Abstract B35: Cumulative results from an investigation of transcriptome differences in breast cancer samples from African American and East African triple-negative breast cancer patients

We report our cumulative results of a multi-year study focusing on the genomic similarities and differences between Triple-negative breast cancer (TNBC) in native African and U.S. African patients. We used a cohort of African-American (AA) TNBC patients from South Florida and an indigenous cohort of Kenyan TNBC patients. Strong U.S. epidemiological data supports breast cancer (BC) as the second leading cause of cancer death among AA women, with a 20% greater mortality rate than that in Caucasian-American women (CA). AA women often present with tumors that are of higher grade and later stage and their relapse-free and overall survival period is significantly lower than CA. Additionally, TNBC has a higher prevalence in AA women. All of these observations lead to a much poorer prognosis for AA BC patients- thus defining the all-encompassing term “disparities in BC in women of African ancestry”. In our study, we used archived formalin fixed paraffin embedded (FFPE) blocks, collected across a stage-matched multi-ethnic U.S. cohort of node-negative TNBC from the University of Miami and similar TNBC samples from the Kijabe Hospital (Kenya). Using 10 μm scrolls from each block, total RNA was isolated, cDNA prepared, and hybridized to a breast cancer enriched gene expression array (Affymetrix Platform BC DSA Research Tool) in collaboration with Almac Diagnostics. Gene expression analysis was conducted using GeneSpring 12.1® analytical software. The raw data, a total of 60,856 gene/probes, was pre-processed using Robust MultiArray Average (RMA) algorithm; background corrected, log2 transformed to the baseline median of all samples and then quintile normalized. The samples that passed final QC were then filtered to remove low-intensity signals ( 2.5), was performed. The resulting dendogram clearly segregated into distinct subgroups based on ethnicity, revealing a pattern of differential gene expression between the cohorts. A list of differentially expressed genes from each cohort (DEG) were selected using ANOVA analysis (fold change > 3.0, p value Citation Format: Julie E. Getz, Mary E. Ahearn, Carmen Gomez, Biju Issac, Jennifer Clarke, Mark D. Pegram, Peter Bird, John D. Carpten, Lisa L. Baumbach. Cumulative results from an investigation of transcriptome differences in breast cancer samples from African American and East African triple-negative breast cancer patients. [abstract]. In: Proceedings of the Sixth AACR Conference: The Science of Cancer Health Disparities; Dec 6–9, 2013; Atlanta, GA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2014;23(11 Suppl):Abstract nr B35. doi:10.1158/1538-7755.DISP13-B35