It is my goal to utilize this funding mechanism to answer a biological question. In the process I will be expanding my knowledge base, by taking courses and workshops in the field of bioinformatics, a discipline that my project relies on heavily, and the field of pathobiology, information I feel will give me a better understanding of the cancers that I intend on studying. I intend to use an array-based method to determine genome copy number fluctuations between two cancer genomes. This method based on genomic representations has been shown to be accurate at detecting deletions and amplifications from primary breast tumors. This method will be used to study the genome copy number fluctuations that occur in primary breast cancer. Furthermore it will be used to compare the copy number fluctuations between ductal carcinoma in situ (DCIS), and invasive ductal carcinoma (IDC). The regions that undergo copy number fluctuations in DCIS will be compared to those in IDC for similarity, to demonstrate whether IDC derives from DCIS. Copy number fluctuations identified for all tumor biopsies will be mapped to a finer resolution than before possible. The regions of the genome identified may represent regions, when mutated contribute to the path to malignancy. These regions will have several uses as markers, for diagnosis, prognosis, and for the identification of gene candidates involved in the path to malignancy.
| Kamalakaran, Sitharthan; Kendall, Jude; Zhao, Xiaoyue et al. (2009) Methylation detection oligonucleotide microarray analysis: a high-resolution method for detection of CpG island methylation. Nucleic Acids Res 37:e89 |
| Chen, Shuaili; Auletta, Theresa; Dovirak, Ostap et al. (2008) Copy number alterations in pancreatic cancer identify recurrent PAK4 amplification. Cancer Biol Ther 7:1793-802 |
| Fu, Baojin; Luo, Mingde; Lakkur, Sindhu et al. (2008) Frequent genomic copy number gain and overexpression of GATA-6 in pancreatic carcinoma. Cancer Biol Ther 7:1593-601 |
| Lakshmi, B; Hall, Ira M; Egan, Christopher et al. (2006) Mouse genomic representational oligonucleotide microarray analysis: detection of copy number variations in normal and tumor specimens. Proc Natl Acad Sci U S A 103:11234-9 |
| Lucito, Robert; Healy, John; Alexander, Joan et al. (2003) Representational oligonucleotide microarray analysis: a high-resolution method to detect genome copy number variation. Genome Res 13:2291-305 |
