comparing amino acid change is useful when analyzing mutations?

Question

[mangfu100]

Hi all

I am wondering that comparing mutation of amino acid change is useful when analyzing mutations?

In my opinion, it might give some knowledge that same amino-acid changes can be grouped together and will be a source of identifying driver mutations in targeted cancer. (Of course, mutations at the same positions is more powerful evidence).

What is your opinion about this topic? Is it a good approach?

[Michael]

I think it is part of the standard approach to look for amino acid changes, that is called variant effect annotation (non-synonymous mutations). There are many other variant effects to look for as well. Search the site for "variant effect prediction".

[mangfu100]

Thanks for your kindly reply.

More detail about my questions, I have a set of nonsynonymous muations in cancer and I would like to know their significance for developing tumorous. So, I came up with ideas that comparing my amino-acid changes from my nonsynonymous mutations with that of mutation that are stored on public sites such as TCGA or COSMIC is a good solution because the amino-acid changes exactly matched frequently in the public databases is more important among them.

[Ram]

Or not. Novel mutations could be useful too. Like Michael says, Variant Effect prediction is a standard part of most analysis pipelines. Check out software like VEP and snpEff. You will have to work on the DNA mutations in the VCF file though. and not on amino acid changes. If you wish to work on amino acid changes, look for tools like PredictSNP to make in silico predictions on the effects of amino acid changes.