Affymetrix chip definition files construction based on custom probe set annotation database

DNA microarrays are used to characterize transcription profiles and identify changes in the cellular processes induced by various chemical and physical factors. In this paper we propose a new tool for the validation of expression measurements, based on the current genome and transcriptome knowledge. It incorporates Affymetrix Chip Definition Files (CDFs) that encode the physical design of the microarray, linking oligonucleotide probes to the respective transcripts, allowing construction of custom CDF libraries based on any probe-transcript relation table. The presented application was used to create PLANdbAffy probe annotation database CDF files which were evaluated by the analysis of two distinct datasets containing expression profiles of breast cancer patients and a technical replicates dataset. Performed re-annotation allowed to identify specific set of genes with increased probe set validity compared to CDF given from Brainarray repository. Obtained signature significantly differentiates patients showing high or low radio-sensitivity, which wasn't possible with standard Affymetrix libraries. Additionally the observed expression levels were more accurately and precisely associated with genes and their corresponding transcripts.