIC results. Too many deleted genes?
gravatar for rin
8 months ago by
rin30 wrote:

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.

snp cnv gistic • 419 views
ADD COMMENTlink written 8 months ago by rin30

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

ADD REPLYlink written 8 months ago by Kevin Blighe44k

Hi Kevin!

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

ADD REPLYlink written 8 months ago by rin30

Hey bro. Oh, you can download the pre-computed GISTIC 2.0 scores from Broad Firebrowse. Take a look at my answer here and follow through to the links: A: Firebrowse Data vs GDC Portal Data

ADD REPLYlink modified 8 months ago • written 8 months ago by Kevin Blighe44k
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