[BioC] Detecting mRNA Expression When Somatic Mutations Have

[Alicia Oshlack]

>
> Message: 10
> Date: Fri, 5 Dec 2008 15:40:16 -0700
> From: "Stephen Piccolo" <steve.piccolo at gmail.com>
> Subject: [BioC] Detecting mRNA Expression When Somatic Mutations Have
> 	Occurred
> To: <Bioconductor at stat.math.ethz.ch>
> Message-ID: <4939adcf.1e068e0a.67c0.ffffd8d7 at mx.google.com>
> Content-Type: text/plain
>
> 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?
>
>
This is similar to what has been observed in between species/strains
experiments and shown in
Gilad Y, Rifkin SA, Bertone P, Gerstein M, White KP.
Genome Res. 2005 May;15(5):674-80.


>
> Any way to get around this?
>
>
If the mutation is only in cancer and you are comparing cancer to wild
type then the best way I can think of would be to try to use a probe
which doesn't contain the mutation.
>
> Know of any papers that discuss this?
>
>
>
> Thanks in advance.
>
>
>
> Regards,
>
> -Steve
>
Cheers,
Alicia