Purpose: Several risk factors for local recurrence of breast cancer after breast conserving therapy (BCT) have been identified. The identification of additional risk factors would be very useful in guiding optimal therapy and also improve understanding of the mechanisms underlying local recurrence. We used cDNA microarray analysis to identify gene expression profiles associated with local recurrence.
Experimental Design: Using 18K cDNA microarrays, gene expression profiles were obtained from 50 patients who underwent BCT. Of these 50 patients 19 developed a local recurrence; the remaining 31 patients were selected as controls as they were free of local recurrence at least 11 years after treatment. For 9/19 patients also the local recurrence was available for gene expression profiling. Unsupervised and supervised methods of classification were used to separate patients in groups corresponding to disease outcome and to study the overall gene expression pattern of primary tumors and their recurrences.
Results: Hierarchical clustering of patients did not show any grouping reflecting local recurrence status. Supervised analysis revealed no significant set of genes that was able to distinguish recurring tumors from non-recurring tumors. Paired-data analysis of primary tumors and local recurrences showed a remarkable similarity in gene expression profile between primary tumors and their recurrences.
Conclusions: No significant differences in gene expression between primary breast cancer tumors in patients with or without local recurrence after breast conserving therapy were identified. Furthermore, analyses of primary tumors and local recurrences show a preservation of the overall gene expression pattern in the local recurrence, even after radiotherapy.
Keywords: gene expression profiling
Overall design: The series contains 50 primary breast carcinomas; 19 of which develop a local recurrence (cases) and 31 remain free from local recurrence for 11 years after therapy (controls).
In addition this studie group contains 9 recurrences that are the actual recurrence of 9 out the 19 cases.
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31 primary tumors without recurrence:
GSM110395, GSM110396, GSM110397, GSM110398, GSM110399, GSM110400, GSM110401, GSM110406, GSM110407, GSM110409, GSM110410, GSM110413, GSM110414, GSM110415, GSM110416, GSM110418, GSM110419, GSM110420, GSM110421, GSM110423, GSM110424, GSM110425, GSM110427, GSM110428, GSM110430, GSM110431, GSM110432, GSM110434, GSM110435, GSM110437, GSM110438
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19 primary tumors with recurrence:
GSM110388, GSM110392, GSM110394, GSM110402, GSM110411, GSM110412, GSM110417, GSM110422, GSM110426, GSM110429, GSM110433, GSM110436, GSM110440, GSM110441, GSM110444, GSM110445, GSM110446, GSM110449, GSM110451
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9 recurrences:
GSM110391, GSM110439, GSM110442, GSM110443, GSM110447, GSM110448, GSM110450, GSM110452, GSM110453
Less...