The present study serves to confirm that key clinical phenotypes of breast cancer can be identified. It has identified that both the luminal and basal breast cancer phenotypes appear to be heterogeneous and contain distinct subgroups. Of importance is the observation that only 62% of breast cancer cases in this cohort have been assigned to the determined phenotypes, while the remaining 38% of cases express mixed or indeterminate characteristics. This latter observation, although previously recognised, has not been emphasised in the past. It has important clinical implications should either cDNA expression or protein expression assays be used for stratification of patients into treatment groups either in clinical trails or for routine clinical management. The clinical phenotypes determined in this study are a new luminal group, luminal N, the new basal subgroups, basal X and basal Y, and the previously well-established luminal A, luminal B and HER2 groups.