A robust classifier of high predictive value to identify good prognosis patients in ER-negative breast cancer

Andrew E Teschendorff¹^,2 and Carlos Caldas¹^,3

¹Breast Cancer Functional Genomics Laboratory, Cancer Research UK Cambridge Research Institute, Cambridge, CB2 0RE, UK.

²Department of Oncology University of Cambridge, Li Ka-Shing Centre, Robinson Way, Cambridge CB2 0RE, UK.

³Cambridge Breast Unit, Addenbrookes Hospital, Cambridge University Hospitals NHS Foundation Trust, Hills Road, Cambridge, UK.

author email corresponding author email

Breast Cancer Research 2008, 10:R73doi:10.1186/bcr2138


Published:	28 August 2008

Abstract

Introduction

Patients with primary operable oestrogen receptor (ER) negative (-) breast cancer account for about 30% of all cases and generally have a worse prognosis than ER-positive (+) patients. Nevertheless, a significant proportion of ER- cases have favourable outcomes and could potentially benefit from a less aggressive course of therapy. However, identification of such patients with a good prognosis remains difficult and at present is only possible through examining histopathological factors.

Methods

Building on a previously identified seven-gene prognostic immune response module for ER- breast cancer, we developed a novel statistical tool based on Mixture Discriminant Analysis in order to build a classifier that could accurately identify ER- patients with a good prognosis.

Results

We report the construction of a seven-gene expression classifier that accurately predicts, across a training cohort of 183 ER- tumours and six independent test cohorts (a total of 469 ER- tumours), ER- patients of good prognosis (in test sets, average predictive value = 94% [range 85 to 100%], average hazard ratio = 0.15 [range 0.07 to 0.36] p < 0.000001) independently of lymph node status and treatment.

Conclusions

This seven-gene classifier could be used in a polymerase chain reaction-based clinical assay to identify ER- patients with a good prognosis, who may therefore benefit from less aggressive treatment regimens.