Cosmic mutation signature
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Entering edit mode
5.7 years ago
agicict ▴ 180

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

 

SNV cosmic mutation signature • 3.5k views
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Entering edit mode
5.7 years ago
trausch ★ 1.6k

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.

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Thank you very much!

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