TCGA MSI status

Question

[jan]

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 ?

Answer 1

[Shicheng Guo]

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

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

Answer 2

[Shicheng Guo]

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

[gcaravagn]

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