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Optimization of a Multiplex RNA-based Expression Assay Using Breast Cancer Archival Material
Published on: August 1, 2018
Breast cancer molecular subtype classifier that incorporates MRI features
Elizabeth J Sutton1, Brittany Z Dashevsky1,2, Jung Hun Oh3
1Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, New York, USA.
Purpose:
To use features extracted from magnetic resonance (MR) images and a machine-learning method to assist in differentiating breast cancer molecular subtypes.
Materials And Methods:
This retrospective Health Insurance Portability and Accountability Act (HIPAA)-compliant study received Institutional Review Board (IRB) approval. We identified 178 breast cancer patients between 2006-2011 with: 1) ERPR + (n = 95, 53.4%), ERPR-/HER2 + (n = 35, 19.6%), or triple negative (TN, n = 48, 27.0%) invasive ductal carcinoma (IDC), and 2) preoperative breast MRI at 1.5T or 3.0T. Shape, texture, and histogram-based features were extracted from each tumor contoured on pre- and three postcontrast MR images using in-house software. Clinical and pathologic features were also collected. Machine-learning-based (support vector machines) models were used to identify significant imaging features and to build models that predict IDC subtype. Leave-one-out cross-validation (LOOCV) was used to avoid model overfitting. Statistical significance was determined using the Kruskal-Wallis test.
Results:
Each support vector machine fit in the LOOCV process generated a model with varying features. Eleven out of the top 20 ranked features were significantly different between IDC subtypes with P < 0.05. When the top nine pathologic and imaging features were incorporated, the predictive model distinguished IDC subtypes with an overall accuracy on LOOCV of 83.4%. The combined pathologic and imaging model's accuracy for each subtype was 89.2% (ERPR+), 63.6% (ERPR-/HER2+), and 82.5% (TN). When only the top nine imaging features were incorporated, the predictive model distinguished IDC subtypes with an overall accuracy on LOOCV of 71.2%. The combined pathologic and imaging model's accuracy for each subtype was 69.9% (ERPR+), 62.9% (ERPR-/HER2+), and 81.0% (TN).
Conclusion:
We developed a machine-learning-based predictive model using features extracted from MRI that can distinguish IDC subtypes with significant predictive power. J. Magn. Reson. Imaging 2016;44:122-129.
