title: Classification and risk stratification of invasive breast carcinomas using a real-time quantitative RT-PCR assay.
abstract: BACKGROUND
  Predicting the clinical course of breast cancer is often difficult because it is a diverse disease comprised of many biological subtypes. Gene expression profiling by microarray analysis has identified breast cancer signatures that are important for prognosis and treatment. In the current article, we use microarray analysis and a real-time quantitative reverse-transcription (qRT)-PCR assay to risk-stratify breast cancers based on biological 'intrinsic' subtypes and proliferation.
  
  
  METHODS
  Gene sets were selected from microarray data to assess proliferation and to classify breast cancers into four different molecular subtypes, designated Luminal, Normal-like, HER2+/ER-, and Basal-like. One-hundred and twenty-three breast samples (117 invasive carcinomas, one fibroadenoma and five normal tissues) and three breast cancer cell lines were prospectively analyzed using a microarray (Agilent) and a qRT-PCR assay comprised of 53 genes. Biological subtypes were assigned from the microarray and qRT-PCR data by hierarchical clustering. A proliferation signature was used as a single meta-gene (log2 average of 14 genes) to predict outcome within the context of estrogen receptor status and biological 'intrinsic' subtype.
  
  
  RESULTS
  We found that the qRT-PCR assay could determine the intrinsic subtype (93% concordance with microarray-based assignments) and that the intrinsic subtypes were predictive of outcome. The proliferation meta-gene provided additional prognostic information for patients with the Luminal subtype (P = 0.0012), and for patients with estrogen receptor-positive tumors (P = 3.4 x 10-6). High proliferation in the Luminal subtype conferred a 19-fold relative risk of relapse (confidence interval = 95%) compared with Luminal tumors with low proliferation.
  
  
  CONCLUSIONS
  A real-time qRT-PCR assay can recapitulate microarray classifications of breast cancer and can risk-stratify patients using the intrinsic subtype and proliferation. The proliferation meta-gene offers an objective and quantitative measurement for grade and adds significant prognostic information to the biological subtypes.
authors.affiliation: The ARUP Institute for Clinical and Experimental Pathology, SLC, Utah, USA.
authors.forename: Laurent
authors.initials: L
authors.lastname: Perreard
authors.forename: Cheng
authors.initials: C
authors.lastname: Fan
authors.forename: John F
authors.initials: JF
authors.lastname: Quackenbush
authors.forename: Michael
authors.initials: M
authors.lastname: Mullins
authors.forename: Nicholas P
authors.initials: NP
authors.lastname: Gauthier
authors.forename: Edward
authors.initials: E
authors.lastname: Nelson
authors.forename: Mary
authors.initials: M
authors.lastname: Mone
authors.forename: Heidi
authors.initials: H
authors.lastname: Hansen
authors.forename: Saundra S
authors.initials: SS
authors.lastname: Buys
authors.forename: Karen
authors.initials: K
authors.lastname: Rasmussen
authors.forename: Alejandra Ruiz
authors.initials: AR
authors.lastname: Orrico
authors.forename: Donna
authors.initials: D
authors.lastname: Dreher
authors.forename: Rhonda
authors.initials: R
authors.lastname: Walters
authors.forename: Joel
authors.initials: J
authors.lastname: Parker
authors.forename: Zhiyuan
authors.initials: Z
authors.lastname: Hu
authors.forename: Xiaping
authors.initials: X
authors.lastname: He
authors.forename: Juan P
authors.initials: JP
authors.lastname: Palazzo
authors.forename: Olufunmilayo I
authors.initials: OI
authors.lastname: Olopade
authors.forename: Aniko
authors.initials: A
authors.lastname: Szabo
authors.forename: Charles M
authors.initials: CM
authors.lastname: Perou
authors.forename: Philip S
authors.initials: PS
authors.lastname: Bernard
mesh_terms: D001943:Breast Neoplasms / Q000145:classification* / Q000453:epidemiology / Q000235:genetics* / Q000401:mortality / Q000473:pathology; D045744:Cell Line, Tumor; D015331:Cohort Studies; D005260:Female; D006801:Humans; D009361:Neoplasm Invasiveness / Q000235:genetics; D020411:Oligonucleotide Array Sequence Analysis; D020133:Reverse Transcriptase Polymerase Chain Reaction / Q000379:methods*; D018570:Risk Assessment; D016019:Survival Analysis