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Initial enthusiasm to explore gene expression profi ling and other high-throughput molecular methods as molecular diagnostic tools for breast cancer has given way to increasing skepticism. Several investigators suggested that these novel analytical methods may not have advanced diagnostic medicine beyond what optimally performed histology and immonohistochemistry (IHC) could deliver. Th ere is some truth in this criticism, particularly when it comes to clinically useful assays that gene expression profi ling methods have yielded. However, this overly simplistic assessment of molecular profi ling overlooks three important contributions that high-throughput gene expression analysis has brought to breast cancer research and treatment. First, results from gene expression profi ling studies have fundamentally changed our conceptual approach to breast cancer. Second, these methods have yielded several commercially available new diagnostic tests that fi ll a previously unmet diagnostic niche and have started to impact routine care, at least in the United States. Th ird, the impact of the large volume of molecular data that these studies have generated will have a lasting impact on breast cancer research. Th e in-depth analysis of the many tantalizing observations made from comprehensive genomic characterization of breast cancers has barely begun. The conceptual impact of molecular profi ling on breast cancer research Gene expression profi ling provided the fi rst glimpse of the true complexity of the molecular machinery of breast cancer. Th e earliest of these studies already revealed large-scale molecular diff erences between estrogen receptor (ER)-positive and ER-negative cancers and also revealed two robust subsets within the ER-positive cancers [1]. Th ese molecular diff erences between breast cancer subsets together with the important clinical diff erences that also distinguish these groups have prompted a conceptual shift in the classifi cation of breast cancer. Breast cancer is no longer considered a single disease with variable ER expression, histology and grade but a collection of genuinely diff erent neoplastic diseases that arise from the breast epithelium. Th e long recognized heterogeneity in ER expression and grade have not led to similar shifts in classifi cation in the past because the scale of molecular diff erences that exist between these disease types remained hidden until highthroughput molecular analytical methods become available. Th e implications of the new classifi cation schema reach far beyond a simple ER-based stratifi cation of breast cancer. Diff erent molecular types of breast cancers will require separate clinical trials, diff erent prognostic

Molecular profiling contributes more than routine histology and immonohistochemistry to breast cancer diagnostics