Date of Award


Document Type

Campus Access Thesis

Degree Name

Master of Science (MS)



First Advisor

David J. Kwiatkowski

Second Advisor

Richard Kesseli

Third Advisor

Linda Huang


Bladder cancer is a complex disease caused by multiple environmental and genetic factors, and is associated with advanced age that causes 15,000 deaths annually in the US population. Bladder cancer arises from transitional cells of the mucosal urothelium with two distinct morphological forms: papillary, a low-grade intraurothelial neoplasia which make up 80% of bladder transitional cell carcinoma (TCC); and non-papillary tumors which make up the remaining 20% and are typically invasive into the muscle layer or beyond. Multiple recurrent mutations in both dominantly acting oncogenes, and tumor suppressor genes have been identified in bladder TCC, as well as genes identified as targets for genomic loss or amplification. We applied a novel technology for the analysis of both mutations and copy number changes in a set of 80 bladder cancers samples. This technology, multiplex inversion probe (MIP) assay by Affymetrix, enabled us to analyze 330,000 single nucleotide polymorphisms (SNPs) for allele ratios and copy number, and to analyze 412 common cancer mutations. Mutation findings were validated by Sanger sequencing in 20 of 33 cases in which the MIP score was greater than or equal to 9.0. Nexus v6.0 was used to visualize and analyze MIP data on copy number and allele frequency. 73 of the 80 TCC samples that met quality control standards were analyzed using Genomic Identification of Significant Targets in Cancer (GISTIC) that identified 44 genomic regions having significant gains or loss (q < 0.1). Subsequent manual review was used to assess reliability and to refine the extent of the regions and the genes contained therein. I then chose to focus on regions of amplification because they usually act in a dominant manner, and are more targetable in general than tumor suppressor genes lost in deletions. My plan is to validate these results using Multiplex Ligation-dependent Probe Amplification (MLPA) on bladder cancer cell lines, and additional clinical samples from bladder cancer patients. Future studies will examine the importance of these amplified genes in bladder cancer development and growth, and will hopefully lead to novel targeted therapy.


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