Question: Cosmic mutation signature
0
gravatar for agicict
4.7 years ago by
agicict160
Korea, Republic Of
agicict160 wrote:

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 mutation signature cosmic • 3.1k views
ADD COMMENTlink modified 4.7 years ago by trausch1.5k • written 4.7 years ago by agicict160
2
gravatar for trausch
4.7 years ago by
trausch1.5k
Germany
trausch1.5k wrote:

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.

ADD COMMENTlink written 4.7 years ago by trausch1.5k
1

Thank you very much!

ADD REPLYlink written 4.7 years ago by agicict160
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2223 users visited in the last hour