Gene expression profiling of peripheral blood cells for early detection of breast cancer

Abstract

Introduction: Early detection of breast cancer is key to successful treatment and patient survival. We have previously reported the potential use of gene expression profiling of peripheral blood cells for early detection of breast cancer. The aim of the present study was to refine these findings using a larger sample size and a commercially available microarray platform.

Methods: Blood samples were collected from 121 females referred for diagnostic mammography following an initial suspicious screening mammogram. Diagnostic work-up revealed that 67 of these women had breast cancer while 54 had no malignant disease. Additionally, nine samples from six healthy female controls were included. Gene expression analyses were conducted using high density oligonucleotide microarrays. Partial Least Squares Regression (PLSR) was used for model building while a leave-one-out (LOO) double cross validation approach was used to identify predictors and estimate their prediction efficiency.

Results: A set of 738 probes that discriminated breast cancer and non-breast cancer samples was identified. By cross validation we achieved an estimated prediction accuracy of 79.5% with a sensitivity of 80.6% and a specificity of 78.3%. The genes deregulated in blood of breast cancer patients are related to functional processes such as defense response, translation, and various metabolic processes, such as lipid- and steroid metabolism.

Conclusions: We have identified a gene signature in whole blood that classifies breast cancer patients and healthy women with good accuracy supporting our previous findings.

Figure 1

Prediction performance. A) Raw prediction scores (breast cancer >0> non-breast cancer). Subjects with breast cancer are indicated by red bars and healthy subjects are indicated by green bars. Among the 67 breast cancer patients, 54 were correctly predicted, while 47 of the 60 healthy samples were assigned to the correct class. False negatives (n = 13) and false positives (n = 13) can be seen in the centre of the figure. Bars marked with * are samples from pregnant women. B) ROC curve based on the double cross-validation results Prediction of the 127 samples based on the 738 probe list. The prediction accuracy is 79.5% and the area under curve (AUC) is 0.88 reflecting a good separation of the two groups.

Figure 2

Interaction map of the core up-regulated genes. Biological network prediction of the 47 core up-regulated genes in blood of breast cancer patients compared to controls, using edge weight cutoff 0.648 (interaction confidence). Genes marked with red asterix are involved in defense response to bacterium.