Node Negative, 61-, T1-2

Recently, a 76-gene prognostic signature able to predict distant metastases in lymph node–negative (N-) breast cancer patients was reported. The aims of this study conducted by TRANSBIG were to independently validate these results and to compare the outcome with clinical risk assessment.

Dataset of microarray experiments from primary breast tumors used to validate the 76-gene signature (VERIDEX). No replicate, no reference sample.

Patients were younger than the age of 61 years (median age, 47 years) and had node-negative, T1-T2 (?5 cm) tumors. Patients in this series had been diagnosed between 1980 and 1998 (median follow-up, 13.6 years) and had been seen at six centers: Institut Gustave Roussy, Villejuif, France (IGR); Karolinska Institute, Stockholm and Uppsala University Hospital, Uppsala, Sweden (KI); Centre René Huguenin, Saint-Cloud, France (CRH); Guy's Hospital, London, United Kingdom (GH); and John Radcliffe Hospital, Oxford, United Kingdom (JRH). Patients with previous malignancies (except basal cell carcinoma) and bilateral synchronous breast tumors were excluded. The corresponding paraffin-embedded tumor samples of these patients were sent to the Department of Pathology at the European Institute of Oncology, Milan, Italy, where ER status (using immunohistochemistry) and histologic grade (using the Elston and Ellis method) were determined by the same pathologist, blinded to the clinical and genomic data. The clinical centers were also visited by two independent auditors who carried out source data verification of all data in the validation series. The validation protocol was finalized in September 2005, and all institutional ethics committees approved the use of the tumor materials for the purposes described in this study.

Frozen samples were sent from the clinical centers to the Netherlands Cancer Institute, Amsterdam, where RNA had been extracted for the previous TRANSBIG validation study of the 70-gene profile on the Agilent platform (7), except for the samples from Centre René Huguenin, for which RNA was sent directly to Amsterdam. To carry out the present study, RNAs were then shipped to the Jules Bordet Institute to perform the microarray analyses using the Affymetrix U133a GeneChip blinded to clinical data and independent of Veridex. The quality of the RNA obtained from each tumor sample was assessed via the RNA profile generated by the Agilent bioanalyzer. RNA amplification, hybridization, and image scanning were done according to standard Affymetrix protocols. Expression values for each gene were calculated using Affymetrix GeneChip analysis software MAS 5.0. For chip normalization, probe sets were scaled to a target intensity of 600, and scale mask filters were not selected. Chips with signal to noise ratio < 24 were excluded. Each probe set was considered as a separate gene.

Desmedt, Christine, Fanny Piette, Sherene Loi, Yixin Wang, Françoise Lallemand, Benjamin Haibe-Kains, Giuseppe Viale, et al. “Strong Time Dependence of the 76-Gene Prognostic Signature for Node-Negative Breast Cancer Patients in the TRANSBIG Multicenter Independent Validation Series.” Clinical Cancer Research 13, no. 11 (June 1, 2007): 3207–14. doi:10.1158/1078-0432.CCR-06-2765.