title: Prediction consistency and clinical presentations of breast cancer molecular subtypes for Han Chinese population.
abstract: BACKGROUND
  Breast cancer is a heterogeneous disease in terms of transcriptional aberrations; moreover, microarray gene expression profiles had defined 5 molecular subtypes based on certain intrinsic genes. This study aimed to evaluate the prediction consistency of breast cancer molecular subtypes from 3 distinct intrinsic gene sets (Sørlie 500, Hu 306 and PAM50) as well as clinical presentations of each molecualr subtype in Han Chinese population.
  
  
  METHODS
  In all, 169 breast cancer samples (44 from Taiwan and 125 from China) of Han Chinese population were gathered, and the gene expression features corresponding to 3 distinct intrinsic gene sets (Sørlie 500, Hu 306 and PAM50) were retrieved for molecular subtype prediction.
  
  
  RESULTS
  For Sørlie 500 and Hu 306 intrinsic gene set, mean-centring of genes and distance-weighted discrimination (DWD) remarkably reduced the number of unclassified cases. Regarding pairwise agreement, the highest predictive consistency was found between Hu 306 and PAM50. In all, 150 and 126 samples were assigned into identical subtypes by both Hu 306 and PAM50 genes, under mean-centring and DWD. Luminal B tended to show a higher nuclear grade and have more HER2 over-expression status than luminal A did. No basal-like breast tumours were ER positive, and most HER2-enriched breast tumours showed HER2 over-expression, whereas, only two-thirds of ER negativity/HER2 over-expression tumros were predicted as HER2-enriched molecular subtype. For 44 Taiwanese breast cancers with survival data, a better prognosis of luminal A than luminal B subtype in ER-postive breast cancers and a better prognosis of basal-like than HER2-enriched subtype in ER-negative breast cancers was observed.
  
  
  CONCLUSIONS
  We suggest that the intrinsic signature Hu 306 or PAM50 be used for breast cancers in the Han Chinese population during molecular subtyping. For the prognostic value and decision making based on intrinsic subtypes, further prospective study with longer survival data is needed.
authors.affiliation: Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei City, Taiwan.
authors.forename: Chi-Cheng
authors.initials: CC
authors.lastname: Huang
authors.forename: Shih-Hsin
authors.initials: SH
authors.lastname: Tu
authors.forename: Heng-Hui
authors.initials: HH
authors.lastname: Lien
authors.forename: Jaan-Yeh
authors.initials: JY
authors.lastname: Jeng
authors.forename: Jung-Sen
authors.initials: JS
authors.lastname: Liu
authors.forename: Ching-Shui
authors.initials: CS
authors.lastname: Huang
authors.forename: Yih-Yiing
authors.initials: YY
authors.lastname: Wu
authors.forename: Chih-Yi
authors.initials: CY
authors.lastname: Liu
authors.forename: Liang-Chuan
authors.initials: LC
authors.lastname: Lai
authors.forename: Eric Y
authors.initials: EY
authors.lastname: Chuang
mesh_terms: D044466:Asian People / Q000235:genetics*; D001943:Breast Neoplasms / Q000145:classification* / Q000235:genetics* / Q000473:pathology; D002681:China; D003710:Demography; D005006:Ethnicity / Q000235:genetics*; D005260:Female; D052138:Genes, Neoplasm / Q000235:genetics; D006801:Humans; D011379:Prognosis; D016019:Survival Analysis; D013624:Taiwan