Gene mutations vs expression data

[cellfree]

Hi everyone,

I have a rather silly question but I'm hoping someone will clear something up in my head.

Why do people study gene mutations in cancer patients (for example) rather than studying their RNA expression levels, since a mutation doesn't necessarily mean a cell will have a varied mRNA output and therefore a phenotypic change?
There must be some advantages to assessing variants at the DNA level rather than at the RNA level, right?

Thanks!

[nucacidhunter]

Main reasons:
1- Gene expression is not consistent and will vary by environment and other factors so an important gene can be missed because at the sampling time it was not expressed
2- Mutations in non-protein coding regions can affect gene regulation
3- A mutation in DNA can be detected by sequencing whole genome or targeted sequencing an not be missed
4- The aim normally is to correlate mutations with disease, response to drugs or condition
5- Library prep from DNA is straight and less expensive in comparison to RNA

[Denise - Open Targets]

There will be pros and cons for both (whether they are technical or biological). The good news is that you can focus on eQTLs, variants that affect the expression of one or more genes (nearby the location of the variant or not).