TCGA, CNV, GISTIC

[Elena Kuzmin, Dr]

Hello,

I was wondering if you have the GISTIC analyzed data of the CNV segmented data for breast cancer TCGA?

Elena

[Michael Noble]

Dear Elena,

Yes, please see this entry in our online FAQ for more details about the multiple ways to access the data used in, and analyses conducted by, Firehose.

Best,

Mike

—

Michael S. Noble

Associate Director for Data Science

Cancer Genome Computational Analysis

The Broad Institute of MIT & Harvard

Manager, Genome Data Analysis Center

The Cancer Genome Atlas

[David Heiman]

Hi Elena,

The GISTIC2 reports give file descriptions:

https://confluence.broadinstitute.org/display/GDAC/FAQ#FAQ-QThatsgreatbuthowdoInavigateallofyourresultsontheweb

We don't add GISTIC2 results to IGV; it is, in fact, the segmented data. Those files are the genome_wide_snp_6-segmented_scna_minus_germline_cnv_hg19 archives.

Regards,

David

--

David Heiman

Run Operations Engineer

TCGA Genome Data Analysis Center

The Broad Institute of MIT and Harvard

415 Main Street

Cambridge, MA 02142

---------- Forwarded message ----------
From: Elena Kuzmin, Dr <elena....@mcgill.ca>
Date: Thu, Aug 4, 2016 at 10:43 AM
Subject: Re: [GDAC-users] TCGA, CNV, GISTIC
To: Michael Noble <mno...@broadinstitute.org>


Hi Michael,

Thank you very much for such a prompt reply. Based on looking at the contents of each file I can roughly guess what they are showing but would you happen to have a description of these files so that I could be sure?  Which of these files gets fed into IGV when it accesses the CNV data from the servers? It is not segmented data but a version of the gistic analyzed data.  

Elena

-- 

Thank You,

Michael S. Noble
Associate Director for Data Science
Cancer Genome Computational Analysis

Broad Institute of MIT and Harvard

Manager, Genome Data Analysis Center
The Cancer Genome Atlas

-- 

Thank You,

Michael S. Noble
Associate Director for Data Science
Cancer Genome Computational Analysis

Broad Institute of MIT and Harvard

[Elena Kuzmin, Dr]

Hi David and Michael, 

Actually I found all the required information but I have one more question, 

This website: https://confluence.broadinstitute.org/display/GDAC/Analysis+Run+Release+Notes

shows these parameters:

Old parameters

• Amplification Threshold: 0.3
• Deletion Threshold: 0.3
• Cap Values: 2.0
• Broad Length Cutoff: 0.5
• Remove X-Chromosome: True
• Join Segment Size: 10
• Maximum Sample Segments: 10000

Whereas this folder GISTIC archive [tar.gz] (71M) on this website https://tcga-data.nci.nih.gov/docs/publications/brca_2012/ 

has this file: gp_execution_log.txt which looks incomplete 

# Created: Sat Dec 03 01:12:38 EST 2011 by achernia

# Job: 2042928    server:  http://cga-genepattern:8090/gp/

# Module: Gistic2_Analysis urn:lsid:broadinstitute.org:cancer.genome.analysis:00264:95

# Parameters: 

#    seg_file = freeze_brca19.seg   /gp/getFile.jsp?job=2042928&file=achernia_run8746718093406872522.tmp%2Ffreeze_brca19.seg

#    markers_file = /xchip/tcga/CancerGenomeAnalysisData/trunk/SNP6_annotations/genome.info.6.0_hg19.na31.minus_autosomal_cnvs.txt

#    refgene_file = /xchip/gistic/variables/GAFs/hg19.gaf.June2011.mat

#    cnv_files = /xchip/gistic/CNV/CNV.hg19.XandYchrom.txt

#    amp_thresh = 0.3

#    del_thresh = 0.3

So am I to conclude that the parameters that were used in the paper are the same ones that are listed at the top of this email?

Thank you for all your help.

Elena

On Aug 4, 2016, at 4:44 PM, Elena Kuzmin, Dr <elena....@mcgill.ca> wrote:

Hi David,

Where can I find what input values were used in GISTIC2 to analyze the data that went into TCGA 2012 paper? I checked both the paper, and the supplement and could not location this information.

Elena

[Elena Kuzmin, Dr]

Hi David,

Where can I find what input values were used in GISTIC2 to analyze the data that went into TCGA 2012 paper? I checked both the paper, and the supplement and could not location this information.

Elena

On Aug 4, 2016, at 11:19 AM, David Heiman <dhe...@broadinstitute.org> wrote: