> > 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