Proper genomic profiling of (BRCA1-mutated) basal-like breast carcinomas requires prior removal of tumor infiltrating lymphocytes

To find BRCA1-associated copy number abberations, the copy number profiles of Familial Basal-like BRCA1-mutated breast carcinomas were compared to Familial Basal-like carcinomas with no pathgogenic BRCA1/2 mutation. This led to the observation of unanticipated heterogeneity of the BRCA1 associated copy number profiles. Gene expression analysis on the same samples identified tumor infiltrating lymphocytes to be responsible for this observation. High number of infiltrating lymphocytes proved to be detrimental for copy number profiling efforts. After optimal sample selection, BRCA1-associated copy number abberations could be detected. Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from fresh frozen primary breast tumors Copy number analysis of Affymetrix 500K SNP arrays was performed for 120 famlial primary breast tumors. 90 Female HAPMAP samples (http://hapmap.ncbi.nlm.nih.gov/) with CEU ancestry were used as baseline.