Validation of a Blood-Based Gene Expression Test for the Detection of Breast Cancer Using an Independent European Cohort.
Authors: D. Tobin, A. Børresen-Dale, M. Kauczynska, A. Hollingsworth, P. Sharma
Journal: Cancer Research (2009)

Abstract We report the development of a gene expression based blood test to detect breast cancer (BC). The test measures RNA species that undergo regulation as a response to the presence of a breast cancer lesion. We have previously presented data from a European/US cohort with accuracies from 75% - 82%. We now report findings from a multi-centre study where a calibration set of 282 subjects was used to create a model for the classification of breast cancer vs non-breast cancer using a European/US cohort. Validation of this model was performed using an independent set of 109 samples collected in 5 sites one of which was independent from the calibration set.MethodsIn a multicentre-study, blood samples were collected from women recruited in 4 groups 1) early stage BC (stage 0-1), 2) late stage BC (stage2+), 3) benign breast lesions, 4) without abnormal mammographic findings. Samples were collected in PAXgene™ tubes and shipped to a central laboratory where RNA extraction and quality control were performed. Gene expression analysis was performed using real time-RT PCR on an AB Prism 7900HT Fast instrument with a microfluidic card containing a BC-specific gene signature in a 96-gene assay format. Modelling was performed using Partial Least Square Regression providing an algorithm for application to gene expression data. Application of the algorithm to subjects in an independent cohort was used to obtain a test score for each subject. A positive test score classified a subject as positive for breast cancer, whilst a negative score classified a subject as negative for breast cancer. A total of 248 samples were used to develop the algorithm and 109 used as an independent validation set to describe it performance.ResultsThe model correctly predicted the class of 78/109 validation samples, resulting in an overall accuracy of 72%. Performance was similar for early and late stage cancer with a sensitivity of 74% for stage 0 and stage 1 breast cancer. No significant difference in diagnostic performance was seen between pre- (71%) and post-menopausal (70%) women indicating the clinical value of our test in younger women. When assessing the efficacy of ductal and lobular cancers only the test showed a sensitivity of73%. The effect of medications were assessed from the information gathered from the subject report forms. The majority of medications were for hypocholesterolaemia, hypertension, diabetes, and asthma. None of the medication groups noted appeared to have a detrimental effect on the ability for the test.ConclusionWe report the validation of the blood-based gene expression test in a European cohort from a multi-centre study. The test shows efficacy for the detection of early breast cancer for both lobular and ductal breast cancer in both pre- and postmenopausal women. The test may be of clinical benefit as an adjuvant to mammography particularly for pre-menopausal women where mammography is known to have limitations. Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 3025.