Published online before print May 31, 2007

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Journal of Molecular Diagnostics 2007, Vol. 9, No. 3
Copyright © 2007 American Society for Investigative Pathology & Association for Molecular Pathology
DOI: 10.2353/jmoldx.2007.060079

Amplification Patterns of Three Genomic Regions Predict Distant Recurrence in Breast Carcinoma

Lisa M. Davis^*, Cole Harris^*, Lei Tang^*, Patti Doherty^*, Peter Hraber^*, Yumiko Sakai^*, Therese Bocklage, Katie Doeden, Bryan Hall, John Alsobrook^*, Ian Rabinowitz, Thomas M. Williams and John Hozier

From Exagen Diagnostics, * Albuquerque; and the Departments of Pathology and Internal Medicine, University of New Mexico, Albuquerque, New Mexico

Currently used clinical and histopathological parameters imprecisely define the risk of distant recurrence in breast cancer, underscoring the need for more informative prognostic markers. In the present fluorescence in situ hybridization study of archived surgical specimens, we derived an algorithm for computing a prognostic index (PI) from DNA copy numbers of three genomic regions (CYP24, PDCD6IP, and BIRC5) for estrogen/progesterone receptor-positive (ER/PR⁺) cancers and a distinct PI (based on NR1D1, SMARCE1, and BIRC5) for estrogen/progesterone receptor-negative (ER/PR^–) cancers. Among independent test cases stratified by PI, recurrence rates were significantly higher among high-risk patients than low-risk patients for both ER/PR⁺ (odds ratio = 9.52, 95% confidence interval >2.12, P = 0.0024) and ER/PR^– (odds ratio = 12.3, 95% confidence interval >1.45, P = 0.0188) cancers. Among the entire population, recurrences were significantly more prevalent for cases with PI above the medians for both ER/PR⁺ (Fisher’s exact, P = 1.19 x 10^–5) and ER/PR^– (P = 0.0025) patients and for the node-negative subsets (ER/PR⁺ node-negative, P = 0.042 and ER/PR^– node-negative, P = 0.039). In conclusion, these markers perform well in comparison with other criteria for recurrence risk assessment and can be used with routinely formalin-fixed, paraffin-embedded surgical specimens.

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