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

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

instability maf microsatellite msi
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written by Jaber • Jaber

1 answer

  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.
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written by Zhenyu Zhang Zhenyu Zhang

Thank you

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

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written by Jaber • Jaber

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