Cosmic mutation signature

Question

[agicict]

Hi

I am trying to get information from somatic nucleotide variant of patients. I hope to make mutation signature like cosmic. (Below is link)

http://cancer.sanger.ac.uk/cosmic/signatures

According to the site, all mutation signature are referred to by the pyrimidine of the mutated Watson-Crick base pair.

So there are only 6 types of nucleotide substitution.

C>A, C>G, C>T, T>A, T>C, and T>G

I am wondering how to count other nucleotide substitutions.

For instance, is G>A substitution considered as C>T substitution and added to C>T substitution?

Or is the change not counted (i.e 0)?

My colleague said that in the case, they are not counted. However, I think that the comment is wrong.

This is because there will be too much loss of information about substitution.

I believe that G>A substitution is considered C>T.

Please give me your opinion.

Thanks

Answer 1

[trausch]

Illumina WGS data is unstranded so you cannot distinguish a G>A mutation from a C>T mutation. You are right counting both of them together in one bin.

[agicict]

Thank you very much!