Question: It's there any GISTIC2.0 like tools?
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gravatar for MatthewP
12 days ago by
MatthewP260
China
MatthewP260 wrote:

GISTIC2.0 can find CNV across a set of samples. I want to know it's there other tools can do the same thing? Thanks.

cnv • 83 views
ADD COMMENTlink modified 12 days ago by jared.andrews073.4k • written 12 days ago by MatthewP260

but wait, GISTIC2.0 is not a CNV caller. It is a tool for driver genes discovery. Can you clarify what you need - cancer driver genes discovery or CNV calling? Why do you need another tool? Because you can not call variants with GISTIC2.0 or because you are not satisfied with the algorithm? I'd say GISTIC2.0 algorithm sounds bullet-proof for me.

ADD REPLYlink modified 12 days ago • written 12 days ago by kuckunniwid330

GISTIC calls CNVs for you, it just doesn't do segmentation. Though yes, it also does driver gene discovery, so a clarification would be nice.

ADD REPLYlink modified 12 days ago • written 12 days ago by jared.andrews073.4k

I am confused. Copy-number estimation is required by GISTIC as input (ftp://ftp.broadinstitute.org/pub/GISTIC2.0/GISTICDocumentation_standalone.htm , segmentation file paragraph). Clearly it requires Seg.CN as input. In which sense it calls CNVs?

ADD REPLYlink written 12 days ago by kuckunniwid330
1

Segmentation is breaking up the genome and estimating CN for each segment. However, these segments may be noisy and aren't stitched together into contiguous regions of CN change by segmentation algorithms alone.

GISTIC (and most other CNV programs/packages) utilize segmentation to perform CNV "calling" and to come up with discrete regions of CN change based on threshold values (often removing low-quality segments e.g. those with very few reads/probes). Often, a comparison to normals will also be done to remove germline changes, particularly if small focal changes are of interest.

This distinction is admittedly somewhat semantic, but generally the "calling" step is where hard thresholds are drawn and integer CN values are assigned. GISTIC does this.

ADD REPLYlink written 12 days ago by jared.andrews073.4k

Ah, I see. That's kinda weird - GISTIC has no idea about the underlying sub-clonal structure, so I'd never use it for calling, but good to know that it also does that, thanks!

ADD REPLYlink written 12 days ago by kuckunniwid330
1
gravatar for jared.andrews07
12 days ago by
jared.andrews073.4k
St. Louis, MO
jared.andrews073.4k wrote:

There are lots of them:

Are just a few off the top of my head. CNVkit is probably the easiest to use out of those and can work on arrays or WGS. There are many others you can find just by searching a bit.

ADD COMMENTlink written 12 days ago by jared.andrews073.4k

Sorry, I misunderstand function of gistic. I thought it's use to identify CNV from multiple samples, like some kind of merge many CNV results.

ADD REPLYlink written 11 days ago by MatthewP260

It kind of does that. It basically finds the recurrent CNVs between samples and tries to tie them back to which genes are affected.

ADD REPLYlink written 11 days ago by jared.andrews073.4k
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