A PLATFORM FOR THE SCREENING OF BREAST CANCER-ASSOCIATED POLYMORPHISIMS USING A PRIMER EXTENSION MICROARRAY

Abstract

It is of great societal and scientific importance to be able to identify low penetrance polymorphic loci and the combinations of allelic variation that give the greatest risk to an individual for the development of breast cancer. Understanding about this variation will be beneficial both for diagnosis, prevention and in the development of drug targets for breast cancer. To this end I propose the creation of a diagnostic platform that will help to identify the risk factors associated with known or suspected polymorphic markers that may influence the progression of breast cancer. The platform that I propose would entail the creation of an oligonucleotide microarray consisting of oligonucleotide detection primers that would anneal to genomic DNA from a donor and detect polymorphic mutations among known and suspected breast cancer-associated alleles. Genomic DNA would be taken from a patient and then amplified. The loci of interest would be copied out of the genomic material by using a multiplexing PCR primer set. The amplified polymorphic loci would then be cleaned up and combined to create a hybridization probe for the microarray. Once the probe is hybridized to the microarray, a polymerase will then be added along with fluorescent-labeled dNTPs and the detection primer would be extended using the labeled dNTPs. This extension would only occur when there is a complete nucleotide match between the sample DNA from the patient and the detection primer's 3' end. A microarray scanner should be able to detect the presence of incorporated labeled nucleotides. The data from large scale studies using this platform coupled with the monitoring of an individual's medical history that has been genotyped using this method, could provide both scientists and clinicians with data available to make a better judgment regarding future risk and prevention of this disease.