Hi all

When analyzing mutation in exome-seq for cancer, it is obvious that non-synonymous mutations is much highly likely to be relevant to cancer-disease than that of synonymous. Therefore I mainly focus on nonsynonymous and have a tendency to get rid of synonymous mutations while doing my research.

At this point, I came up with ideas that it might be a reasonable to analyze the non-nonsynonymous mutations (synonymous, UTR, etc..) which have lots of sequence coverage and high allele frequencies reported.

Assume that I find the recurrent mutations across samples with high allele ratio and read depth, but are synonymous or UTR or ncRNA whatever, can you continue to examine them for downstream analysis even though they are not non-synonymous?