Confounding effects in "a six-gene signature predicting breast cancer lung metastasis": reply.

Molecular signatures have begun to elucidate the biological and molecular mechanisms underlying the phenotypic diversity of breast tumors. Breast tumors are characterized by five different molecular subtypes that are associated with distinct clinical outcomes in terms of prognosis, treatment response, and site of relapse. In particular, the basal-like and luminal B subtypes of tumors are more aggressive and have a higher tendency to metastasize to the lung than do the other subtypes. Given this difference in metastatic profiles of breast tumors, the six-gene signature (6GS) that we showed to be predictive of lung relapse was reexamined in the context of the tumor subtypes. This first analysis suggested that the 6GS is a surrogate for molecular subtype, discriminating basal-like tumors rather than tumors that metastasize to the lung. Here, we show that the 6GS discriminates the two overlapping features, the basal-like subtype and the tendency to metastasize to the lung. Nevertheless, the 6GS predicts lung metastases of breast tumors independent of the molecular subtypes.