title: Comparison of prognostic gene profiles using qRT-PCR in paraffin samples: a retrospective study in patients with early breast cancer.
abstract: BACKGROUND
  Gene profiling may improve prognostic accuracy in patients with early breast cancer, but this technology is not widely available. We used commercial assays for qRT-PCR to assess the performance of the gene profiles included in the 70-Gene Signature, the Recurrence Score and the Two-Gene Ratio.
  
  
  METHODS
  153 patients with early breast cancer and a minimum follow-up of 5 years were included. All tumours were positive for hormonal receptors and 38% had positive lymph nodes; 64% of patients received adjuvant chemotherapy. RNA was extracted from formalin-fixed paraffin-embedded (FFPE) specimens using a specific kit. qRT-PCR amplifications were performed with TaqMan Gene Expression Assays products. We applied the three gene-expression-based models to our patient cohort to compare the predictions derived from these gene sets.
  
  
  RESULTS
  After a median follow-up of 91 months, 22% of patients relapsed. The distant metastasis-free survival (DMFS) at 5 years was calculated for each profile. For the 70-Gene Signature, DMFS was 95% -good prognosis- versus 66% -poor prognosis. In the case of the Recurrence Score, DMFS was 98%, 81% and 69% for low, intermediate and high-risk groups, respectively. Finally, for the Two-Gene Ratio, DMFS was 86% versus 70%. The 70-Gene Signature and the Recurrence Score were highly informative in identifying patients with distant metastasis, even in multivariate analysis.
  
  
  CONCLUSIONS
  Commercially available assays for qRT-PCR can be used to assess the prognostic utility of previously published gene expression profiles in FFPE material from patients with early breast cancer. Our results, with the use of a different platform and with different material, confirm the robustness of the 70-Gene Signature and represent an independent test for the Recurrence Score, using different primer/probe sets.
authors: Service of Oncology, Hospital La Paz, Madrid, Spain. eespinosa00@terra.es
authors: Enrique
authors: E
authors: Espinosa
authors: Iker
authors: I
authors: Sánchez-Navarro
authors: Angelo
authors: A
authors: Gámez-Pozo
authors: Alvaro Pinto
authors: AP
authors: Marin
authors: David
authors: D
authors: Hardisson
authors: Rosario
authors: R
authors: Madero
authors: Andrés
authors: A
authors: Redondo
authors: Pilar
authors: P
authors: Zamora
authors: Belén
authors: B
authors: San José Valiente
authors: Marta
authors: M
authors: Mendiola
authors: Manuel
authors: M
authors: González Barón
authors: Juan Angel
authors: JA
authors: Fresno Vara
mesh_terms: D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D001943:Breast Neoplasms / Q000175:diagnosis* / Q000235:genetics*; D018572:Disease-Free Survival; D005260:Female; D020869:Gene Expression Profiling; D006801:Humans; D008207:Lymphatic Metastasis; D008875:Middle Aged; D011379:Prognosis; D012008:Recurrence; D015203:Reproducibility of Results; D012189:Retrospective Studies; D020133:Reverse Transcriptase Polymerase Chain Reaction / Q000379:methods*