DNA arrays as predictors of efficacy of adjuvant/neoadjuvant chemotherapy in breast cancer patients: Current data and issues on study design

Chemotherapy provides variable benefit to patients with breast cancer, with usually modest but occasionally severe side effects. Hence, there is a need to identify predictive biomarkers for its efficacy. DNA arrays have been used in this setting as potential novel predictive diagnostic tools. Several gene signatures and single gene markers were proposed to predict response to chemotherapy. Although this technology offers interesting perspectives through large-scale analysis of the transcriptome, its ability to identify clinically relevant predictors is highly dependent on study design. In the present manuscript, we will review currently available results of breast cancer pharmacogenomics and focus on aspects of study design that are critical to reliably identify predictive biomarkers using DNA array technology. We will discuss whether studies should be done in the overall, unselected breast cancer population or in specific homogeneous molecular subclasses. Next, we will compare advantages and limitations of cohort-based and case-control studies. The choice of end-point to discriminate between sensitive and resistant patients will also be examined.