[BioC] Detecting mRNA Expression When Somatic Mutations Have Occurred

[Wolfgang Huber]

Dear Stephen

this is a very appropriate question. Such mutations can (and often will) 
affect hybridisation efficiency. Mostly this seems to be "swept under 
the carpet" in the microarray RNA profiling field, but the fact has also 
been used since the early days of microarrays for genotyping, e.g. by 
Elizabeth Winzeler et al. Direct Allelic Variation Scanning of the Yeast 
Genome, Science 281 (1998) [1]. An application of this effect is in the 
detection of allele-specific expression levels, e.g. Ronald et al. [2]

I've heard people doing eQTL analysis (where this effect would induce 
spurios "cis-effects") saying that their microarrays were designed to 
avoid at least the common polymorphims (SNPs), but looking e.g. at this 
technical report:
http://www.illumina.com/downloads/WholeGenomeExpressionTechnicalBulletin.pdf
there is some explanation of their probe design, but I saw no mention of 
this problem (?).

Eventually, this problem will be solved (or circumvented) by RNA-Seq.

Best wishes
      Wolfgang

[1] http://www.sciencemag.org/cgi/content/full/281/5380/1194
[2] http://genome.cshlp.org/content/15/2/284.abstract

----------------------------------------------------
Wolfgang Huber, EMBL-EBI, http://www.ebi.ac.uk/huber

Stephen Piccolo ha scritto:
> I'm guessing this question will show my naivete, but I wanted to see if
> anyone could point me in the right direction.
> 
>  
> 
> Let's say you have a gene like KRAS that gets a DNA point mutation
> (missense) in a tumor cell, and that cell clonally expands. Then let's say
> you use a microarray to try to detect mRNA expression for that gene (and
> others).
> 
>  
> 
> Will the mutation affect your ability to detect mRNA expression for KRAS? Or
> in other words, will the expression level be detected as lower because the
> RNA sequence was different than the reference sequence on the chip?
> 
>  
> 
> Any way to get around this?
> 
>  
> 
> Know of any papers that discuss this?
> 
>  
> 
> Thanks in advance.
> 
>  
> 
> Regards,
> 
> -Steve
> 
>  
> 
> ----------------------------------------------------------------------------
> ------------------
> 
> Stephen Piccolo
> 
>  
> 
> PhD Student
> 
> Department of Biomedical Informatics, University of Utah
> 
> 26 South 2000 East
> 
> Suite 5700 HSEB
> 
> Salt Lake City, UT 84112-5750
> 
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