How to calculate TMB - GDCquery ?

Question

[Negatyvna]

I would like to ask, can I calculate the TMB based on the information I got from these two functions? Do I need to download any more information?

query1 <- GDCquery( project = "TCGA-COAD", data.category = "Simple Nucleotide Variation", data.type = "Masked Somatic Mutation", legacy=F)

muts <- GDCprepare(query1)

clin <- GDCquery_clinic("TCGA-COAD","clinical")

I would like any suggestions, thanks.

Answer 1

[Kevin Blighe]

Hi, please see this previous answer, which also contains a link to a few published works on TMB: How to calculate Tumor Mutation Burden (TMB) for TCGA samples

In brief, it seems like you have the correct data; however, keep in mind that TMB is a general term, and that people calculate it in diverse ways.

Note also that, under the FDA, pembrolizumab (Keytruda®) is approved for use in 'TMB - high' tumours. To them, TMB-High equates to ≥10 mutations/megabase (mut/Mb)].

Kevin

[Negatyvna]

Thank you very much for your answer.

[Kevin Blighe]

You are welcome, Negatyvna