Epidemiological evidence from different studies has shown that genes harboring sequence variations may modify breast cancer risk inBRCA1andBRCA2mutation carriers. Current attempts to identify genetic modifiers ofBRCA1andBRCA2associated risk have focused on a candidate gene-based approach or the development of large genome-wide association studies. However, both methods have notable limitations. This chapter describes a novel approach for analyzing gene expression differences to prioritize candidate modifier genes for single nucleotide polymorphism association studies. The advantage that gives this strategy an edge over other candidate gene-based studies is its potential to identify candidate genes that interact with exogenous risk factors to cause or modify cancer, without detailed a priori knowledge of the molecular pathways involved.
