Our group has reported several intrinsic gene sets important for identifying subtypes of breast cancer with clinical significance. 1 Sørlie T Tibshirani R Parker J et al. Repeated observation of breast tumor subtypes in independent gene expression data sets. Proc Natl Acad Sci USA. 2003; 100: 8418-8423 Crossref PubMed Scopus (4148) Google Scholar , 2 Hu Z Fan C Oh DS et al. The molecular portraits of breast tumors are conserved across microarray platforms. BMC Genomics. 2006; 7: 96 Crossref PubMed Scopus (1108) Google Scholar , 3 Parker JS Mullins M Cheang MC et al. Supervised risk predictor of breast cancer based on intrinsic subtypes. J Clin Oncol. 2009; 27: 116-167 Crossref Scopus (11) Google Scholar In these studies we have explored and published methods for sample classification across different genomic platforms and tissue qualities. In 2009, we suggested the use of a standardised gene set (PAM50) for subtype classification to improve the classification concordance reported by investigators. 3 Parker JS Mullins M Cheang MC et al. Supervised risk predictor of breast cancer based on intrinsic subtypes. J Clin Oncol. 2009; 27: 116-167 Crossref Scopus (11) Google Scholar However, a standardised gene set does not completely resolve discrepancies between researchers since the genes might be quantitatively measured using different platforms and normalisation methods. Weigelt and co-workers 4 Weigelt B Mackay A A'hern R et al. Breast cancer molecular profiling with single sample predictors: a retrospective analysis. Lancet Oncol. 2010; 11: 339-349 Summary Full Text Full Text PDF PubMed Scopus (277) Google Scholar applied three different intrinsic gene sets to four data sets using one prediction method and showed a range of agreement. Because of the level of discordance that was reported, they concluded that identification of the intrinsic subtypes is not ready for clinical implementation. We disagree with this interpretation.