Multi-ethnic comparisons of genome-wide alterations in breast cancer using paraffin embedded samples.

A75 Approximately 178,000 US women will be identified with invasive breast cancer (BC) this year; about 41,000 will die from the disease. It is recognized that ethnic-specific disparities in stage of presentation/survival rates exist in BC patients. These disparities remain an enigma. To investigate a possible genetic basis, we are extending our study of genomic changes in BC samples from African-American (AA) women to a multi-ethnic cohort consisting of 20 each African-American, Hispanic and non-Hispanic white (Cauc) women matched for age of diagnosis, cancer stage, and hormone receptor status. Tissue samples are evaluated for gene expression differences, as well as DNA copy number (CNV)/chromosome alterations by CGH arrays. After successful completion of a pilot study to test feasibility of using paraffin embedded tissue (FFPE) samples from three AA and three Cauc BC pathology specimens, we have embarked on the larger three ethnic cohort study. We present here results of our initial study focusing on triple negative (ER-/PR-/Her2-) patients. Pathology specimens were freshly cut from FFPE blocks and marked by a pathologist as to normal versus tumor tissue. Almac Diagnostics isolated RNA, generated labeled cDNA, and hybridized tumor and normal cDNA to Almac Diagnostics proprietary Breast Cancer DSA Research Tool. To date, 18 triple negative cases have been studied - five AA, four Cauc and nine Hispanic patients. Each patient had self matched gene expression studies (tumor vs. normal). A main goal of this study was to identify the differentially expressed genes between the tumor and normal that are common or unique among the three ethnic groups. Using the FFPE samples, approximately 17516 transcripts (~30%) were expressed on the Breast Cancer DSA with intensity significantly higher than background. Thirty percent is a significantly higher than average proportion for FFPE tissues (average usually 20-25%). For the normal tissue samples, 9399 transcripts were detected in all three ethnic groups, while in tumor tissue samples, 10,296 transcripts were detected. There were also selected transcripts (hundreds to a thousand) that were detected in one or two ethnic groups only. Using two-way ANOVA (disease state and ethnicity) and a p-value cutoff of 0.01, a subset of 6479 highly consistent/significant genes were selected and further used in data quality control. Data QC indicated patient samples clustered well with respect to both ethnicity and normal versus tumor tissue. Additional methods of analysis included K-mean 2-Dimensional clustering and Principal Component Analysis. From these analyses of this limited sample set, we have already identified ethnic-specific expression patterns in tumor specimens. We are mapping clusters of differentially-expressed genes into pathway analysis. Our immediate plan is to extend this study to the full 60 sample cohort, as well as to assess CNV by CGH arrays. It is our hope that the completed study will result in an increased understanding of the biological basis of ethnic-specific BC disparities, leading ultimately to individualized, ethnic-specific diagnostic and therapeutic approaches.