Question: GISTIC 2.0 markers
0
gravatar for noshadho
14 months ago by
noshadho10
noshadho10 wrote:

Hi all,

I am using GISTIC2.0 for a segmented file I have (Segmented using CBS). I can't understand what is marker file. What does a marker represent here? how dp we choose markers?

Thanks

ADD COMMENTlink modified 14 months ago by Kevin Blighe67k • written 14 months ago by noshadho10
3
gravatar for Kevin Blighe
14 months ago by
Kevin Blighe67k
Republic of Ireland
Kevin Blighe67k wrote:

The markers file contains the positions of the probes before segmentation was performed. You do not have to supply a markers file with GISTIC versions > 2.0.23.

To understand the purpose of this file, one can cite the original published work (I have highlighted the important points in bold for you):

Some genes are affected by non-overlapping deletions, either on different alleles in one sample or across multiple samples. For such genes, a marker-based score does not weight the presence of all deletions affecting that gene, despite the fact that these events are likely to have similarly deleterious effects on gene function. We have developed a modified scoring and permutation procedure, termed GeneGISTIC, that scores genes rather than markers (Supplementary Methods in Additional file 1). In each sample, we assign each gene the minimal copy number of any marker contained within that gene, and then sum across all samples to compute the gene score. Because genes covering more markers are more likely to achieve a more extreme value by chance, the permutation procedure is adjusted to account for gene size; the score for a gene covering n markers is compared against a size-specific null distribution generated by computing minima overall running windows of size n in each sample and then randomly permuting these minimal values across the genome.

[source: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3218867/]

Kevin

ADD COMMENTlink written 14 months ago by Kevin Blighe67k

Hi Kevin,

Just revisiting this because I am facing a similar problem. It seems GISTIC 2.0 still requires a segmentation file, which takes in a "Num Markers" field. Do you know how to address this if we are using sequencing data?

ADD REPLYlink written 10 weeks ago by vctrm6720

Hi Kevin, do you use bins for your data? If I am using bins (like dividing genome into 10k, 20k, etc bins), I would pass on the number of bins each segment contains (because that is how many measurements we have for that segment). If not bins(like in a targeted panel or wxs sample), I would just pass on the number of targeted regions at each segment.

ADD REPLYlink written 10 weeks ago by noshadho10

I am no expert on GISTIC, unfortunately. I prefer to use another similar program, called GAIA. You may reach out to the GISTIC developers.

ADD REPLYlink modified 10 weeks ago • written 10 weeks ago by Kevin Blighe67k

Do you know of any other programs that would work with CNV profiles derived from sequencing data, as opposed to array data?

ADD REPLYlink written 9 weeks ago by vctrm6720
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