How to calculate Mutation Frequency for each Gene using TCGA SNV data?

Question

[mausamkumravat]

Hi, I've downloaded SNV data (.maf file) for TCGA-SKCM. There is no column in data for mutation frequency. Now, for each gene I've to calculate mutation frequency. How can I do that? Someone please suggest any approach to calculate Mutation Frequency for each gene using TCGA SNV data. Thanks!

[Kevin Blighe]

Just out of curiosity: to what, do you believe, the mutation frequency actually relates? When you answer, you should then know how to calculate it.

Things to consider:

1. which mutation type are you going to include in the calculation? - missense, intronic, UTR, spilcing?
2. are you going to adjust for gene length? - larger genes will accumulate more mutations
3. are you going to segregate by any clinical features, e.g., Stage I, II, III, or IV?
4. are you going to segregate based on transitions versus transversions?
5. are you going to segregate based on mutational signatures?

You may also be interested in MutSig.

Kevin