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The recognition of molecular subtypes of breast cancer based on gene expression analysis creates opportunities and challenges for future clinical research. Clinical trials must be designed to evaluate results among patients with different subtypes of breast cancer. Increasingly, clinical trials may be designed to target specific subtypes such as trials among HER2-positive patients or basal-like patients only. Such trials can identify activity of novel agents and regimens among these subgroups that might be obscured in a trial including all patients with breast cancer. However, the challenge will be to recruit sufficient number of patients with the less frequent subtype in question. This will likely require increased collaboration between multiple centers, and cooperative group studies targeting the different subtypes of breast cancer. In reality, the current understanding of breast cancer subtypes is the first generation of such studies; ongoing efforts will doubtless refine our understanding of subtypes within the categories already identified. Hopefully, increasingly sophisticated understanding of biological pathways at play in individual tumors will allow for truly tailored therapy in the future.

In addition, the techniques of gene expression analysis discussed above are currently quite cumbersome. Improved techniques are needed, so that molecular subtypes of breast cancer can readily be identified in the clinic and this information can be used to guide discussions of prognosis and management decisions. This may involve development of gene array chips that can be processed rapidly in standard pathology labs or refined use of IHC surrogates that reliably differentiate molecular subtypes. One of the most important avenues of research to emerge from this work will be the identification of individual genes or groups of genes that drive cancer pathogenesis for the different subtypes. Evaluating single genes or groups of genes can lead to better understanding of the biology of cancer and may identify therapeutic targets or means of monitoring response to therapy.

Finally, recognition of the molecular subtypes should allow us to better understand the relationship between genetic and environmental causes of cancer leading to improvements in cancer detection and prevention. As with response to therapy, an environmental risk for one subtype of cancer could be obscured in a study evaluating the relationship between that risk factor and all breast cancers.

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