Comparison of Prognostic Gene Profiles Using qRT-PCR in Paraffin Samples: A Retrospective Study in Patients with Early Breast Cancer

Abstract

IntroductionGene 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.Methods153 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.ResultsAfter 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.ConclusionCommercially 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.

Tumor-Associated Macrophages in SHH Subgroup of Medulloblastomas

“…Our group and others have demonstrated the clinical utility of these TLDA assays in childhood and adult clinical trials (34,35). Although current techniques such as IHC, FISH, and cytogenetics could be used to identify only a portion of medulloblastomas subgroups (21,23), our proposed 31-gene signature provides a rapid and highly accurate assay for determining these subgroups.…”

“…To identify the subgroups in a larger cohort of medulloblastoma patients and to validate expression of inflammation-related genes, we developed a robust and clinically applicable assay using the TLDA technology, a system currently being evaluated in neuroblastoma and used in breast cancer clinical trials (34,35). We built a medulloblastoma-specific TLDA card containing 39 tumor-related and six inflammation-related genes (CD163, CSF1R, MMD, CD4, ALCAM, and CXCR4) that were observed as significantly deregulated among medulloblastoma subgroups in our HuEx microarray analysis (Supplementary Table S2).…”

Biomarkers vs conventional histological analysis to detect lymph node micrometastases in bladder cancer: a real improvement?

“…Until recently, RT‐qPCR was used only to analyse fresh‐frozen tissue samples, which yield high quality and quantity RNA. However, the recent use of this technique to analyse formalin‐fixed paraffin‐embedded (FFPE) samples has greatly facilitated retrospective studies in which correlations with surveillance and outcome are possible [5–9]. In addition, novel combined methodologies, such as the cDNA preamplification technique before gene expression analysis, allow the analysis of clinical samples that yield scarce amounts of RNA [10].…”

<p>Decision of Adjuvant Systemic Treatment in HR+ HER2- Early Invasive Breast Cancer: Which Biomarkers Could Help?</p>

“…Most studies showed a significant association between Oncotype DX ® and breast cancer outcome: in ER+ pN0 patients without systemic treatment,46 in ER+ pN0 patients treated with ET alone,31,36,40,42,44–47 and in patients treated with chemotherapy and ET 34,41,43,46,48. An association between the RS and patients’ outcome was also found in ER+ pN+ patients 35,36,41,43,44,49,50. Only three retrospective studies evaluated the Oncotype DX ® in the target population of strictly ER+, HER2- patients 51–53.…”