Breast cancer subtype intertumor heterogeneity: MRI-based features predict results of a genomic assay

Precision diagnostics based on machine learning-derived imaging signatures

The complexity of modern multi-parametric MRI has increasingly challenged conventional interpretations of such images. Machine learning has emerged as a powerful approach to integrating diverse and complex imaging data into signatures of diagnostic and predictive value. It has also allowed us to progress from group comparisons to imaging biomarkers that offer value on an individual basis. We review several directions of research around this topic, emphasizing the use of machine learning in personalized predictions of clinical outcome, in breaking down broad umbrella diagnostic categories into more detailed and precise subtypes, and in non-invasively estimating cancer molecular characteristics. These methods and studies contribute to the field of precision medicine, by introducing more specific diagnostic and predictive biomarkers of clinical outcome, therefore pointing to better matching of treatments to patients.

Tumour heterogeneity revealed by unsupervised decomposition of dynamic contrast-enhanced magnetic resonance imaging is associated with underlying gene expression patterns and poor survival in breast cancer patients

BACKGROUND

Heterogeneity is a common finding within tumours. We evaluated the imaging features of tumours based on the decomposition of tumoural dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) data to identify their prognostic value for breast cancer survival and to explore their biological importance.

METHODS

Imaging features (n = 14), such as texture, histogram distribution and morphological features, were extracted to determine their associations with recurrence-free survival (RFS) in patients in the training cohort (n = 61) from The Cancer Imaging Archive (TCIA). The prognostic value of the features was evaluated in an independent dataset of 173 patients (i.e. the reproducibility cohort) from the TCIA I-SPY 1 TRIAL dataset. Radiogenomic analysis was performed in an additional cohort, the radiogenomic cohort (n = 87), using DCE-MRI from TCGA-BRCA and corresponding gene expression data from The Cancer Genome Atlas (TCGA). The MRI tumour area was decomposed by convex analysis of mixtures (CAM), resulting in 3 components that represent plasma input, fast-flow kinetics and slow-flow kinetics. The prognostic MRI features were associated with the gene expression module in which the pathway was analysed. Furthermore, a multigene signature for each prognostic imaging feature was built, and the prognostic value for RFS and overall survival (OS) was confirmed in an additional cohort from TCGA.

RESULTS

Three image features (i.e. the maximum probability from the precontrast MR series, the median value from the second postcontrast series and the overall tumour volume) were independently correlated with RFS (p values of 0.0018, 0.0036 and 0.0032, respectively). The maximum probability feature from the fast-flow kinetics subregion was also significantly associated with RFS and OS in the reproducibility cohort. Additionally, this feature had a high correlation with the gene expression module (r = 0.59), and the pathway analysis showed that Ras signalling, a breast cancer-related pathway, was significantly enriched (corrected p value = 0.0044). Gene signatures (n = 43) associated with the maximum probability feature were assessed for associations with RFS (p = 0.035) and OS (p = 0.027) in an independent dataset containing 1010 gene expression samples. Among the 43 gene signatures, Ras signalling was also significantly enriched.

CONCLUSIONS

Dynamic pattern deconvolution revealed that tumour heterogeneity was associated with poor survival and cancer-related pathways in breast cancer.

Lymph Node Imaging in Patients with Primary Breast Cancer: Concurrent Diagnostic Tools

The detection of lymph node metastasis affects the management of patients with primary breast cancer significantly in terms of staging, treatment, and prognosis. The main goal for the radiologist is to determine and detect the presence of metastatic disease in nonpalpable axillary lymph nodes with a positive predictive value that is high enough to initially select patients for upfront axillary lymph node dissection. Features that are suggestive of axillary adenopathy may be seen with different imaging modalities, but ultrasound is the method of choice for evaluating axillary lymph nodes and for performing image-guided lymph node interventions. This review aims to provide a comprehensive overview of the available imaging modalities for lymph node assessment in patients diagnosed with primary breast cancer. IMPLICATIONS FOR PRACTICE: The detection of lymph node metastasis affects the management of patients with primary breast cancer. The main goal for the radiologist is to detect lymph node metastasis in patients to allow for the selection of patients who should undergo upfront axillary lymph node dissection. Features that are suggestive of axillary adenopathy may be seen with mammography, computed tomography, and magnetic resonance imaging, but ultrasonography is the imaging modality of choice for evaluating axillary lymph nodes. A normal axillary lymph node is characterized by a reniform shape, a maximal cortical thickness of 3 mm without focal bulging, smooth margins, and, depending on size, a discernable central fatty hilum.

Reliability of tumor segmentation in glioblastoma: Impact on the robustness of MRI-radiomic features

PURPOSE

The use of radiomic features as biomarkers of treatment response and outcome or as correlates to genomic variations requires that the computed features are robust and reproducible. Segmentation, a crucial step in radiomic analysis, is a major source of variability in the computed radiomic features. Therefore, we studied the impact of tumor segmentation variability on the robustness of MRI radiomic features.

METHOD

Fluid-attenuated inversion recovery (FLAIR) and contrast-enhanced T1-weighted (T1WI_CE ) MRI of 90 patients diagnosed with glioblastoma were segmented using a semiautomatic algorithm and an interactive segmentation with two different raters. We analyzed the robustness of 108 radiomic features from five categories (intensity histogram, gray-level co-occurrence matrix, gray-level size-zone matrix (GLSZM), edge maps, and shape) using intra-class correlation coefficient (ICC) and Bland and Altman analysis.

RESULTS

Our results show that both segmentation methods are reliable with ICC ≥ 0.96 and standard deviation (SD) of mean differences between the two raters (SD_diffs ) ≤ 30%. Features computed from the histogram and co-occurrence matrices were found to be the most robust (ICC ≥ 0.8 and SD_diffs  ≤ 30% for most features in these groups). Features from GLSZM were shown to have mixed robustness. Edge, shape, and GLSZM features were the most impacted by the choice of segmentation method with the interactive method resulting in more robust features than the semiautomatic method. Finally, features computed from T1WI_CE and FLAIR images were found to have similar robustness when computed with the interactive segmentation method.

CONCLUSION

Semiautomatic and interactive segmentation methods using two raters are both reliable. The interactive method produced more robust features than the semiautomatic method. We also found that the robustness of radiomic features varied by categories. Therefore, this study could help motivate segmentation methods and feature selection in MRI radiomic studies.

Machine learning in breast MRI

Machine-learning techniques have led to remarkable advances in data extraction and analysis of medical imaging. Applications of machine learning to breast MRI continue to expand rapidly as increasingly accurate 3D breast and lesion segmentation allows the combination of radiologist-level interpretation (eg, BI-RADS lexicon), data from advanced multiparametric imaging techniques, and patient-level data such as genetic risk markers. Advances in breast MRI feature extraction have led to rapid dataset analysis, which offers promise in large pooled multiinstitutional data analysis. The object of this review is to provide an overview of machine-learning and deep-learning techniques for breast MRI, including supervised and unsupervised methods, anatomic breast segmentation, and lesion segmentation. Finally, it explores the role of machine learning, current limitations, and future applications to texture analysis, radiomics, and radiogenomics. Level of Evidence: 3 Technical Efficacy Stage: 2 J. Magn. Reson. Imaging 2019. J. Magn. Reson. Imaging 2020;52:998-1018.

Assessment of the Spatial Heterogeneity of Breast Cancers: Associations Between Computed Tomography and Immunohistochemistry

BACKGROUND

Tumour heterogeneity is considered an important mechanism of treatment failure. Imaging-based assessment of tumour heterogeneity is showing promise but the relationship between these mathematically derived measures and accepted 'gold standards' of tumour biology such as immunohistochemical measures is not established.

METHODS

A total of 20 women with primary breast cancer underwent a research dynamic contrast-enhanced computed tomography prior to treatment with data being available for 15 of these. Texture analysis was performed of the primary tumours to extract 13 locoregional and global parameters. Immunohistochemical analysis associations were assessed by the Spearman rank correlation.

RESULTS

Hypoxia-inducible factor-1α was correlated with first-order kurtosis (r = -0.533, P = .041) and higher order neighbourhood grey-tone difference matrix coarseness (r = 0.54, P = .038). Vascular maturity-related smooth muscle actin was correlated with higher order grey-level run-length long-run emphasis (r = -0.52, P = .047), fractal dimension (r = 0.613, P = .015), and lacunarity (r = -0.634, P = .011). Micro-vessel density, reflecting angiogenesis, was also associated with lacunarity (r = 0.547, P = .035).

CONCLUSIONS

The associations suggest a biological basis for these image-based heterogeneity features and support the use of imaging, already part of standard care, for assessing intratumoural heterogeneity.

Radiomics signature on 3T dynamic contrast-enhanced magnetic resonance imaging for estrogen receptor-positive invasive breast cancers: Preliminary results for correlation with Oncotype DX recurrence scores

To evaluate the ability of a radiomics signature based on 3T dynamic contrast-enhanced (DCE) magnetic resonance imaging (MRI) to distinguish between low and non-low Oncotype DX (OD) risk groups in estrogen receptor (ER)-positive invasive breast cancers.Between May 2011 and March 2016, 67 women with ER-positive invasive breast cancer who performed preoperative 3T MRI and OD assay were included. We divided the patients into low (OD recurrence score [RS] <18) and non-low risk (RS ≥18) groups. Extracted radiomics features included 8 morphological, 76 histogram-based, and 72 higher-order texture features. A radiomics signature (Rad-score) was generated using the least absolute shrinkage and selection operator (LASSO). Univariate and multivariate logistic regression analyses were performed to investigate the association between clinicopathologic factors, MRI findings, and the Rad-score with OD risk groups, and the areas under the receiver operating characteristic curves (AUC) were used to assess classification performance of the Rad-score.The Rad-score was constructed for each tumor by extracting 10 (6.3%) from 158 radiomics features. A higher Rad-score (odds ratio [OR], 65.209; P <.001), Ki-67 expression (OR, 17.462; P = .007), and high p53 (OR = 8.449; P = .077) were associated with non-low OD risk. The Rad-score classified low and non-low OD risk with an AUC of 0.759.The Rad-score showed the potential for discrimination between low and non-low OD risk groups in patients with ER-positive invasive breast cancers.

Neo-adjuvant chemoradiotherapy response prediction using MRI based ensemble learning method in rectal cancer patients

OBJECTIVES

The aim of this study was to investigate and validate the performance of individual and ensemble machine learning models (EMLMs) based on magnetic resonance imaging (MRI) to predict neo-adjuvant chemoradiation therapy (nCRT) response in rectal cancer patients. We also aimed to study the effect of Laplacian of Gaussian (LOG) filter on EMLMs predictive performance.

METHODS

98 rectal cancer patients were divided into a training (n = 53) and a validation set (n = 45). All patients underwent MRI a week before nCRT. Several features from intensity, shape and texture feature sets were extracted from MR images. SVM, Bayesian network, neural network and KNN classifiers were used individually and together for response prediction. Predictive performance was evaluated using the area under the receiver operator characteristic (ROC) curve (AUC).

RESULTS

Patients' nCRT responses included 17 patients with Grade 0, 28 with Grade 1, 34 with Grade 2, and 19 with Grade 3 according to AJCC/CAP pathologic grading. In without preprocessing MR Image the best result was for Bayesian network classifier with AUC and accuracy of 75.2% and 80.9% respectively, which was confirmed in the validation set with an AUC and accuracy of 74% and 79% respectively. In EMLMs the best result was for 4 (SVM.NN.BN.KNN) classifier EMLM with AUC and accuracy of 97.8% and 92.8% in testing and 95% and 90% in validation set respectively.

CONCLUSIONS

In conclusion, we observed that machine learning methods can used to predict nCRT response in patients with rectal cancer. Preprocessing LOG filters and EL models can improve the prediction process.

The Potential Use of DCE-MRI Texture Analysis to Predict HER2 2+ Status

Purpose: To evaluate the ability of texture analysis of breast dynamic contrast enhancement-magnetic resonance (DCE-MR) images in differentiating human epidermal growth factor receptor 2 (HER2) 2+ status of breast tumors. Methods: A total of 73 cases were retrospectively selected. HER2 2+ status was confirmed by fluorescence in situ hybridization. For each case, 279 textural features were derived. A student's t-test or Mann-Whitney U test was used to select features with statistically significant differences between HER2 2+ positive and negative groups. A principal component analysis was applied to eliminate feature correlation. Three machine learning classifiers, logistic regression (LR), quadratic discriminant analysis (QDA), and a support vector machine (SVM), were trained and tested using a leave-one-out cross-validation method. The area under a receiver operating characteristic curve (AUC) was measured to assess the classifier's performance. Results: The AUCs for the different classifiers were satisfactory, ranging from 0.808 to 0.865. The classification methods derived with LR and SVM demonstrated similarly high performances, and the accuracy levels were 81.06 and 81.18%, respectively. The AUC for the classifier derived with SVM was the highest (0.865), and a marked specificity (88.90%) was presented. For the classifier with LR, the AUC was 0.851, and the corresponding sensitivity (94.44%) was the highest. Conclusion: The texture analysis for breast DCE-MRI proposed in this study demonstrated potential utility in HER2 2+ status discrimination.

Feasibility of an ADC-based radiomics model for predicting pelvic lymph node metastases in patients with stage IB-IIA cervical squamous cell carcinoma

OBJECTIVES

To investigate the prediction value of a radiomics model based on apparent diffusion coefficient (ADC) maps for pelvic lymph node metastasis (PLNM) in patients with stage IB-IIA cervical squamous cell carcinoma (CSCC).

METHODS

A total of 153 stage IB-IIA CSCC patients who underwent preoperative MRI including DWI from January 2015 to October 2017 were retrospectively studied and divided into a training cohort ( n = 102) and a validation cohort ( n = 51). Radiomics features were extracted from the ADC maps. The one-way ANOVA method, Mann-Whitney U test and Pearson's correlation analysis were used for selecting radiomics features. Logistic regression analyses were used to develop the model. ROC analyses were used to evaluate the prediction performance of the model.

RESULTS

Clinical stage, tumor diameter, and MR-reported lymph node (LN) status were significantly associated with LN status ( p < 0.05 for both the training and validation cohorts). The radiomics model, which incorporated clinical stage, MR-reported LN status, and grey-level non-uniformity, showed good predictive performance in the training group (AUC 0.864; 95% CI, 0.782 - 0.924) and the validation group (AUC 0.870; 95% CI, 0.747 - 0.948). The performance of the radiomics model was significantly better than that of each predictive factor alone.

CONCLUSION

The presented radiomics model, a non-invasive preoperative prediction tool, has the potential to have more predictive efficacy than clinical and radiological factors for differentiating between metastatic and non-metastatic lymph nodes.

ADVANCES IN KNOWLEDGE

A radiomics model derived from the ADC maps of primary lesions demonstrated good performance for predicting PLNM in stage IB-IIA CSCC patients and may help to improve clinical decision-making.

Role of texture analysis in breast MRI as a cancer biomarker: A review

Breast cancer is a known heterogeneous disease. Current clinically utilized histopathologic biomarkers may undersample tumor heterogeneity, resulting in higher rates of misdiagnosis for breast cancer. MRI can provide a whole-tumor sampling of disease burden and is widely utilized in clinical care. Texture analysis can provide a localized description of breast cancer, with particular emphasis on quantifying breast lesion heterogeneity. The object of this review is to provide an overview of texture analysis applications towards breast cancer diagnosis, prognosis, and treatment response evaluation and review the role of image-based texture features as noninvasive prognostic and predictive biomarkers. Level of Evidence: 5 Technical Efficacy: Stage 2 J. Magn. Reson. Imaging 2019;49:927-938.

Application of Radiomics and Decision Support Systems for Breast MR Differential Diagnosis

Over the years, MR systems have evolved from imaging modalities to advanced computational systems producing a variety of numerical parameters that can be used for the noninvasive preoperative assessment of breast pathology. Furthermore, the combination with state-of-the-art image analysis methods provides a plethora of quantifiable imaging features, termed radiomics that increases diagnostic accuracy towards individualized therapy planning. More importantly, radiomics can now be complemented by the emerging deep learning techniques for further process automation and correlation with other clinical data which facilitate the monitoring of treatment response, as well as the prediction of patient's outcome, by means of unravelling of the complex underlying pathophysiological mechanisms which are reflected in tissue phenotype. The scope of this review is to provide applications and limitations of radiomics towards the development of clinical decision support systems for breast cancer diagnosis and prognosis.

Magnetic resonance imaging and molecular features associated with tumor-infiltrating lymphocytes in breast cancer

Background

We sought to investigate associations between dynamic contrast-enhanced (DCE) magnetic resonance imaging (MRI) features and tumor-infiltrating lymphocytes (TILs) in breast cancer, as well as to study if MRI features are complementary to molecular markers of TILs.

Methods

In this retrospective study, we extracted 17 computational DCE-MRI features to characterize tumor and parenchyma in The Cancer Genome Atlas cohort (n = 126). The percentage of stromal TILs was evaluated on H&E-stained histological whole-tumor sections. We first evaluated associations between individual imaging features and TILs. Multiple-hypothesis testing was corrected by the Benjamini-Hochberg method using false discovery rate (FDR). Second, we implemented LASSO (least absolute shrinkage and selection operator) and linear regression nested with tenfold cross-validation to develop an imaging signature for TILs. Next, we built a composite prediction model for TILs by combining imaging signature with molecular features. Finally, we tested the prognostic significance of the TIL model in an independent cohort (I-SPY 1; n = 106).

Results

Four imaging features were significantly associated with TILs (P < 0.05 and FDR < 0.2), including tumor volume, cluster shade of signal enhancement ratio (SER), mean SER of tumor-surrounding background parenchymal enhancement (BPE), and proportion of BPE. Among molecular and clinicopathological factors, only cytolytic score was correlated with TILs (ρ = 0.51; 95% CI, 0.36–0.63; P = 1.6E-9). An imaging signature that linearly combines five features showed correlation with TILs (ρ = 0.40; 95% CI, 0.24–0.54; P = 4.2E-6). A composite model combining the imaging signature and cytolytic score improved correlation with TILs (ρ = 0.62; 95% CI, 0.50–0.72; P = 9.7E-15). The composite model successfully distinguished low vs high, intermediate vs high, and low vs intermediate TIL groups, with AUCs of 0.94, 0.76, and 0.79, respectively. During validation (I-SPY 1), the predicted TILs from the imaging signature separated patients into two groups with distinct recurrence-free survival (RFS), with log-rank P = 0.042 among triple-negative breast cancer (TNBC). The composite model further improved stratification of patients with distinct RFS (log-rank P = 0.0008), where TNBC with no/minimal TILs had a worse prognosis.

Conclusions

Specific MRI features of tumor and parenchyma are associated with TILs in breast cancer, and imaging may play an important role in the evaluation of TILs by providing key complementary information in equivocal cases or situations that are prone to sampling bias.

Electronic supplementary material

The online version of this article (10.1186/s13058-018-1039-2) contains supplementary material, which is available to authorized users.

Convolutional Neural Network Using a Breast MRI Tumor Dataset Can Predict Oncotype Dx Recurrence Score

BACKGROUND

Oncotype Dx is a validated genetic analysis that provides a recurrence score (RS) to quantitatively predict outcomes in patients who meet the criteria of estrogen receptor positive / human epidermal growth factor receptor-2 negative (ER+/HER2-)/node negative invasive breast carcinoma. Although effective, the test is invasive and expensive, which has motivated this investigation to determine the potential role of radiomics.

HYPOTHESIS

We hypothesized that convolutional neural network (CNN) can be used to predict Oncotype Dx RS using an MRI dataset.

STUDY TYPE

Institutional Review Board (IRB)-approved retrospective study from January 2010 to June 2016.

POPULATION

In all, 134 patients with ER+/HER2- invasive ductal carcinoma who underwent both breast MRI and Oncotype Dx RS evaluation. Patients were classified into three groups: low risk (group 1, RS <18), intermediate risk (group 2, RS 18-30), and high risk (group 3, RS >30).

FIELD STRENGTH/SEQUENCE

1.5T and 3.0T. Breast MRI, T₁ postcontrast.

ASSESSMENT

Each breast tumor underwent 3D segmentation. In all, 1649 volumetric slices in 134 tumors (mean 12.3 slices/tumor) were evaluated. A CNN consisted of four convolutional layers and max-pooling layers. Dropout at 50% was applied to the second to last fully connected layer to prevent overfitting. Three-class prediction (group 1 vs. group 2 vs. group 3) and two-class prediction (group 1 vs. group 2/3) models were performed.

STATISTICAL TESTS

A 5-fold crossvalidation test was performed using 80% training and 20% testing. Diagnostic accuracy, sensitivity, specificity, and receiver operating characteristic (ROC) area under the curve (AUC) were evaluated.

RESULTS

The CNN achieved an overall accuracy of 81% (95% confidence interval [CI] ± 4%) in three-class prediction with specificity 90% (95% CI ± 5%), sensitivity 60% (95% CI ± 6%), and the area under the ROC curve was 0.92 (SD, 0.01). The CNN achieved an overall accuracy of 84% (95% CI ± 5%) in two-class prediction with specificity 81% (95% CI ± 4%), sensitivity 87% (95% CI ± 5%), and the area under the ROC curve was 0.92 (SD, 0.01).

DATA CONCLUSION

It is feasible for current deep CNN architecture to be trained to predict Oncotype DX RS.

LEVEL OF EVIDENCE

4 Technical Efficacy: Stage 2 J. Magn. Reson. Imaging 2019;49:518-524.

Precision Medicine and Radiogenomics in Breast Cancer: New Approaches toward Diagnosis and Treatment

Precision medicine is medicine optimized to the genotypic and phenotypic characteristics of an individual and, when present, his or her disease. It has a host of targets, including genes and their transcripts, proteins, and metabolites. Studying precision medicine involves a systems biology approach that integrates mathematical modeling and biology genomics, transcriptomics, proteomics, and metabolomics. Moreover, precision medicine must consider not only the relatively static genetic codes of individuals, but also the dynamic and heterogeneous genetic codes of cancers. Thus, precision medicine relies not only on discovering identifiable targets for treatment and surveillance modification, but also on reliable, noninvasive methods of identifying changes in these targets over time. Imaging via radiomics and radiogenomics is poised for a central role. Radiomics, which extracts large volumes of quantitative data from digital images and amalgamates these together with clinical and patient data into searchable shared databases, potentiates radiogenomics, which is the combination of genetic and radiomic data. Radiogenomics may provide voxel-by-voxel genetic information for a complete, heterogeneous tumor or, in the setting of metastatic disease, set of tumors and thereby guide tailored therapy. Radiogenomics may also quantify lesion characteristics, to better differentiate between benign and malignant entities, and patient characteristics, to better stratify patients according to risk for disease, thereby allowing for more precise imaging and screening. This report provides an overview of precision medicine and discusses radiogenomics specifically in breast cancer. ^© RSNA, 2018.

Radiomics Signature on Magnetic Resonance Imaging: Association with Disease-Free Survival in Patients with Invasive Breast Cancer

Purpose: To develop a radiomics signature based on preoperative MRI to estimate disease-free survival (DFS) in patients with invasive breast cancer and to establish a radiomics nomogram that incorporates the radiomics signature and MRI and clinicopathological findings.Experimental Design: We identified 294 patients with invasive breast cancer who underwent preoperative MRI. Patients were randomly divided into training (n = 194) and validation (n = 100) sets. A radiomics signature (Rad-score) was generated using an elastic net in the training set, and the cutoff point of the radiomics signature to divide the patients into high- and low-risk groups was determined using receiver-operating characteristic curve analysis. Univariate and multivariate Cox proportional hazards model and Kaplan-Meier analysis were used to determine the association of the radiomics signature, MRI findings, and clinicopathological variables with DFS. A radiomics nomogram combining the Rad-score and MRI and clinicopathological findings was constructed to validate the radiomic signatures for individualized DFS estimation.Results: Higher Rad-scores were significantly associated with worse DFS in both the training and validation sets (P = 0.002 and 0.036, respectively). The radiomics nomogram estimated DFS [C-index, 0.76; 95% confidence interval (CI); 0.74-0.77] better than the clinicopathological (C-index, 0.72; 95% CI, 0.70-0.74) or Rad-score-only nomograms (C-index, 0.67; 95% CI, 0.65-0.69).Conclusions: The radiomics signature is an independent biomarker for the estimation of DFS in patients with invasive breast cancer. Combining the radiomics nomogram improved individualized DFS estimation. Clin Cancer Res; 24(19); 4705-14. ©2018 AACR.

Breast cancer MRI radiomics: An overview of algorithmic features and impact of inter-reader variability in annotating tumors

PURPOSE

To review features used in MRI radiomics of breast cancer and study the inter-reader stability of the features.

METHODS

We implemented 529 algorithmic features that can be extracted from tumor and fibroglandular tissue (FGT) in breast MRIs. The features were identified based on a review of the existing literature with consideration of their usage, prognostic ability, and uniqueness. The set was then extended so that it comprehensively describes breast cancer imaging characteristics. The features were classified into 10 groups based on the type of data used to extract them and the type of calculation being performed. For the assessment of inter-reader variability, four fellowship-trained readers annotated tumors on preoperative dynamic contrast-enhanced MRIs for 50 breast cancer patients. Based on the annotations, an algorithm automatically segmented the image and extracted all features resulting in one set of features for each reader. For a given feature, the inter-reader stability was defined as the intraclass correlation coefficient (ICC) computed using the feature values obtained through all readers for all cases.

RESULTS

The average inter-reader stability for all features was 0.8474 (95% CI: 0.8068-0.8858). The mean inter-reader stability was lower for tumor-based features (0.6348, 95% CI: 0.5391-0.7257) than FGT-based features (0.9984, 95% CI: 0.9970-0.9992). The feature group with the highest inter-reader stability quantifies breast and FGT volume. The feature group with the lowest inter-reader stability quantifies variations in tumor enhancement.

CONCLUSIONS

Breast MRI radiomics features widely vary in terms of their stability in the presence of inter-reader variability. Appropriate measures need to be taken for reducing this variability in tumor-based radiomics.

MRI for the Staging and Evaluation of Response to Therapy in Breast Cancer

Breast magnetic resonance imaging (MRI) is the most sensitive of the available imaging modalities to characterize breast cancer. Breast MRI has gained clinical acceptance for screening high-risk patients, but its role in the preoperative imaging of breast cancer patients remains controversial. This review focuses on the current indications for staging breast MRI, the evidence for and against the role of breast MRI in the preoperative staging workup, and the evaluation of treatment response of breast cancer patients.

A study of association of Oncotype DX recurrence score with DCE-MRI characteristics using multivariate machine learning models

PURPOSE

To determine whether multivariate machine learning models of algorithmically assessed magnetic resonance imaging (MRI) features from breast cancer patients are associated with Oncotype DX (ODX) test recurrence scores.

METHODS

A set of 261 female patients with invasive breast cancer, pre-operative dynamic contrast enhanced magnetic resonance (DCE-MR) images and available ODX score at our institution was identified. A computer algorithm extracted a comprehensive set of 529 features from the DCE-MR images of these patients. The set of patients was divided into a training set and a test set. Using the training set we developed two machine learning-based models to discriminate (1) high ODX scores from intermediate and low ODX scores, and (2) high and intermediate ODX scores from low ODX scores. The performance of these models was evaluated on the independent test set.

RESULTS

High against low and intermediate ODX scores were predicted by the multivariate model with AUC 0.77 (95% CI 0.56-0.98, p < 0.003). Low against intermediate and high ODX score was predicted with AUC 0.51 (95% CI 0.41-0.61, p = 0.75).

CONCLUSION

A moderate association between imaging and ODX score was identified. The evaluated models currently do not warrant replacement of ODX with imaging alone.

Non-invasive tumor genotyping using radiogenomic biomarkers, a systematic review and oncology-wide pathway analysis

With targeted treatments playing an increasing role in oncology, the need arises for fast non-invasive genotyping in clinical practice. Radiogenomics is a rapidly evolving field of research aimed at identifying imaging biomarkers useful for non-invasive genotyping. Radiogenomic genotyping has the advantage that it can capture tumor heterogeneity, can be performed repeatedly for treatment monitoring, and can be performed in malignancies for which biopsy is not available. In this systematic review of 187 included articles, we compiled a database of radiogenomic associations and unraveled networks of imaging groups and gene pathways oncology-wide. Results indicated that ill-defined tumor margins and tumor heterogeneity can potentially be used as imaging biomarkers for 1p/19q codeletion in glioma, relevant for prognosis and disease profiling. In non-small cell lung cancer, FDG-PET uptake and CT-ground-glass-opacity features were associated with treatment-informing traits including EGFR-mutations and ALK-rearrangements. Oncology-wide gene pathway analysis revealed an association between contrast enhancement (imaging) and the targetable VEGF-signalling pathway. Although the need of independent validation remains a concern, radiogenomic biomarkers showed potential for prognosis prediction and targeted treatment selection. Quantitative imaging enhanced the potential of multiparametric radiogenomic models. A wealth of data has been compiled for guiding future research towards robust non-invasive genomic profiling.

Appearance Constrained Semi-Automatic Segmentation from DCE-MRI is Reproducible and Feasible for Breast Cancer Radiomics: A Feasibility Study

We present a segmentation approach that combines GrowCut (GC) with cancer-specific multi-parametric Gaussian Mixture Model (GCGMM) to produce accurate and reproducible segmentations. We evaluated GCGMM using a retrospectively collected 75 invasive ductal carcinoma with ERPR+ HER2− (n = 15), triple negative (TN) (n = 9), and ER-HER2+ (n = 57) cancers with variable presentation (mass and non-mass enhancement) and background parenchymal enhancement (mild and marked). Expert delineated manual contours were used to assess the segmentation performance using Dice coefficient (DSC), mean surface distance (mSD), Hausdorff distance, and volume ratio (VR). GCGMM segmentations were significantly more accurate than GrowCut (GC) and fuzzy c-means clustering (FCM). GCGMM’s segmentations and the texture features computed from those segmentations were the most reproducible compared with manual delineations and other analyzed segmentation methods. Finally, random forest (RF) classifier trained with leave-one-out cross-validation using features extracted from GCGMM segmentation resulted in the best accuracy for ER-HER2+ vs. ERPR+/TN (GCGMM 0.95, expert 0.95, GC 0.90, FCM 0.92) and for ERPR + HER2− vs. TN (GCGMM 0.92, expert 0.91, GC 0.77, FCM 0.83).

DCE-MRI Pharmacokinetic-Based Phenotyping of Invasive Ductal Carcinoma: A Radiomic Study for Prediction of Histological Outcomes

Breast cancer is a disease affecting an increasing number of women worldwide. Several efforts have been made in the last years to identify imaging biomarker and to develop noninvasive diagnostic tools for breast tumor characterization and monitoring, which could help in patients' stratification, outcome prediction, and treatment personalization. In particular, radiomic approaches have paved the way to the study of the cancer imaging phenotypes. In this work, a group of 49 patients with diagnosis of invasive ductal carcinoma was studied. The purpose of this study was to select radiomic features extracted from a DCE-MRI pharmacokinetic protocol, including quantitative maps of ktrans, kep, ve, iAUC, and R1 and to construct predictive models for the discrimination of molecular receptor status (ER+/ER-, PR+/PR-, and HER2+/HER2-), triple negative (TN)/non-triple negative (NTN), ki67 levels, and tumor grade. A total of 163 features were obtained and, after feature set reduction step, followed by feature selection and prediction performance estimations, the predictive model coefficients were computed for each classification task. The AUC values obtained were 0.826 ± 0.006 for ER+/ER-, 0.875 ± 0.009 for PR+/PR-, 0.838 ± 0.006 for HER2+/HER2-, 0.876 ± 0.007 for TN/NTN, 0.811 ± 0.005 for ki67+/ki67-, and 0.895 ± 0.006 for lowGrade/highGrade. In conclusion, DCE-MRI pharmacokinetic-based phenotyping shows promising for discrimination of the histological outcomes.

MRI features predictive of negative surgical margins in patients with HER2 overexpressing breast cancer undergoing breast conservation

Here we develop a tool to predict resectability of HER2+ breast cancer at breast conservation surgery (BCS) utilizing features identified on preoperative breast MRI. We identified patients with HER2+ breast cancer who obtained pre-operative breast MRI and underwent BCS between 2002–2013. From the contoured tumor on pre-operative MRI, shape, histogram, and co-occurrence and size zone matrix texture features were extracted. In univariate analysis, Spearman’s correlation coefficient (Rs) was used to assess the correlation between each image feature and an endpoint (surgical re-excision). For multivariate modeling, we employed a support vector machine (SVM) method in a manner of leave-one-out cross-validation (LOOCV). Of 109 patients with HER2+breast cancer who underwent BCS, 39% underwent surgical re-excision. 62% had residual cancer at re-excision. In univariate analysis, solidity (Rs = −0.32, p = 0.009) and extent (Rs = −0.29, p = 0.019) were significantly associated with re-excision. Skewness in post-contrast 1, 2, and 3 (Rs = 0.25, p = 0.045; Rs = 0.30, p = 0.015; Rs = 0.28, p = 0.026) and kurtosis in post-contrast 1 (Rs = 0.26, p = 0.035) were also statistically significant. LOOCV-based SVM test achieved 74.4% specificity and 71.4% sensitivity when 21 features were used. Thus, tumor texture, histogram and morphological MRI features may assist surgical planning, encouraging wide margins or mastectomy in patients who may otherwise go on to re-excision.

MRI texture analysis in differentiating luminal A and luminal B breast cancer molecular subtypes - a feasibility study

Background

The aim of this study was to use texture analysis (TA) of breast magnetic resonance (MR) images to assist in differentiating estrogen receptor (ER) positive breast cancer molecular subtypes.

Methods

Twenty-seven patients with histopathologically proven invasive ductal breast cancer were selected in preliminary study. Tumors were classified into molecular subtypes: luminal A (ER-positive and/or progesterone receptor (PR)-positive, human epidermal growth factor receptor type 2 (HER2) -negative, proliferation marker Ki-67 < 20 and low grade (I)) and luminal B (ER-positive and/or PR-positive, HER2-positive or HER2-negative with high Ki-67 ≥ 20 and higher grade (II or III)). Co-occurrence matrix -based texture features were extracted from each tumor on T1-weighted non fat saturated pre- and postcontrast MR images using TA software MaZda. Texture parameters and tumour volumes were correlated with tumour prognostic factors.

Results

Textural differences were observed mainly in precontrast images. The two most discriminative texture parameters to differentiate luminal A and luminal B subtypes were sum entropy and sum variance (p = 0.003). The AUCs were 0.828 for sum entropy (p = 0.004), and 0.833 for sum variance (p = 0.003), and 0.878 for the model combining texture features sum entropy, sum variance (p = 0.001). In the LOOCV, the AUC for model combining features sum entropy and sum variance was 0.876. Sum entropy and sum variance showed positive correlation with higher Ki-67 index. Luminal B types were larger in volume and moderate correlation between larger tumour volume and higher Ki-67 index was also observed (r = 0.499, p = 0.008).

Conclusions

Texture features which measure randomness, heterogeneity or smoothness and homogeneity may either directly or indirectly reflect underlying growth patterns of breast tumours. TA and volumetric analysis may provide a way to evaluate the biologic aggressiveness of breast tumours and provide aid in decisions regarding therapeutic efficacy.

DCE-MRI texture analysis with tumor subregion partitioning for predicting Ki-67 status of estrogen receptor-positive breast cancers

BACKGROUND

Breast tumor heterogeneity is related to risk factors that lead to worse prognosis, yet such heterogeneity has not been well studied.

PURPOSE

To predict the Ki-67 status of estrogen receptor (ER)-positive breast cancer patients via analysis of tumor heterogeneity with subgroup identification based on patterns of dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI).

STUDY TYPE

Retrospective study.

POPULATION

Seventy-seven breast cancer patients with ER-positive breast cancer were investigated, of whom 51 had low Ki-67 expression.

FIELD STRENGTH/SEQUENCE

T₁ -weighted 3.0T DCE-MR images.

ASSESSMENT

Each tumor was partitioned into multiple subregions using three methods based on patterns of dynamic enhancement: 1) time to peak (TTP), 2) peak enhancement rate (PER), and 3) kinetic pattern clustering (KPC). In each tumor subregion, 18 texture features were computed.

STATISTICAL TESTING

Univariate and multivariate logistic regression analyses were performed using a leave-one-out-based cross-validation (LOOCV) method. The partitioning results were compared with the same feature extraction methods across the whole tumor.

RESULTS

In the univariate analysis, the best-performing feature was the texture statistic of sum variance in the tumor subregion with early TTP for differentiating between patients with high and low Ki-67 expression (area under the receiver operating characteristic curves, AUC = 0.748). Multivariate analysis showed that features from the tumor subregion associated with early TTP yielded the highest performance (AUC = 0.807) among the subregions for predicting the Ki-67 status. Among all regions, the tumor area with high PER at a precontrast MR image achieved the highest performance (AUC = 0.722), while the subregion that exhibited the highest overall enhancement rate based on KPC had an AUC of 0.731. These three models based on intratumoral texture analysis significantly (P < 0.01) outperformed the model using features from the whole tumor (AUC = 0.59).

DATA CONCLUSION

Texture analysis of intratumoral heterogeneity has the potential to serve as a valuable clinical marker to enhance the prediction of breast cancer prognosis.

LEVEL OF EVIDENCE

4 Technical Efficacy: Stage 3 J. Magn. Reson. Imaging 2017.

Effects of MRI scanner parameters on breast cancer radiomics

PURPOSE

To assess the impact of varying magnetic resonance imaging (MRI) scanner parameters on the extraction of algorithmic features in breast MRI radiomics studies.

METHODS

In this retrospective study, breast imaging data for 272 patients were analyzed with magnetic resonance (MR) images. From the MR images, we assembled and implemented 529 algorithmic features of breast tumors and fibrograndular tissue (FGT). We divided the features into 10 groups based on the type of data used for the feature extraction and the nature of the extracted information. Three scanner parameters were considered: scanner manufacturer, scanner magnetic field strength, and slice thickness. We assessed the impact of each of the scanner parameters on each of the feature by testing whether the feature values are systematically diverse for different values of these scanner parameters. A two-sample t-test has been used to establish whether the impact of a scanner parameter on values of a feature is significant and receiver operating characteristics have been used for to establish the extent of that effect.

RESULTS

On average, higher proportion (69% FGT versus 20% tumor) of FGT related features were affected by the three scanner parameters. Of all feature groups and scanner parameters, the feature group related to the variation in FGT enhancement was found to be the most sensitive to the scanner manufacturer (AUC = 0.81 ± 0.14).

CONCLUSIONS

Features involving calculations from FGT are particularly sensitive to the scanner parameters.

Diffusion-weighted MRI characteristics associated with prognostic pathological factors and recurrence risk in invasive ER+/HER2- breast cancers

BACKGROUND

Hormone receptor-positive breast cancer is the most common subtype; better tools to identify which patients in this group would derive clear benefit from chemotherapy are needed.

PURPOSE

To evaluate the prognostic potential of diffusion-weighted MRI (DWI) by investigating associations with pathologic biomarkers and a genomic assay for 10-year recurrence risk.

STUDY TYPE

Retrospective.

SUBJECTS

In all, 107 consecutive patients (from 2/2010 to 1/2013) with estrogen receptor (ER)-positive/HER2neu-negative invasive breast cancer who had the 21-gene recurrence score (RS) test (Oncotype DX, Genomic Health).

FIELD STRENGTH/SEQUENCE

Each subject underwent presurgical 3T breast MRI, which included DWI (b = 0, 800 s/mm² ).

ASSESSMENT

Apparent diffusion coefficient (ADC) and contrast-to-noise ratio (CNR) were measured for each lesion by a fifth year radiology resident. Pathological markers (Nottingham histologic grade, Ki-67, RS) were determined from pathology reports. Medical records were reviewed to assess recurrence-free survival.

STATISTICAL TESTS

RS was stratified into low (<18), moderate (18-30), and high (>30)-risk groups. Associations of DWI characteristics with pathologic biomarkers were evaluated by binary or ordinal logistic regression, as appropriate, with adjustment for multiple comparisons. Post-hoc comparisons between specific groups were also performed.

RESULTS

ADCmean (odds ratio [OR] = 0.61 per 1 standard deviation [SD] increase, adj. P = 0.044) and CNR (OR = 1.76 per 1-SD increase, adj. P = 0.026) were significantly associated with increasing tumor grade. DWI CNR was also significantly associated with a high (Ki-67 ≥14%) proliferation rate (OR = 2.55 per 1-SD increase, adj. P = 0.026). While there were no statistically significant linear associations in ADC (adj. P = 0.80-0.85) and CNR (adj. P = 0.56) across all three RS groups by ordinal logistic regression, post-hoc analyses suggested that high RS lesions exhibited lower ADCmean (P = 0.037) and ADCmax (P = 0.004) values and higher CNR (P = 0.008) compared to lesions with a low or moderate RS.

DATA CONCLUSION

DWI characteristics correlated with tumor grade, proliferation index, and RS, and may potentially help to identify those with highest recurrence risk and most potential benefit from chemotherapy.

LEVEL OF EVIDENCE

3 Technical Efficacy Stage 3 J. Magn. Reson. Imaging 2017.

Increased hippocampal fissure width is a sensitive indicator of rat hippocampal atrophy

OBJECTIVES

Volume loss within the hippocampus is known as the most replicated finding of structural brain imaging studies of neuropsychiatric diseases. Although voxel-based auto or semi-auto volumetric measurements are widely used in the determination of the human hippocampus, the detection of hippocampal atrophy in rats is still a dilemma as it relies on a relatively primitive and complex approach. In this study, we aimed to develop a convenient way to measure the atrophy of the hippocampus in rats.

METHODS

Twenty-four male Wistar rats were exposed to chronic unpredictable mild stress (CUMS) and a wheel running test (WRT) to simulate the conditions of hippocampal volume atrophy and improvement. The hippocampal volume and hippocampal fissure (HiF) width were dynamically measured using 7 T structural magnetic resonance imaging (MRI) with the grayscale method at week 0, 2, 4, and 8. The changes in the hippocampal volume and HiF width in rats were compared. In addition, hematoxylin-eosin (HE) staining of the HiF was used to verify the MRI findings.

RESULTS

The hippocampal volume and the HiF width presented opposite trends based on the MRI findings and the histology data. The atrophy of the hippocampal subfields was closely related to the corresponding increase in the HiF width.

CONCLUSION

Determination of the HiF width may serve as a sensitive and convenient indicator of rat hippocampal atrophy.

Biomarkers and Imaging of Breast Cancer

OBJECTIVE

The goals of this review are to provide background information on the definitions and applications of the general term "biomarker" and to highlight the specific roles of breast imaging biomarkers in research and clinical breast cancer care. A search was conducted of the main electronic biomedical databases (PubMed, Cochrane, Embase, MEDLINE [Ovid], Scopus, and Web of Science). The search was focused on review literature in general radiology and biomedical sciences and on reviews and primary research articles on biomarkers in breast imaging over the 15 years ending in June 2017. The keywords included "biomarker," "trial endpoints," "breast imaging," "breast cancer," "radiomics," and "precision medicine" in the titles and abstracts of the papers.

CONCLUSION

Clinical breast care and breast cancer-related research rely on imaging biomarkers for decision support. In the era of precision medicine and big data, the practice of radiology is likely to change. A closer integration of breast imaging with related biomedical fields and the creation of large integrated and shareable databases of clinical, molecular, and imaging biomarkers should allow the field to continue guiding breast cancer care and research.

Breast MRI radiomics: comparison of computer- and human-extracted imaging phenotypes

Background

In this study, we sought to investigate if computer-extracted magnetic resonance imaging (MRI) phenotypes of breast cancer could replicate human-extracted size and Breast Imaging-Reporting and Data System (BI-RADS) imaging phenotypes using MRI data from The Cancer Genome Atlas (TCGA) project of the National Cancer Institute.

Methods

Our retrospective interpretation study involved analysis of Health Insurance Portability and Accountability Act-compliant breast MRI data from The Cancer Imaging Archive, an open-source database from the TCGA project. This study was exempt from institutional review board approval at Memorial Sloan Kettering Cancer Center and the need for informed consent was waived. Ninety-one pre-operative breast MRIs with verified invasive breast cancers were analysed. Three fellowship-trained breast radiologists evaluated the index cancer in each case according to size and the BI-RADS lexicon for shape, margin, and enhancement (human-extracted image phenotypes [HEIP]). Human inter-observer agreement was analysed by the intra-class correlation coefficient (ICC) for size and Krippendorff’s α for other measurements. Quantitative MRI radiomics of computerised three-dimensional segmentations of each cancer generated computer-extracted image phenotypes (CEIP). Spearman’s rank correlation coefficients were used to compare HEIP and CEIP.

Results

Inter-observer agreement for HEIP varied, with the highest agreement seen for size (ICC 0.679) and shape (ICC 0.527). The computer-extracted maximum linear size replicated the human measurement with p < 10⁻¹². CEIP of shape, specifically sphericity and irregularity, replicated HEIP with both p values < 0.001. CEIP did not demonstrate agreement with HEIP of tumour margin or internal enhancement.

Conclusions

Quantitative radiomics of breast cancer may replicate human-extracted tumour size and BI-RADS imaging phenotypes, thus enabling precision medicine.

Background, current role, and potential applications of radiogenomics

With the genomic revolution in the early 1990s, medical research has been driven to study the basis of human disease on a genomic level and to devise precise cancer therapies tailored to the specific genetic makeup of a tumor. To match novel therapeutic concepts conceived in the era of precision medicine, diagnostic tests must be equally sufficient, multilayered, and complex to identify the relevant genetic alterations that render cancers susceptible to treatment. With significant advances in training and medical imaging techniques, image analysis and the development of high-throughput methods to extract and correlate multiple imaging parameters with genomic data, a new direction in medical research has emerged. This novel approach has been termed radiogenomics. Radiogenomics aims to correlate imaging characteristics (ie, the imaging phenotype) with gene expression patterns, gene mutations, and other genome-related characteristics and is designed to facilitate a deeper understanding of tumor biology and capture the intrinsic tumor heterogeneity. Ultimately, the goal of radiogenomics is to develop imaging biomarkers for outcome that incorporate both phenotypic and genotypic metrics. Due to the noninvasive nature of medical imaging and its ubiquitous use in clinical practice, the field of radiogenomics is rapidly evolving and initial results are encouraging. In this article, we briefly discuss the background and then summarize the current role and the potential of radiogenomics in brain, liver, prostate, gynecological, and breast tumors.

LEVEL OF EVIDENCE

5 Technical Efficacy: Stage 2 J. Magn. Reson. Imaging 2017;47:604-620.

Features from Computerized Texture Analysis of Breast Cancers at Pretreatment MR Imaging Are Associated with Response to Neoadjuvant Chemotherapy

Purpose To evaluate whether features from texture analysis of breast cancers were associated with pathologic complete response (pCR) after neoadjuvant chemotherapy and to explore the association between texture features and tumor subtypes at pretreatment magnetic resonance (MR) imaging. Materials and Methods Institutional review board approval was obtained. This retrospective study included 85 patients with 85 breast cancers who underwent breast MR imaging before neoadjuvant chemotherapy between April 10, 2008, and March 12, 2015. Two-dimensional texture analysis was performed by using software at T2-weighted MR imaging and contrast material-enhanced T1-weighted MR imaging. Quantitative parameters were compared between patients with pCR and those with non-pCR and between patients with triple-negative breast cancer and those with non-triple-negative cancer. Multiple logistic regression analysis was used to determine independent parameters. Results Eighteen tumors (22%) were triple-negative breast cancers. pCR was achieved in 30 of the 85 tumors (35%). At univariate analysis, mean pixel intensity with spatial scaling factor (SSF) of 2 and 4 on T2-weighted images and kurtosis on contrast-enhanced T1-weighted images showed a significant difference between triple-negative breast cancer and non-triple-negative breast cancer (P = .009, .003, and .001, respectively). Kurtosis (SSF, 2) on T2-weighted images showed a significant difference between pCR and non-pCR (P = .015). At multiple logistic regression, kurtosis on T2-weighted images was independently associated with pCR in non-triple-negative breast cancer (P = .033). A multivariate model incorporating T2-weighted and contrast-enhanced T1-weighted kurtosis showed good performance for the identification of triple-negative breast cancer (area under the receiver operating characteristic curve, 0.834). Conclusion At pretreatment MR imaging, kurtosis appears to be associated with pCR to neoadjuvant chemotherapy in non-triple-negative breast cancer and may be a promising biomarker for the identification of triple-negative breast cancer. ^© RSNA, 2017.

BI-RADS 3-5 microcalcifications can preoperatively predict breast cancer HER2 and Luminal a molecular subtype

Purpose

To investigate associations between breast cancer molecular subtype and the patterns of mammographically detected calcifications.

Results

Identified were 93 (19.1%) Luminal A, 242 (49.9%) Luminal B, 108 (22.2%) HER2 and 42 (8.7%) basal subtypes. In univariate analysis, the clinicopathological parameters and BI-RADS 3–5 microcalcifications, which consisted 9 selected features was significantly associated with breast cancer molecular subtype (all P < 0.05). Among subtypes, multivariate analysis showed that calcification >2 cm in range (OR: 1.878, 95% CI: 1.150 to 3.067) and calcification > 0.5 mm in diameter (OR:2.206, 95% CI: 1.235 to 3.323) was independently predictive of HER2 subtype. The model showed good discrimination for predicting HER2 subtype, with a C-index of 0.704. In addition, multivariate analysis showed that calcification morphology (amorphour or coarse heterogenous calcifications OR: 2.847, 95% CI: 1.526 to 5.312) was independently predictive of Luminal A subtype. The model showed good discrimination for predicting Luminal A subtype, with a C-index of 0.74. And we demonstrated that amorphour or coarse heterogenous calcifications were associated with a higher incidence of Luminal A subtype than pleomorphic or fine linear or branching calcifications. There was no significant difference between breast cancer subtypes (Luminal B vs. other; Basal vs. other) and the patterns of mammographically detected calcifications.

Materials and Methods

Mammographic images of 485 female patients were included. The correlation between mammographic imaging features and breast cancer subtype was analyzed using Chi-square test, univariate and binary logistic regression analysis.

Conclusions

This study shows that BI-RADS 3–5 microcalcifications can be conveniently used to facilitate the preoperative prediction of HER2 and Luminal A molecular subtype in patients with infiltrating ductal carcinoma.

An Assessment of Imaging Informatics for Precision Medicine in Cancer

Objectives: Precision medicine requires the measurement, quantification, and cataloging of medical characteristics to identify the most effective medical intervention. However, the amount of available data exceeds our current capacity to extract meaningful information. We examine the informatics needs to achieve precision medicine from the perspective of quantitative imaging and oncology. Methods: The National Cancer Institute (NCI) organized several workshops on the topic of medical imaging and precision medicine. The observations and recommendations are summarized herein. Results: Recommendations include: use of standards in data collection and clinical correlates to promote interoperability; data sharing and validation of imaging tools; clinician's feedback in all phases of research and development; use of open-source architecture to encourage reproducibility and reusability; use of challenges which simulate real-world situations to incentivize innovation; partnership with industry to facilitate commercialization; and education in academic communities regarding the challenges involved with translation of technology from the research domain to clinical utility and the benefits of doing so. Conclusions: This article provides a survey of the role and priorities for imaging informatics to help advance quantitative imaging in the era of precision medicine. While these recommendations were drawn from oncology, they are relevant and applicable to other clinical domains where imaging aids precision medicine.

Qualitative Radiogenomics: Association between Oncotype DX Test Recurrence Score and BI-RADS Mammographic and Breast MR Imaging Features

Purpose To evaluate the association between Breast Imaging Reporting and Data System (BI-RADS) mammographic and magnetic resonance (MR) imaging features and breast cancer recurrence risk in patients with estrogen receptor-positive breast cancer who underwent the Oncotype DX assay. Materials and Methods In this institutional review board-approved and HIPAA-compliant protocol, 408 patients diagnosed with invasive breast cancer between 2004 and 2013 who underwent the Oncotype DX assay were identified. Mammographic and MR imaging features were retrospectively collected according to the BI-RADS lexicon. Linear regression assessed the association between imaging features and Oncotype DX test recurrence score (ODxRS), and post hoc pairwise comparisons assessed ODxRS means by using imaging features. Results Mammographic breast density was inversely associated with ODxRS (P ≤ .05). Average ODxRS for density category A was 24.4 and that for density category D was 16.5 (P < .02). Both indistinct mass margins and fine linear branching calcifications at mammography were significantly associated with higher ODxRS (P < .01 and P < .03, respectively). Masses with indistinct margins had an average ODxRS of 31.3, which significantly differed from the ODxRS of 18.5 for all other mass margins (P < .01). The average ODxRS for fine linear branching calcifications was 29.6, whereas the ODxRS for all other suspicious calcification morphologies was 19.4 (P < .03). Average ODxRS was significantly higher for irregular mass margins at MR imaging compared with spiculated mass margins (24.0 vs 17.6; P < .02). The presence of nonmass enhancement at MR imaging was associated with lower ODxRS than was its absence (16.4 vs 19.9; P < .05). Conclusion The BI-RADS features of mammographic breast density, calcification morphology, mass margins at mammography and MR imaging, and nonmass enhancement at MR imaging have the potential to serve as imaging biomarkers of breast cancer recurrence risk. Further prospective studies involving larger patient cohorts are needed to validate these preliminary findings. ^© RSNA, 2017 Online supplemental material is available for this article.

Heterogeneous Enhancement Patterns of Tumor-adjacent Parenchyma at MR Imaging Are Associated with Dysregulated Signaling Pathways and Poor Survival in Breast Cancer

Purpose To identify the molecular basis of quantitative imaging characteristics of tumor-adjacent parenchyma at dynamic contrast material-enhanced magnetic resonance (MR) imaging and to evaluate their prognostic value in breast cancer. Materials and Methods In this institutional review board-approved, HIPAA-compliant study, 10 quantitative imaging features depicting tumor-adjacent parenchymal enhancement patterns were extracted and screened for prognostic features in a discovery cohort of 60 patients. By using data from The Cancer Genome Atlas (TCGA), a radiogenomic map for the tumor-adjacent parenchymal tissue was created and molecular pathways associated with prognostic parenchymal imaging features were identified. Furthermore, a multigene signature of the parenchymal imaging feature was built in a training cohort (n = 126), and its prognostic relevance was evaluated in two independent cohorts (n = 879 and 159). Results One image feature measuring heterogeneity (ie, information measure of correlation) was significantly associated with prognosis (false-discovery rate < 0.1), and at a cutoff of 0.57 stratified patients into two groups with different recurrence-free survival rates (log-rank P = .024). The tumor necrosis factor signaling pathway was identified as the top enriched pathway (hypergeometric P < .0001) among genes associated with the image feature. A 73-gene signature based on the tumor profiles in TCGA achieved good association with the tumor-adjacent parenchymal image feature (R² = 0.873), which stratified patients into groups regarding recurrence-free survival (log-rank P = .029) and overall survival (log-rank P = .042) in an independent TCGA cohort. The prognostic value was confirmed in another independent cohort (Gene Expression Omnibus GSE 1456), with log-rank P = .00058 for recurrence-free survival and log-rank P = .0026 for overall survival. Conclusion Heterogeneous enhancement patterns of tumor-adjacent parenchyma at MR imaging are associated with the tumor necrosis signaling pathway and poor survival in breast cancer. ^© RSNA, 2017 Online supplemental material is available for this article.

Unsupervised Clustering of Quantitative Image Phenotypes Reveals Breast Cancer Subtypes with Distinct Prognoses and Molecular Pathways

Purpose: To identify novel breast cancer subtypes by extracting quantitative imaging phenotypes of the tumor and surrounding parenchyma and to elucidate the underlying biologic underpinnings and evaluate the prognostic capacity for predicting recurrence-free survival (RFS).Experimental Design: We retrospectively analyzed dynamic contrast-enhanced MRI data of patients from a single-center discovery cohort (n = 60) and an independent multicenter validation cohort (n = 96). Quantitative image features were extracted to characterize tumor morphology, intratumor heterogeneity of contrast agent wash-in/wash-out patterns, and tumor-surrounding parenchyma enhancement. On the basis of these image features, we used unsupervised consensus clustering to identify robust imaging subtypes and evaluated their clinical and biologic relevance. We built a gene expression-based classifier of imaging subtypes and tested their prognostic significance in five additional cohorts with publically available gene expression data but without imaging data (n = 1,160).Results: Three distinct imaging subtypes, that is, homogeneous intratumoral enhancing, minimal parenchymal enhancing, and prominent parenchymal enhancing, were identified and validated. In the discovery cohort, imaging subtypes stratified patients with significantly different 5-year RFS rates of 79.6%, 65.2%, 52.5% (log-rank P = 0.025) and remained as an independent predictor after adjusting for clinicopathologic factors (HR, 2.79; P = 0.016). The prognostic value of imaging subtypes was further validated in five independent gene expression cohorts, with average 5-year RFS rates of 88.1%, 74.0%, 59.5% (log-rank P from <0.0001 to 0.008). Each imaging subtype was associated with specific dysregulated molecular pathways that can be therapeutically targeted.Conclusions: Imaging subtypes provide complimentary value to established histopathologic or molecular subtypes and may help stratify patients with breast cancer. Clin Cancer Res; 23(13); 3334-42. ©2017 AACR.

Apparent diffusion coefficient in estrogen receptor-positive and lymph node-negative invasive breast cancers at 3.0T DW-MRI: A potential predictor for an oncotype Dx test recurrence score

PURPOSE

To measure the apparent diffusion coefficient (ADC) values in estrogen receptor-positive (ER+) and axillary lymph node-negative (LN-) invasive breast cancer and investigate the correlation of ADC with Oncotype Dx test recurrence scores (ODxRS).

MATERIALS AND METHODS

This was a Health Insurance Portability and Accountability Act (HIPAA)-compliant single-site retrospective study. Patients underwent preoperative 3.0T MRI scans with additional diffusion-weighted imaging sequential scans (b = 0, 600 and b = 0, 1000 s/mm² ) from January 2011 to 2013. The study population included 31 ER+/LN- invasive breast cancers, which underwent ODxRS genomic testing. ADC₆₀₀ and ADC₁₀₀₀ parametric maps were generated, and ADC values were calculated from a user-drawn region of interest. ODxRS predicts 10-year recurrence risk in individual patients: low (RS <18), intermediate (RS: 18-30), or high (RS >30). All breast lesions, including subgroups of invasive ductal carcinoma (IDC) lesions and mass-only lesions were dichotomized by RS scores, low-risk versus intermediate/high-risk, and statistical analysis was performed using Mann-Whitney's test (statistical significance at P < 0.05) and receiver operating characteristic (ROC) curves. Multivariate analysis was also performed.

RESULTS

Invasive breast cancers, when scored as low-risk by ODxRS, had significantly higher ADC values compared with intermediate/high-risk lesions for both ADC₆₀₀ (P = 0.007) and ADC₁₀₀₀ (P = 0.008) mean values. This was true both when analyzing only mass-lesions (P = 0.03 and 0.01) or only IDCs (P = 0.001 and 0.009).

CONCLUSION

Preliminary findings suggest that lesion ADC values correlate with recurrence risk likelihood stratified using ODxRS. Hence, ADC is a potential surrogate biomarker for tumor aggressiveness.

LEVEL OF EVIDENCE

3 Technical Efficacy: Stage 5 J. Magn. Reson. Imaging 2018;47:401-409.

Role of Imaging in the Era of Precision Medicine

Precision medicine is an emerging approach for treating medical disorders, which takes into account individual variability in genetic and environmental factors. Preventive or therapeutic interventions can then be directed to those who will benefit most from targeted interventions, thereby maximizing benefits and minimizing costs and complications. Precision medicine is gaining increasing recognition by clinicians, healthcare systems, pharmaceutical companies, patients, and the government. Imaging plays a critical role in precision medicine including screening, early diagnosis, guiding treatment, evaluating response to therapy, and assessing likelihood of disease recurrence. The Association of University Radiologists Radiology Research Alliance Precision Imaging Task Force convened to explore the current and future role of imaging in the era of precision medicine and summarized its finding in this article. We review the increasingly important role of imaging in various oncological and non-oncological disorders. We also highlight the challenges for radiology in the era of precision medicine.

Radiogenomic Analysis of Oncological Data: A Technical Survey

In the last few years, biomedical research has been boosted by the technological development of analytical instrumentation generating a large volume of data. Such information has increased in complexity from basic (i.e., blood samples) to extensive sets encompassing many aspects of a subject phenotype, and now rapidly extending into genetic and, more recently, radiomic information. Radiogenomics integrates both aspects, investigating the relationship between imaging features and gene expression. From a methodological point of view, radiogenomics takes advantage of non-conventional data analysis techniques that reveal meaningful information for decision-support in cancer diagnosis and treatment. This survey is aimed to review the state-of-the-art techniques employed in radiomics and genomics with special focus on analysis methods based on molecular and multimodal probes. The impact of single and combined techniques will be discussed in light of their suitability in correlation and predictive studies of specific oncologic diseases.

Computer-aided heterogeneity analysis in breast MR imaging assessment of ductal carcinoma in situ: Correlating histologic grade and receptor status

PURPOSE

To identify breast MR imaging biomarkers to predict histologic grade and receptor status of ductal carcinoma in situ (DCIS).

MATERIALS AND METHODS

Informed consent was waived in this Health Insurance Portability and Accountability Act-compliant Institutional Review Board-approved study. Case inclusion was conducted from 7332 consecutive breast MR studies from January 1, 2009, to December 31, 2012. Excluding studies with benign diagnoses, studies without visible abnormal enhancement, and pathology containing invasive disease yielded 55 MR-imaged pathology-proven DCIS seen on 54 studies. Twenty-eight studies (52%) were performed at 1.5 Tesla (T); 26 (48%) at 3T. Regions-of-interest representing DCIS were segmented for precontrast, first and fourth postcontrast, and subtracted first and fourth postcontrast images on the open-source three-dimensional (3D) Slicer software. Fifty-seven metrics of each DCIS were obtained, including distribution statistics, shape, morphology, Renyi dimensions, geometrical measure, and texture, using the 3D Slicer HeterogeneityCAD module. Statistical correlation of heterogeneity metrics with DCIS grade and receptor status was performed using univariate Mann-Whitney test.

RESULTS

Twenty-four of the 55 DCIS (44%) were high nuclear grade (HNG); 44 (80%) were estrogen receptor (ER) positive. Human epidermal growth factor receptor-2 (HER2) was amplified in 10/55 (18%), nonamplified in 34/55 (62%), unknown/equivocal in 8/55 (15%). Surface area-to-volume ratio showed significant difference (P < 0.05) between HNG and non-HNG DCIS. No metric differentiated ER status (0.113 < p ≤ 1.000). Seventeen metrics showed significant differences between HER2-positive and HER2-negative DCIS (0.016 < P < 0.050).

CONCLUSION

Quantitative heterogeneity analysis of DCIS suggests the presence of MR imaging biomarkers in classifying DCIS grade and HER2 status. Validation with larger samples and prospective studies is needed to translate these results into clinical applications.

LEVEL OF EVIDENCE

3 Technical Efficacy: Stage 3 J. Magn. Reson. Imaging 2017;46:1748-1759.

Identifying relations between imaging phenotypes and molecular subtypes of breast cancer: Model discovery and external validation

PURPOSE

To determine whether dynamic contrast enhancement magnetic resonance imaging (DCE-MRI) characteristics of the breast tumor and background parenchyma can distinguish molecular subtypes (ie, luminal A/B or basal) of breast cancer.

MATERIALS AND METHODS

In all, 84 patients from one institution and 126 patients from The Cancer Genome Atlas (TCGA) were used for discovery and external validation, respectively. Thirty-five quantitative image features were extracted from DCE-MRI (1.5 or 3T) including morphology, texture, and volumetric features, which capture both tumor and background parenchymal enhancement (BPE) characteristics. Multiple testing was corrected using the Benjamini-Hochberg method to control the false-discovery rate (FDR). Sparse logistic regression models were built using the discovery cohort to distinguish each of the three studied molecular subtypes versus the rest, and the models were evaluated in the validation cohort.

RESULTS

On univariate analysis in discovery and validation cohorts, two features characterizing tumor and two characterizing BPE were statistically significant in separating luminal A versus nonluminal A cancers; two features characterizing tumor were statistically significant for separating luminal B; one feature characterizing tumor and one characterizing BPE reached statistical significance for distinguishing basal (Wilcoxon P < 0.05, FDR < 0.25). In discovery and validation cohorts, multivariate logistic regression models achieved an area under the receiver operator characteristic curve (AUC) of 0.71 and 0.73 for luminal A cancer, 0.67 and 0.69 for luminal B cancer, and 0.66 and 0.79 for basal cancer, respectively.

CONCLUSION

DCE-MRI characteristics of breast cancer and BPE may potentially be used to distinguish among molecular subtypes of breast cancer.

LEVEL OF EVIDENCE

3 Technical Efficacy: Stage 3 J. Magn. Reson. Imaging 2017;46:1017-1027.

Radiomic analysis reveals DCE-MRI features for prediction of molecular subtypes of breast cancer

The purpose of this study was to investigate the role of features derived from breast dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) and to incorporated clinical information to predict the molecular subtypes of breast cancer. In particular, 60 breast cancers with the following four molecular subtypes were analyzed: luminal A, luminal B, human epidermal growth factor receptor-2 (HER2)-over-expressing and basal-like. The breast region was segmented and the suspicious tumor was depicted on sequentially scanned MR images from each case. In total, 90 features were obtained, including 88 imaging features related to morphology and texture as well as dynamic features from tumor and background parenchymal enhancement (BPE) and 2 clinical information-based parameters, namely, age and menopausal status. An evolutionary algorithm was used to select an optimal subset of features for classification. Using these features, we trained a multi-class logistic regression classifier that calculated the area under the receiver operating characteristic curve (AUC). The results of a prediction model using 24 selected features showed high overall classification performance, with an AUC value of 0.869. The predictive model discriminated among the luminal A, luminal B, HER2 and basal-like subtypes, with AUC values of 0.867, 0.786, 0.888 and 0.923, respectively. An additional independent dataset with 36 patients was utilized to validate the results. A similar classification analysis of the validation dataset showed an AUC of 0.872 using 15 image features, 10 of which were identical to those from the first cohort. We identified clinical information and 3D imaging features from DCE-MRI as candidate biomarkers for discriminating among four molecular subtypes of breast cancer.

Exploring the complementarity of THz pulse imaging and DCE-MRIs: Toward a unified multi-channel classification and a deep learning framework

We provide a comprehensive account of recent advances in biomedical image analysis and classification from two complementary imaging modalities: terahertz (THz) pulse imaging and dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI). The work aims to highlight underlining commonalities in both data structures so that a common multi-channel data fusion framework can be developed. Signal pre-processing in both datasets is discussed briefly taking into consideration advances in multi-resolution analysis and model based fractional order calculus system identification. Developments in statistical signal processing using principal component and independent component analysis are also considered. These algorithms have been developed independently by the THz-pulse imaging and DCE-MRI communities, and there is scope to place them in a common multi-channel framework to provide better software standardization at the pre-processing de-noising stage. A comprehensive discussion of feature selection strategies is also provided and the importance of preserving textural information is highlighted. Feature extraction and classification methods taking into consideration recent advances in support vector machine (SVM) and extreme learning machine (ELM) classifiers and their complex extensions are presented. An outlook on Clifford algebra classifiers and deep learning techniques suitable to both types of datasets is also provided. The work points toward the direction of developing a new unified multi-channel signal processing framework for biomedical image analysis that will explore synergies from both sensing modalities for inferring disease proliferation.

Progress in the clinical detection of heterogeneity in breast cancer

Breast cancer is currently the most common form of cancer and the second‐leading cause of death from cancer in women. Though considerable progress has been made in the treatment of breast cancer, the heterogeneity of tumors (both inter‐ and intratumor) remains a considerable diagnostic and prognostic challenge. From clinical observation to genetic mutations, the history of understanding the heterogeneity of breast cancer is lengthy and detailed. Effectively detecting heterogeneity in breast cancer is important during treatment. Various methods of depicting this heterogeneity are now available and include genetic, pathologic, and imaging analysis. These methods allow characterization of the heterogeneity of breast cancer on a genetic level, providing greater insight during the process of establishing an effective therapeutic plan. This study reviews how the understanding of tumor heterogeneity in breast cancer evolved, and further summarizes recent advances in the detection and monitoring of this heterogeneity in patients with breast cancer.