Question: Is DNA or RNA better to get somatic mutation profile for neoantigen estimation?
0
gravatar for CY
11 months ago by
CY270
United States
CY270 wrote:

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

somatic mutation • 561 views
ADD COMMENTlink modified 10 months ago by sophiespo90 • written 11 months ago by CY270

What is a neoantigen?

ADD REPLYlink written 10 months ago by karl.stamm3.4k
1
gravatar for sophiespo
10 months ago by
sophiespo90
Vancouver
sophiespo90 wrote:

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.

ADD COMMENTlink written 10 months ago by sophiespo90

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

ADD REPLYlink written 10 months ago by arta540

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

ADD REPLYlink written 10 months ago by CY270
0
gravatar for CY
10 months ago by
CY270
United States
CY270 wrote:

Can anyone share some comments? Really appreciate

ADD COMMENTlink written 10 months ago by CY270
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