Significantly mutated genes without control

Question

[aikaterini.symeonidi]

Dear all,

I was wondering if there is a tool to identify significantly mutated genes in tumor only samples, i.e. without knowing if the SNPs are somatic or germline. I believe that OncogeneFM for example works only for somatic mutations, as does MutSig. Please correct me if I am wrong.

Thank you

Answer 1

[smilefreak]

Could you look at something like CADD scores http://cadd.gs.washington.edu/ across the genes. For instance, if a gene contained a overrepresentation of high cadd scores, which you could test using permutation, you could argue that it was significantly mutated in your cancer samples.

Does any one have any thoughts on whether this is useful.

From the website of CADD scores.

C-scores strongly correlate with allelic diversity, pathogenicity of both coding and non-coding variants, and experimentally measured regulatory effects, and also highly rank causal variants within individual genome sequences. Finally, C-scores of complex trait-associated variants from genome-wide association studies (GWAS) are significantly higher than matched controls and correlate with study sample size, likely reflecting the increased accuracy of larger GWAS.