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How to calculate TMB - GDCquery ?

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.

gdcquery_clinic gdcquery
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updated by Kevin Blighe Kevin Blighe • written by Negatyvna • Negatyvna

1 answer

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

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written by Kevin Blighe Kevin Blighe

Thank you very much for your answer.

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written by Negatyvna • Negatyvna

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