Question: TCGA MSI status
1
gravatar for jan
3.3 years ago by
jan120
Sydney, Australia
jan120 wrote:

Hi,

Im trying to find the MSI-status for TCGA samples and couldn't find the information in clinical/clinical supplement and biospecimen/biospecimen supplement files.

What i need looks something like this:

https://wiki.nci.nih.gov/display/TCGA/Microsatellite+data

Where can I find these information in the new TCGA portal ?

clinical msi tcga • 4.0k views
ADD COMMENTlink modified 3.3 years ago by Shicheng Guo8.1k • written 3.3 years ago by jan120
1
gravatar for Shicheng Guo
3.3 years ago by
Shicheng Guo8.1k
Shicheng Guo8.1k wrote:

How to obtain Microsatellite Instability (MSI) status for TCGA tumor samples:

Extracting progression models for TCGA MSI/MSS colorectal tumors from the COADREAD project with the TRONCO package

http://biorxiv.org/content/biorxiv/suppl/2015/09/23/027359.DC1/027359-2.pdf

ADD COMMENTlink modified 3.3 years ago • written 3.3 years ago by Shicheng Guo8.1k
1

Sheldon is right. If you use the R code that we provide with the release of the Pipeline for Cancer Inference, it will fetch all the clinical information that you need. The code has a lot of comments, and you should be able to find where we extract the MSI/MSS clinical status from TCGA data

https://sites.google.com/site/troncopackage/examples/colorectal

ADD REPLYlink written 3.2 years ago by gcaravagn60
0
gravatar for Shicheng Guo
3.3 years ago by
Shicheng Guo8.1k
Shicheng Guo8.1k wrote:

MSIseq: Software for Assessing Microsatellite Instability from Catalogs of Somatic Mutations

http://www.nature.com/articles/srep13321

ADD COMMENTlink written 3.3 years ago by Shicheng Guo8.1k
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