Deep Radiogenomics Sequencing for Breast Tumor Gene-Phenotype Decoding Using Dynamic Contrast Magnetic Resonance Imaging

Abstract

PurposeWe aim to perform radiogenomic profiling of breast cancer tumors using dynamic contrast magnetic resonance imaging (MRI) for the estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER2) genes.MethodsThe dataset used in the current study consists of imaging data of 922 biopsy-confirmed invasive breast cancer patients with ER, PR, and HER2 gene mutation status. Breast MR images, including a T1-weighted pre-contrast sequence and three post-contrast sequences, were enrolled for analysis. All images were corrected using N4 bias correction algorithms. Based on all images and tumor masks, a bounding box of 128 x 128 x 68 was chosen to include all tumor regions. All networks were implemented in 3D fashion with input sizes of 128 x 128 x 68, and four images were input to each network for multi-channel analysis. Data were randomly split into train/validation (80) and test set (20) with stratification in class (patient-wise), and all metrics were reported in 20 of the untouched test dataset.ResultsFor ER prediction, SEResNet50 achieved an AUC mean of 0.695 (CI95: 0.610-0.775), a sensitivity of 0.564, and a specificity of 0.787. For PR prediction, ResNet34 achieved an AUC mean of 0.658 (95 CI: 0.573-0.741), a sensitivity of 0.593, and a specificity of 0.734. For HER2 prediction, SEResNext101 achieved an AUC mean of 0.698 (95 CI: 0.560-0.822), a sensitivity of 0.750, and a specificity of 0.625.ConclusionThe current study demonstrated the feasibility of imaging gene-phenotype decoding in breast tumors using MR images and deep learning algorithms with moderate performance.