Question: Is DNA or RNA better to get somatic mutation profile for neoantigen estimation?
0
gravatar for CY
7 days ago by
CY80
United States
CY80 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 • 128 views
ADD COMMENTlink modified 4 days ago by sophiespo10 • written 7 days ago by CY80

What is a neoantigen?

ADD REPLYlink written 4 days ago by karl.stamm3.2k
1
gravatar for sophiespo
4 days ago by
sophiespo10
BC Cancer Agency Genome Sciences Centre
sophiespo10 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 4 days ago by sophiespo10

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

ADD REPLYlink written 4 days ago by arta180

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 3 days ago by CY80
0
gravatar for CY
4 days ago by
CY80
United States
CY80 wrote:

Can anyone share some comments? Really appreciate

ADD COMMENTlink written 4 days ago by CY80
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