Comparison of Gene Expression and DNA Copy Number Data to Identify Amplicons in Breast Cancer

Abstract:
Breast Cancer is one of the primary causes of death in women in the world. Many genes have been implicated in the predisposition to this disease. In this experiment, chromosomal copy number changes were analyzed alongside gene expression. Using CGH technology, changes in DNA copy number in four tumors were used to detect areas of DNA Amplification. Gene expression levels found on 250k SNP arrays were inspected to match areas of increased expression with the previously found amplicons. Areas of correlated expression were sought in the hopes of locating specific genes being over-expressed, with the possibility they are driver genes of the amplicon, and therefore possible oncogenes. Of the eighteen amplicons found, four yielded posivtive correlation results (correlation hugher than 0.6 within a 1 megabase genomic window). The amplicons on Chromosomes 17, 12, 8, and 6 were analyzed in more detail.

I can now honestly say that I am FINISHED with my dissertation, as I submitted it for printing this morning. I still need to do our "portfolio entry" (they love making us 'reflect', as practice for later), as well as fill out a questionnaire, pick up the printed version, and hand it in; but the hard bit is over! Today is alll relaxation, and getting ready for the parties of the week.

If anyone wants to check out the full dissertation (no idea why you would), drop me a line and I'll send it your way.

-AMiB