Is It Possible to Calculate Microsatellite Instability (MSI) Directly from MAF Files or TCGA Data?

Question

[Jaber]

Greetings,

I'm trying to calculate MSI in tumor samples from TCGA-READ, I have access to MAF files. I would like to determine if it's possible to directly calculate MSI status using MAF files or any other available TCGA datasets.

Appreciate any advice, Thanks

Answer 1

[Zhenyu Zhang]

1. There are existing clinical MSI test data from TCGA-READ. They like exist in those TCGA clinical files, either in those biotabs or xml, from GDC.
2. I am pretty sure there are existing TCGA-READ papers that have called MSI
3. GDC has MSI called. The results are msi_status currently either on the aligned reads node or copy number segment node, if you know how to use the GDC API.

[Jaber]

Thank you

Will look it up and I am sure I can find it.