Is DNA or RNA better to get somatic mutation profile for neoantigen estimation?

Question

[CY]

Basically, my goal is estimating neoantigen amount. For this purpose, I think both methods have their advantage and disadvantage

Using DNA for mutation detection ignores the expression information. Not all variant are expressed

By using RNA for mutation detection, we can take expression level into account and give different weight to each somatic mutation on its capability to produce neoantigen. However, one single RNA-Seq only represents the expression at a single time point.

Both of them have bias. I think which methods is better depends on if the gene expression across tumor genome vary significantly.

Any comments are appreciate

[karl.stamm]

What is a neoantigen?

Answer 1

[sophiespo]

Personally, I would design my experiment to use both if I could. I would use DNA sequencing to perform identication of mutations and prediction of neoantigens, then use RNAseq to quantify expression of the neoantigens. Lack of expression of a predicted neoantigen may be just as interesting as finding expression of another.

[arta]

I agree with Smith, by combining them you have ability to decrease the noise.

[CY]

Yes, That would be best, The question is what we can do for the best if we only have, say RNA-Seq data.

Answer 2

[CY]

Can anyone share some comments? Really appreciate