Journal Article
. 2009 Jun;4(6).
doi: 10.1371/journal.pone.0005911.

Comparison of prognostic gene profiles using qRT-PCR in paraffin samples: a retrospective study in patients with early breast cancer

Enrique Espinosa 1 Iker Sánchez-Navarro  Angelo Gámez-Pozo  Alvaro Pinto Marin  David Hardisson  Rosario Madero  Andrés Redondo  Pilar Zamora  Belén San José Valiente  Marta Mendiola  Manuel González Barón  Juan Angel Fresno Vara  
  • PMID: 19547727
  •     30 References
  •     6 citations


Introduction: 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.

Conclusion: 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.

Predictive accuracy and explained variation in Cox regression.
M Schemper, R Henderson.
Biometrics, 2000 Apr 28; 56(1). PMID: 10783803
Prognostic and predictive value of the 21-gene recurrence score assay in postmenopausal women with node-positive, oestrogen-receptor-positive breast cancer on chemotherapy: a retrospective analysis of a randomised trial.
Kathy S Albain, William E Barlow, +20 authors, Breast Cancer Intergroup of North America.
Lancet Oncol, 2009 Dec 17; 11(1). PMID: 20005174    Free PMC article.
Highly Cited.
Gene expression profiling predicts clinical outcome of breast cancer.
Laura J van 't Veer, Hongyue Dai, +13 authors, Stephen H Friend.
Nature, 2002 Feb 02; 415(6871). PMID: 11823860
Highly Cited.
A new mathematical model for relative quantification in real-time RT-PCR.
M W Pfaffl.
Nucleic Acids Res, 2001 May 09; 29(9). PMID: 11328886    Free PMC article.
Highly Cited.
A gene-expression signature as a predictor of survival in breast cancer.
Marc J van de Vijver, Yudong D He, +18 authors, René Bernards.
N Engl J Med, 2002 Dec 20; 347(25). PMID: 12490681
Highly Cited.
Measurement of gene expression in archival paraffin-embedded tissues: development and performance of a 92-gene reverse transcriptase-polymerase chain reaction assay.
Maureen Cronin, Mylan Pho, +5 authors, Joffre B Baker.
Am J Pathol, 2003 Dec 26; 164(1). PMID: 14695316    Free PMC article.
Highly Cited.
A two-gene expression ratio predicts clinical outcome in breast cancer patients treated with tamoxifen.
Xiao-Jun Ma, Zuncai Wang, +27 authors, Dennis C Sgroi.
Cancer Cell, 2004 Jun 15; 5(6). PMID: 15193263
Highly Cited.
Overall C as a measure of discrimination in survival analysis: model specific population value and confidence interval estimation.
Michael J Pencina, Ralph B D'Agostino.
Stat Med, 2004 Jun 24; 23(13). PMID: 15211606
Highly Cited.
Multivariable prognostic models: issues in developing models, evaluating assumptions and adequacy, and measuring and reducing errors.
F E Harrell, K L Lee, D B Mark.
Stat Med, 1996 Feb 28; 15(4). PMID: 8668867
Highly Cited. Review.
A multigene assay to predict recurrence of tamoxifen-treated, node-negative breast cancer.
Soonmyung Paik, Steven Shak, +12 authors, Norman Wolmark.
N Engl J Med, 2004 Dec 14; 351(27). PMID: 15591335
Highly Cited.
Population-based validation of the prognostic model ADJUVANT! for early breast cancer.
Ivo A Olivotto, Chris D Bajdik, +6 authors, Karen A Gelmon.
J Clin Oncol, 2005 Apr 20; 23(12). PMID: 15837986
Highly Cited.
Genes that mediate breast cancer metastasis to lung.
Andy J Minn, Gaorav P Gupta, +7 authors, Joan Massagué.
Nature, 2005 Jul 29; 436(7050). PMID: 16049480    Free PMC article.
Highly Cited.
Reliable gene expression measurements from degraded RNA by quantitative real-time PCR depend on short amplicons and a proper normalization.
Janine Antonov, Darlene R Goldstein, +5 authors, Rolf Jaggi.
Lab Invest, 2005 Jun 14; 85(8). PMID: 15951835
Breast cancer prognosis determined by gene expression profiling: a quantitative reverse transcriptase polymerase chain reaction study.
E Espinosa, J A Fresno Vara, +9 authors, M González Barón.
J Clin Oncol, 2005 Sep 01; 23(29). PMID: 16129846
Gene expression profiling in breast cancer: understanding the molecular basis of histologic grade to improve prognosis.
Christos Sotiriou, Pratyaksha Wirapati, +17 authors, Mauro Delorenzi.
J Natl Cancer Inst, 2006 Feb 16; 98(4). PMID: 16478745
Highly Cited.
Gene expression and benefit of chemotherapy in women with node-negative, estrogen receptor-positive breast cancer.
Soonmyung Paik, Gong Tang, +11 authors, Norman Wolmark.
J Clin Oncol, 2006 May 25; 24(23). PMID: 16720680
Highly Cited.
A population-based study of tumor gene expression and risk of breast cancer death among lymph node-negative patients.
Laurel A Habel, Steven Shak, +12 authors, Charles P Quesenberry.
Breast Cancer Res, 2006 Jun 02; 8(3). PMID: 16737553    Free PMC article.
Highly Cited.
Concordance among gene-expression-based predictors for breast cancer.
Cheng Fan, Daniel S Oh, +5 authors, Charles M Perou.
N Engl J Med, 2006 Aug 11; 355(6). PMID: 16899776
Highly Cited.
Validation and clinical utility of a 70-gene prognostic signature for women with node-negative breast cancer.
Marc Buyse, Sherene Loi, +18 authors, TRANSBIG Consortium.
J Natl Cancer Inst, 2006 Sep 07; 98(17). PMID: 16954471
Highly Cited.
The HOXB13:IL17BR expression index is a prognostic factor in early-stage breast cancer.
Xiao-Jun Ma, Susan G Hilsenbeck, +6 authors, Mark G Erlander.
J Clin Oncol, 2006 Sep 30; 24(28). PMID: 17008703
Gene expression profiling: does it add predictive accuracy to clinical characteristics in cancer prognosis?
Daniela Dunkler, Stefan Michiels, Michael Schemper.
Eur J Cancer, 2007 Jan 30; 43(4). PMID: 17257824
Estimation of predictive accuracy in survival analysis using R and S-PLUS.
Lara Lusa, Rosalba Miceli, Luigi Mariani.
Comput Methods Programs Biomed, 2007 Jul 03; 87(2). PMID: 17601627
Progress and promise: highlights of the international expert consensus on the primary therapy of early breast cancer 2007.
A Goldhirsch, W C Wood, +4 authors, 10th St. Gallen conference.
Ann Oncol, 2007 Aug 07; 18(7). PMID: 17675394
Highly Cited. Review.
Critical review of microarray-based prognostic tests and trials in breast cancer.
Serge Koscielny.
Curr Opin Obstet Gynecol, 2008 Jan 17; 20(1). PMID: 18197005
A five-gene molecular grade index and HOXB13:IL17BR are complementary prognostic factors in early stage breast cancer.
Xiao-Jun Ma, Ranelle Salunga, +8 authors, Dennis Sgroi.
Clin Cancer Res, 2008 May 03; 14(9). PMID: 18451222
Prognostic utility of the 21-gene assay in hormone receptor-positive operable breast cancer compared with classical clinicopathologic features.
Lori J Goldstein, Robert Gray, +12 authors, Joseph A Sparano.
J Clin Oncol, 2008 Aug 06; 26(25). PMID: 18678838    Free PMC article.
Highly Cited.
Meta-analysis of gene expression profiles in breast cancer: toward a unified understanding of breast cancer subtyping and prognosis signatures.
Pratyaksha Wirapati, Christos Sotiriou, +10 authors, Mauro Delorenzi.
Breast Cancer Res, 2008 Jul 30; 10(4). PMID: 18662380    Free PMC article.
Highly Cited.
A comprehensive analysis of prognostic signatures reveals the high predictive capacity of the proliferation, immune response and RNA splicing modules in breast cancer.
Fabien Reyal, Martin H van Vliet, +10 authors, Lodewyk F A Wessels.
Breast Cancer Res, 2008 Nov 19; 10(6). PMID: 19014521    Free PMC article.
The 70-gene prognosis-signature predicts disease outcome in breast cancer patients with 1-3 positive lymph nodes in an independent validation study.
Stella Mook, Marjanka K Schmidt, +10 authors, TRANSBIG Consortium.
Breast Cancer Res Treat, 2008 Jul 29; 116(2). PMID: 18661261
Who should not receive adjuvant chemotherapy? International databases.
J Bergh, M Holmquist.
J Natl Cancer Inst Monogr, 2002 Jan 05; (30). PMID: 11773301
An 8-gene qRT-PCR-based gene expression score that has prognostic value in early breast cancer.
Iker Sánchez-Navarro, Angelo Gámez-Pozo, +11 authors, Enrique Espinosa.
BMC Cancer, 2010 Jun 30; 10. PMID: 20584321    Free PMC article.
Identification of reference genes across physiological states for qRT-PCR through microarray meta-analysis.
Wei-Chung Cheng, Cheng-Wei Chang, +4 authors, Ian C Hsu.
PLoS One, 2011 Mar 11; 6(2). PMID: 21390309    Free PMC article.
Gene expression profiling for guiding adjuvant chemotherapy decisions in women with early breast cancer: an evidence-based and economic analysis.
Medical Advisory Secretariat.
Ont Health Technol Assess Ser, 2010 Jan 01; 10(23). PMID: 23074401    Free PMC article.
Comparison of Accuracy of Whole-Exome Sequencing with Formalin-Fixed Paraffin-Embedded and Fresh Frozen Tissue Samples.
Ensel Oh, Yoon-La Choi, +5 authors, Young Kee Shin.
PLoS One, 2015 Dec 08; 10(12). PMID: 26641479    Free PMC article.
Decision of Adjuvant Systemic Treatment in HR+ HER2- Early Invasive Breast Cancer: Which Biomarkers Could Help?
Marie Alexandre, Aurélie Maran-Gonzalez, +6 authors, Séverine Guiu.
Cancer Manag Res, 2019 Dec 19; 11. PMID: 31849525    Free PMC article.
Tumor-associated macrophages in SHH subgroup of medulloblastomas.
Ashley S Margol, Nathan J Robison, +13 authors, Shahab Asgharzadeh.
Clin Cancer Res, 2014 Oct 26; 21(6). PMID: 25344580    Free PMC article.