Finding and Applying SNP information for probes in Human Affymetrix GeneChips. Dr. Jennifer W. Weller Bioinformatics and Computational Biology George Mason University Feb 7 , 2005 at 4:30 ABSTRACT Affymetrix microarrays use a multi-position representation of a gene by placing a number of 25-nt probes along the length of each transcript. The signal across these probes is then normalized in according to one of a number of strategies in order to provide a gene-level concentration equivalent for use in comparative expression studies. Our group has been investigating the effect of individual probe characteristics on the estimation of final concentration, primarily with a goal of understanding biophysical effects. In the course of removing what we think of as confounding factors we realized that a relatively large number of probes ( 5%) contain recognized SNPs. One effect of this is that in some cases a so-called Mismatch probe will in fact be the Perfectmatch, and in other cases neither probe will provide a good estimate of the concentration of the transcript. If the probe value is inaccurately estimated, it will give a skewed contribution to the overall transcript level. We have made several assessments of the SNP effect, which will be presented in the seminar.