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Lee HJ, Lee JH, Lee JE, Na YM, Park MH, Lee JS, Lim HS. Prediction of early clinical response to neoadjuvant chemotherapy in Triple-negative breast cancer: Incorporating Radiomics through breast MRI. Sci Rep 2024; 14:21691. [PMID: 39289507 PMCID: PMC11408492 DOI: 10.1038/s41598-024-72581-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Accepted: 09/09/2024] [Indexed: 09/19/2024] Open
Abstract
This study assessed pretreatment breast MRI coupled with machine learning for predicting early clinical responses to neoadjuvant chemotherapy (NAC) in triple-negative breast cancer (TNBC), focusing on identifying non-responders. A retrospective analysis of 135 TNBC patients (107 responders, 28 non-responders) treated with NAC from January 2015 to October 2022 was conducted. Non-responders were defined according to RECIST guidelines. Data included clinicopathologic factors and clinical MRI findings, with radiomics features from contrast-enhanced T1-weighted images, to train a stacking ensemble of 13 machine learning models. For subgroup analysis, propensity score matching was conducted to adjust for clinical disparities in NAC response. The efficacy of the models was evaluated using the area under the receiver-operating-characteristic curve (AUROC) before and after matching. The model combining clinicopathologic factors and clinical MRI findings achieved an AUROC of 0.752 (95% CI 0.644-0.860) for predicting non-responders, while radiomics-based models showed 0.749 (95% CI 0.614-0.884). An integrated model of radiomics, clinicopathologic factors, and clinical MRI findings reached an AUROC of 0.802 (95% CI 0.699-0.905). After propensity score matching, the hierarchical order of key radiomics features remained consistent. Our study demonstrated the potential of using machine learning models based on pretreatment MRI to non-invasively predict TNBC non-responders to NAC.
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Affiliation(s)
- Hyo-Jae Lee
- Department of Radiology, Chonnam National University Hospital, Gwangju, Republic of Korea
| | - Jeong Hoon Lee
- Department of Radiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Jong Eun Lee
- Department of Radiology and the Research Institute of Radiology, Asan Medical Center, Seoul, Republic of Korea
| | - Yong Min Na
- Department of Surgery, Chonnam National University Hwasun Hospital, Hwasun, Republic of Korea
| | - Min Ho Park
- Department of Surgery, Chonnam National University Hwasun Hospital, Hwasun, Republic of Korea
- Chonnam National University Medical School, Gwangju, Republic of Korea
| | - Ji Shin Lee
- Department of Pathology, Chonnam National University Hwasun Hospital, Hwasun, Republic of Korea
- Chonnam National University Medical School, Gwangju, Republic of Korea
| | - Hyo Soon Lim
- Department of Radiology, Chonnam National University Hwasun Hospital, Hwasun, Republic of Korea.
- Chonnam National University Medical School, Gwangju, Republic of Korea.
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Lyu S, Zhang M, Yu J, Zhu J, Zhang B, Gao L, Jin D, Chen Q. Application of radiomics model based on ultrasound image features in the prediction of carpal tunnel syndrome severity. Skeletal Radiol 2024; 53:1389-1397. [PMID: 38289532 DOI: 10.1007/s00256-024-04594-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Revised: 01/12/2024] [Accepted: 01/14/2024] [Indexed: 05/15/2024]
Abstract
OBJECTIVE The aim of our study is to develop and validate a radiomics model based on ultrasound image features for predicting carpal tunnel syndrome (CTS) severity. METHODS This retrospective study included 237 CTS hands (106 for mild symptom, 68 for moderate symptom and 63 for severe symptom). There were no statistically significant differences among the three groups in terms of age, gender, race, etc. The data set was randomly divided into a training set and a test set in a ratio of 7:3. Firstly, a senior musculoskeletal ultrasound expert measures the cross-sectional area of median nerve (MN) at the scaphoid-pisiform level. Subsequently, a recursive feature elimination (RFE) method was used to identify the most discriminative radiomic features of each MN at the entrance of the carpal tunnel. Eventually, a random forest model was employed to classify the selected features for prediction. To evaluate the performance of the model, the confusion matrix, receiver operating characteristic (ROC) curves, and F1 values were calculated and plotted correspondingly. RESULTS The prediction capability of the radiomics model was significantly better than that of ultrasound measurements when 10 robust features were selected. The training set performed perfect classification with 100% accuracy for all participants, while the testing set performed accurate classification of severity for 76.39% of participants with F1 values of 80.00, 63.40, and 84.80 for predicting mild, moderate, and severe CTS, respectively. Comparably, the F1 values for mild, moderate, and severe CTS predicted based on the MN cross-sectional area were 76.46, 57.78, and 64.00, respectively.. CONCLUSION This radiomics model based on ultrasound images has certain value in distinguishing the severity of CTS, and was slightly superior to using only MN cross-sectional area for judgment. Although its diagnostic efficacy was still inferior to that of neuroelectrophysiology. However, this method was non-invasive and did not require additional costs, and could provide additional information for clinical physicians to develop diagnosis and treatment plans.
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Affiliation(s)
- Shuyi Lyu
- Department of Ultrasound, Haishu District, Ningbo NO.2 Hospital, No. 41, Northwest Street, Ningbo, Zhejiang, 315010, People's Republic of China
- Department of Ultrasound, Zhenhai Hospital of Traditional Chinese Medicine, No.51, Huancheng W Rd, Zhenhai District, Ningbo, 315200, Zhejiang, People's Republic of China
| | - Meiwu Zhang
- Department of Ultrasound, Haishu District, Ningbo NO.2 Hospital, No. 41, Northwest Street, Ningbo, Zhejiang, 315010, People's Republic of China
| | - Jianjun Yu
- Department of Neuroelectrophysiology, Haishu District, Ningbo NO.2 Hospital, No. 41, Northwest Street, Ningbo, Zhejiang, 315010, People's Republic of China
| | - Jiazhen Zhu
- Department of Radiology, Haishu District, Ningbo NO.2 Hospital, No. 41, Northwest Street, Ningbo, Zhejiang, 315010, People's Republic of China
| | - Baisong Zhang
- Department of Ultrasound, Haishu District, Ningbo NO.2 Hospital, No. 41, Northwest Street, Ningbo, Zhejiang, 315010, People's Republic of China
| | - Libo Gao
- Department of Ultrasound, Haishu District, Ningbo NO.2 Hospital, No. 41, Northwest Street, Ningbo, Zhejiang, 315010, People's Republic of China
| | - Dingkelei Jin
- Department of Ultrasound, Haishu District, Ningbo NO.2 Hospital, No. 41, Northwest Street, Ningbo, Zhejiang, 315010, People's Republic of China
- Hangzhou Medical College, Binjiang District, Hangzhou, 310051, People's Republic of China
| | - Qiaojie Chen
- Department of Orthopaedics, Haishu District, Ningbo NO.2 Hospital, No. 41, Northwest Street, Ningbo, Zhejiang, 315010, People's Republic of China.
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Liu Z, Mu C, Zhu W. Metagenomics-based inference of microbial metabolism towards neuroactive amino acids and the response to antibiotics in piglet colon. Amino Acids 2023; 55:1333-1347. [PMID: 37581868 DOI: 10.1007/s00726-023-03311-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 07/30/2023] [Indexed: 08/16/2023]
Abstract
Gut-derived neuroactive metabolites from amino acids perform a broad range of physiological roles in the body. However, the interaction between microbiota and epithelium in the metabolism of amino acids with neuroactive properties remains unclear in the colon of piglets. To investigate the microbial and epithelial metabolism, metagenomics and mucosal metabolomics were performed using colonic samples from 12 ileum-canulated piglets subjected to a 25-day infusion with saline or antibiotics. We categorized 23 metabolites derived from the metabolism of tryptophan, glutamate, and tyrosine, known as precursors of neuroactive metabolites. Microbial enzymes involved in the kynurenine synthesis via arylformamidase, 4-aminobutyric acid (GABA) synthesis via putrescine aminotransferase, and tyramine synthesis via tyrosine decarboxylase were identified in Clostridiales bacterium, uncultured Blautia sp., and Methanobrevibacter wolinii, respectively. Antibiotics significantly affected the microbiota involved in tryptophan-kynurenine and glutamate-GABA metabolism. An increase in the relative abundance of putrescine aminotransferase and Blautia sp. correlated positively with an increase in luminal GABA concentration. Overall, our findings provide new insights into the microbial ability to metabolize key amino acids that are precursors of neuroactive metabolites.
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Affiliation(s)
- Ziyu Liu
- Laboratory of Gastrointestinal Microbiology, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- National Center for International Research on Animal Gut Nutrition, National Experimental Teaching Demonstration Center of Animal Science, Nanjing Agricultural University, Nanjing, China
| | - Chunlong Mu
- Laboratory of Gastrointestinal Microbiology, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China.
- National Center for International Research on Animal Gut Nutrition, National Experimental Teaching Demonstration Center of Animal Science, Nanjing Agricultural University, Nanjing, China.
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Canada.
| | - Weiyun Zhu
- Laboratory of Gastrointestinal Microbiology, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- National Center for International Research on Animal Gut Nutrition, National Experimental Teaching Demonstration Center of Animal Science, Nanjing Agricultural University, Nanjing, China
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Sung P, Lee JY, Cheun JH, Choi IS, Park JH, Park JH, Kim BH, Oh S, Chu AJ, Hwang KT. Prognostic Implication of Focal Breast Edema on Preoperative Breast Magnetic Resonance Imaging in Breast Cancer Patients. J Breast Cancer 2023; 26:479-491. [PMID: 37704381 PMCID: PMC10625867 DOI: 10.4048/jbc.2023.26.e35] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 07/17/2023] [Accepted: 07/29/2023] [Indexed: 09/15/2023] Open
Abstract
PURPOSE In this study, we investigated the prognostic implications of focal breast edema on preoperative breast magnetic resonance imaging (MRI) in patients with breast cancer. METHODS Data of 899 patients with breast cancer at a single institution were retrospectively analyzed. The patients were divided into an edema-positive group (EPG) and an edema-negative group (ENG) based on the presence of peritumoral, prepectoral, or subcutaneous edema. Two radiologists evaluated the presence or absence of focal edema and its subtypes on preoperative breast MRI. Clinicopathologic characteristics and survival outcomes were compared between the two groups and among the three subtypes using Pearson's χ² test, Kaplan-Meier estimator, and Cox proportional hazards model. RESULTS There were 399 (44.4%) and 500 (55.6%) patients in the EPG and ENG, respectively. The EPG showed significantly higher rates of axillary lymph node metastasis (55.6% vs. 19.2%, p < 0.001) and lymphovascular invasion (LVI) (57.9% vs. 12.6%, p < 0.001) than the ENG. Patients in the EPG showed significantly worse overall survival (OS) rate (log-rank p < 0.001; hazard ratio [HR], 4.83; 95% confidence interval [CI], 2.56-9.11) and recurrence-free survival rate (log-rank p < 0.001; HR, 3.00; 95% CI, 1.94-4.63) than those in the ENG. After adjusting for other variables, focal breast edema remained a significant factor affecting the OS rate, regardless of the edema type. Specifically, the presence of subcutaneous edema emerged as the strongest predictor for OS with the highest HR (p < 0.001; HR, 9.10; 95% CI, 3.05-27.15). CONCLUSION Focal breast edema on preoperative breast MRI implies a higher possibility of LVI and axillary lymph node metastasis, which can lead to a poor prognosis. A detailed description of focal breast edema, especially subcutaneous edema, on preoperative breast MRI may provide prognostic predictions. More intensive surveillance is required for patients with breast cancer and focal preoperative breast edema.
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Affiliation(s)
- Pamela Sung
- Department of Radiology, Seoul Metropolitan Government-Seoul National University Boramae Medical Center, Seoul, Korea
| | - Jong Yoon Lee
- Department of Radiology, Seoul Metropolitan Government-Seoul National University Boramae Medical Center, Seoul, Korea
| | - Jong-Ho Cheun
- Department of Surgery, Seoul Metropolitan Government-Seoul National University Boramae Medical Center, Seoul, Korea
| | - In Sil Choi
- Department of Internal Medicine, Seoul Metropolitan Government-Seoul National University Boramae Medical Center, Seoul, Korea
| | - Jin Hyun Park
- Department of Internal Medicine, Seoul Metropolitan Government-Seoul National University Boramae Medical Center, Seoul, Korea
| | - Jeong Hwan Park
- Department of Pathology, Seoul Metropolitan Government-Seoul National University Boramae Medical Center, Seoul, Korea
| | - Byoung Hyuck Kim
- Department of Radiation Oncology, Seoul Metropolitan Government-Seoul National University Boramae Medical Center, Seoul, Korea
| | - Sohee Oh
- Medical Research Collaborating Center, Seoul Metropolitan Government-Seoul National University Boramae Medical Center, Seoul, Korea
| | - A Jung Chu
- Department of Radiology, Seoul Metropolitan Government-Seoul National University Boramae Medical Center, Seoul, Korea.
| | - Ki-Tae Hwang
- Department of Surgery, Seoul Metropolitan Government-Seoul National University Boramae Medical Center, Seoul, Korea
- Department of Surgery, Seoul National University College of Medicine, Seoul, Korea.
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Furtney I, Bradley R, Kabuka MR. Patient Graph Deep Learning to Predict Breast Cancer Molecular Subtype. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2023; 20:3117-3127. [PMID: 37379184 PMCID: PMC10623656 DOI: 10.1109/tcbb.2023.3290394] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/30/2023]
Abstract
Breast cancer is a heterogeneous disease consisting of a diverse set of genomic mutations and clinical characteristics. The molecular subtypes of breast cancer are closely tied to prognosis and therapeutic treatment options. We investigate using deep graph learning on a collection of patient factors from multiple diagnostic disciplines to better represent breast cancer patient information and predict molecular subtype. Our method models breast cancer patient data into a multi-relational directed graph with extracted feature embeddings to directly represent patient information and diagnostic test results. We develop a radiographic image feature extraction pipeline to produce vector representation of breast cancer tumors in DCE-MRI and an autoencoder-based genomic variant embedding method to map variant assay results to a low-dimensional latent space. We leverage related-domain transfer learning to train and evaluate a Relational Graph Convolutional Network to predict the probabilities of molecular subtypes for individual breast cancer patient graphs. Our work found that utilizing information from multiple multimodal diagnostic disciplines improved the model's prediction results and produced more distinct learned feature representations for breast cancer patients. This research demonstrates the capabilities of graph neural networks and deep learning feature representation to perform multimodal data fusion and representation in the breast cancer domain.
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Yue WY, Zhang HT, Gao S, Li G, Sun ZY, Tang Z, Cai JM, Tian N, Zhou J, Dong JH, Liu Y, Bai X, Sheng FG. Predicting Breast Cancer Subtypes Using Magnetic Resonance Imaging Based Radiomics With Automatic Segmentation. J Comput Assist Tomogr 2023; 47:729-737. [PMID: 37707402 PMCID: PMC10510832 DOI: 10.1097/rct.0000000000001474] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 02/02/2023] [Indexed: 05/21/2023]
Abstract
OBJECTIVE The aim of the study is to demonstrate whether radiomics based on an automatic segmentation method is feasible for predicting molecular subtypes. METHODS This retrospective study included 516 patients with confirmed breast cancer. An automatic segmentation-3-dimensional UNet-based Convolutional Neural Networks, trained on our in-house data set-was applied to segment the regions of interest. A set of 1316 radiomics features per region of interest was extracted. Eighteen cross-combination radiomics methods-with 6 feature selection methods and 3 classifiers-were used for model selection. Model classification performance was assessed using the area under the receiver operating characteristic curve (AUC), accuracy, sensitivity, and specificity. RESULTS The average dice similarity coefficient value of the automatic segmentation was 0.89. The radiomics models were predictive of 4 molecular subtypes with the best average: AUC = 0.8623, accuracy = 0.6596, sensitivity = 0.6383, and specificity = 0.8775. For luminal versus nonluminal subtypes, AUC = 0.8788 (95% confidence interval [CI], 0.8505-0.9071), accuracy = 0.7756, sensitivity = 0.7973, and specificity = 0.7466. For human epidermal growth factor receptor 2 (HER2)-enriched versus non-HER2-enriched subtypes, AUC = 0.8676 (95% CI, 0.8370-0.8982), accuracy = 0.7737, sensitivity = 0.8859, and specificity = 0.7283. For triple-negative breast cancer versus non-triple-negative breast cancer subtypes, AUC = 0.9335 (95% CI, 0.9027-0.9643), accuracy = 0.9110, sensitivity = 0.4444, and specificity = 0.9865. CONCLUSIONS Radiomics based on automatic segmentation of magnetic resonance imaging can predict breast cancer of 4 molecular subtypes noninvasively and is potentially applicable in large samples.
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Affiliation(s)
- Wen-Yi Yue
- From the Fifth Medical Center of Chinese PLA General Hospital
- Chinese PLA General Medical School
| | - Hong-Tao Zhang
- From the Fifth Medical Center of Chinese PLA General Hospital
| | - Shen Gao
- From the Fifth Medical Center of Chinese PLA General Hospital
| | - Guang Li
- Keya Medical Technology Co, Ltd, Beijing, China
| | - Ze-Yu Sun
- Keya Medical Technology Co, Ltd, Beijing, China
| | - Zhe Tang
- Keya Medical Technology Co, Ltd, Beijing, China
| | - Jian-Ming Cai
- From the Fifth Medical Center of Chinese PLA General Hospital
| | - Ning Tian
- From the Fifth Medical Center of Chinese PLA General Hospital
| | - Juan Zhou
- From the Fifth Medical Center of Chinese PLA General Hospital
| | - Jing-Hui Dong
- From the Fifth Medical Center of Chinese PLA General Hospital
| | - Yuan Liu
- From the Fifth Medical Center of Chinese PLA General Hospital
| | - Xu Bai
- From the Fifth Medical Center of Chinese PLA General Hospital
| | - Fu-Geng Sheng
- From the Fifth Medical Center of Chinese PLA General Hospital
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Chiacchiaretta P, Mastrodicasa D, Chiarelli AM, Luberti R, Croce P, Sguera M, Torrione C, Marinelli C, Marchetti C, Domenico A, Cocco G, Di Credico A, Russo A, D’Eramo C, Corvino A, Colasurdo M, Sensi SL, Muzi M, Caulo M, Delli Pizzi A. MRI-Based Radiomics Approach Predicts Tumor Recurrence in ER + /HER2 - Early Breast Cancer Patients. J Digit Imaging 2023; 36:1071-1080. [PMID: 36698037 PMCID: PMC10287859 DOI: 10.1007/s10278-023-00781-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 01/11/2023] [Accepted: 01/13/2023] [Indexed: 01/26/2023] Open
Abstract
Oncotype Dx Recurrence Score (RS) has been validated in patients with ER + /HER2 - invasive breast carcinoma to estimate patient risk of recurrence and guide the use of adjuvant chemotherapy. We investigated the role of MRI-based radiomics features extracted from the tumor and the peritumoral tissues to predict the risk of tumor recurrence. A total of 62 patients with biopsy-proved ER + /HER2 - breast cancer who underwent pre-treatment MRI and Oncotype Dx were included. An RS > 25 was considered discriminant between low-intermediate and high risk of tumor recurrence. Two readers segmented each tumor. Radiomics features were extracted from the tumor and the peritumoral tissues. Partial least square (PLS) regression was used as the multivariate machine learning algorithm. PLS β-weights of radiomics features included the 5% features with the largest β-weights in magnitude (top 5%). Leave-one-out nested cross-validation (nCV) was used to achieve hyperparameter optimization and evaluate the generalizable performance of the procedure. The diagnostic performance of the radiomics model was assessed through receiver operating characteristic (ROC) analysis. A null hypothesis probability threshold of 5% was chosen (p < 0.05). The exploratory analysis for the complete dataset revealed an average absolute correlation among features of 0.51. The nCV framework delivered an AUC of 0.76 (p = 1.1∙10-3). When combining "early" and "peak" DCE images of only T or TST, a tendency toward statistical significance was obtained for TST with an AUC of 0.61 (p = 0.05). The 47 features included in the top 5% were balanced between T and TST (23 and 24, respectively). Moreover, 33/47 (70%) were texture-related, and 25/47 (53%) were derived from high-resolution images (1 mm). A radiomics-based machine learning approach shows the potential to accurately predict the recurrence risk in early ER + /HER2 - breast cancer patients.
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Affiliation(s)
- Piero Chiacchiaretta
- Advanced Computing Core, Center of Advanced Studies and Technology (CAST), “G. d’Annunzio” University of Chieti-Pescara, Chieti, Italy
- Department of Innovative Technologies in Medicine and Odonoiatry, “G. d’Annunzio” University, Chieti, Italy
| | | | - Antonio Maria Chiarelli
- Department of Neuroscience, Imaging and Clinical Sciences, “G. d’Annunzio” University, Chieti, Italy
| | - Riccardo Luberti
- Unit of Radiology, “Santissima Annunziata” Hospital, Chieti, Italy
| | - Pierpaolo Croce
- Department of Neuroscience, Imaging and Clinical Sciences, “G. d’Annunzio” University, Chieti, Italy
| | - Mario Sguera
- Unit of Radiology, “Santissima Annunziata” Hospital, Chieti, Italy
| | | | | | - Chiara Marchetti
- Unit of Radiology, “Santissima Annunziata” Hospital, Chieti, Italy
| | | | - Giulio Cocco
- Unit of Ultrasound in Internal Medicine, Department of Medicine and Science of Aging, “G. D’Annunzio” University, Chieti, Italy
| | | | | | | | - Antonio Corvino
- Motor Science and Wellness Department, University of Naples “Parthenope”, 80133 Naples, Italy
| | - Marco Colasurdo
- Department of Neuroscience, Imaging and Clinical Sciences, “G. d’Annunzio” University, Chieti, Italy
| | - Stefano L. Sensi
- Advanced Computing Core, Center of Advanced Studies and Technology (CAST), “G. d’Annunzio” University of Chieti-Pescara, Chieti, Italy
- Department of Neuroscience, Imaging and Clinical Sciences, “G. d’Annunzio” University, Chieti, Italy
| | - Marzia Muzi
- Breast Unit, “Gaetano Bernabeo” Hospital, Ortona, Italy
| | - Massimo Caulo
- Department of Neuroscience, Imaging and Clinical Sciences, “G. d’Annunzio” University, Chieti, Italy
| | - Andrea Delli Pizzi
- Department of Innovative Technologies in Medicine and Odonoiatry, “G. d’Annunzio” University, Chieti, Italy
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Uysal E, Topaloğlu ÖF, Arı A, Özer H, Koplay M. Can magnetic resonance imaging texture analysis change the breast imaging reporting and data system category of breast lesions? Clin Imaging 2023; 97:44-49. [PMID: 36889114 DOI: 10.1016/j.clinimag.2023.02.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 02/19/2023] [Accepted: 02/28/2023] [Indexed: 03/07/2023]
Abstract
PURPOSE This study aimed to reveal magnetic resonance imaging (MRI) texture analysis (TA)'s contribution to categorizing breast lesions according to the Breast Imaging-Reporting and Data System (BI-RADS) lexicon. METHOD Two hundred and seventeen women with BI-RADS category 3, 4, and 5 lesions on breast MRI were included in the study. For TA, the region of interest was drawn manually to encompass the entire lesion on the fat-suppressed T2W and the first post-contrast T1W images. To identify the independent predictors of breast cancer, multivariate logistic regression analyses were performed using texture parameters. Estimated benign and malignant groups were formed according to the TA regression model. RESULTS Texture parameters extracted from T2WI, including median, gray-level co-occurrence matrix (GLCM) contrast, GLCM correlation, GLCM joint entropy, GLCM sum entropy, and GLCM sum of squares, and parameters extracted from T1WI, including maximum, GLCM contrast, GLCM joint entropy, GLCM sum entropy, were independent predictors of breast cancer. In the estimated new groups according to the TA regression model, 19 (91%) of the benign 4a lesions were downgraded to BI-RADS category 3. CONCLUSIONS The addition of quantitative parameters obtained by MRI TA to BI-RADS criteria significantly increased the accuracy rate in differentiating benign and malignant breast lesions. When categorizing BI-RADS 4a lesions, the use of MRI TA in addition to conventional imaging findings may reduce unnecessary biopsy rates.
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Affiliation(s)
- Emine Uysal
- Department of Radiology, Faculty of Medicine, Selçuk University, Selçuklu, Konya, Turkey.
| | - Ömer Faruk Topaloğlu
- Department of Radiology, Faculty of Medicine, Selçuk University, Selçuklu, Konya, Turkey
| | - Ayşe Arı
- Department of Radiology, Faculty of Medicine, Selçuk University, Selçuklu, Konya, Turkey
| | - Halil Özer
- Department of Radiology, Faculty of Medicine, Selçuk University, Selçuklu, Konya, Turkey
| | - Mustafa Koplay
- Department of Radiology, Faculty of Medicine, Selçuk University, Selçuklu, Konya, Turkey
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Ji Y, Whitney HM, Li H, Liu P, Giger ML, Zhang X. Differences in Molecular Subtype Reference Standards Impact AI-based Breast Cancer Classification with Dynamic Contrast-enhanced MRI. Radiology 2023; 307:e220984. [PMID: 36594836 PMCID: PMC10068887 DOI: 10.1148/radiol.220984] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 10/20/2022] [Accepted: 11/01/2022] [Indexed: 01/04/2023]
Abstract
Background Breast cancer tumors can be identified as different luminal molecular subtypes depending on either immunohistochemical (IHC) staining or St Gallen criteria that includes Ki-67. Purpose To characterize molecular subtypes and understand the impact of disagreement among IHC and St Gallen molecular subtype reference standards on artificial intelligence classification of luminal A and luminal B tumors with use of radiomic features extracted from dynamic contrast-enhanced (DCE) MRI scans. Materials and Methods In this retrospective study, 28 radiomic features previously extracted from DCE-MRI scans of breast tumors imaged between February 2015 and October 2017 were examined in the following groups: (a) tumors classified as luminal A by both reference standards ("agreement"), (b) tumors classified as luminal A by IHC and luminal B by St Gallen ("disagreement"), and (c) tumors classified as luminal B by both ("agreement"). Luminal A or luminal B tumor classification with use of radiomic features was conducted with use of three sets: (a) IHC molecular subtyping, (b) St Gallen molecular subtyping, and (c) agreement tumors. The Kruskal-Wallis test was followed by the Mann-Whitney U test to determine pair-wise differences of radiomic features among agreement and disagreement tumors. Fivefold cross-validation with use of stepwise feature selection and linear discriminant analysis classified tumors in each set, with performance measured with use of area under the receiver operating characteristic curve (AUC). Results A total of 877 breast cancer tumors from 872 women (mean age, 48 years [range, 19-75 years]) were analyzed. Six features (sphericity, irregularity, surface area to volume ratio, variance of radial gradient histogram, sum average, volume of most enhancing voxels) were different (P ≤ .001) among agreement and disagreement tumors. AUC (median, 0.74 [95% CI: 0.68, 0.80]) was higher than when using tumors subtyped by either reference standard (IHC, 0.66 [0.60, 0.71], P = .003; St Gallen, 0.62 [0.58, 0.67], P = .001). Conclusion Differences in reference standards can hinder artificial intelligence classification performance of luminal molecular subtypes with dynamic contrast-enhanced MRI. © RSNA, 2023 Supplemental material is available for this article. See also the editorial by Bae in this issue.
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Affiliation(s)
- Yu Ji
- From the Department of Radiology, The Second Hospital of Tianjin
Medical University, No. 23 Pingjiang Rd, Hexi District, Tianjin, China 300211
(Y.J., X.Z.); National Clinical Research Center for Cancer, Tianjin Medical
University Cancer Institute and Hospital, Tianjin, China (Y.J., P.L.);
Department of Radiology, The University of Chicago, Chicago, Ill (H.M.W., H.L.,
M.L.G.); and Department of Physics, Wheaton College, Wheaton, Ill
(H.M.W.)
| | - Heather M. Whitney
- From the Department of Radiology, The Second Hospital of Tianjin
Medical University, No. 23 Pingjiang Rd, Hexi District, Tianjin, China 300211
(Y.J., X.Z.); National Clinical Research Center for Cancer, Tianjin Medical
University Cancer Institute and Hospital, Tianjin, China (Y.J., P.L.);
Department of Radiology, The University of Chicago, Chicago, Ill (H.M.W., H.L.,
M.L.G.); and Department of Physics, Wheaton College, Wheaton, Ill
(H.M.W.)
| | - Hui Li
- From the Department of Radiology, The Second Hospital of Tianjin
Medical University, No. 23 Pingjiang Rd, Hexi District, Tianjin, China 300211
(Y.J., X.Z.); National Clinical Research Center for Cancer, Tianjin Medical
University Cancer Institute and Hospital, Tianjin, China (Y.J., P.L.);
Department of Radiology, The University of Chicago, Chicago, Ill (H.M.W., H.L.,
M.L.G.); and Department of Physics, Wheaton College, Wheaton, Ill
(H.M.W.)
| | - Peifang Liu
- From the Department of Radiology, The Second Hospital of Tianjin
Medical University, No. 23 Pingjiang Rd, Hexi District, Tianjin, China 300211
(Y.J., X.Z.); National Clinical Research Center for Cancer, Tianjin Medical
University Cancer Institute and Hospital, Tianjin, China (Y.J., P.L.);
Department of Radiology, The University of Chicago, Chicago, Ill (H.M.W., H.L.,
M.L.G.); and Department of Physics, Wheaton College, Wheaton, Ill
(H.M.W.)
| | - Maryellen L. Giger
- From the Department of Radiology, The Second Hospital of Tianjin
Medical University, No. 23 Pingjiang Rd, Hexi District, Tianjin, China 300211
(Y.J., X.Z.); National Clinical Research Center for Cancer, Tianjin Medical
University Cancer Institute and Hospital, Tianjin, China (Y.J., P.L.);
Department of Radiology, The University of Chicago, Chicago, Ill (H.M.W., H.L.,
M.L.G.); and Department of Physics, Wheaton College, Wheaton, Ill
(H.M.W.)
| | - Xuening Zhang
- From the Department of Radiology, The Second Hospital of Tianjin
Medical University, No. 23 Pingjiang Rd, Hexi District, Tianjin, China 300211
(Y.J., X.Z.); National Clinical Research Center for Cancer, Tianjin Medical
University Cancer Institute and Hospital, Tianjin, China (Y.J., P.L.);
Department of Radiology, The University of Chicago, Chicago, Ill (H.M.W., H.L.,
M.L.G.); and Department of Physics, Wheaton College, Wheaton, Ill
(H.M.W.)
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Lyu S, Zhang Y, Zhang M, Jiang M, Yu J, Zhu J, Zhang B. Ultrasound-based radiomics in the diagnosis of carpal tunnel syndrome: The influence of regions of interest delineation method on mode. JOURNAL OF CLINICAL ULTRASOUND : JCU 2023; 51:498-506. [PMID: 36341718 DOI: 10.1002/jcu.23387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 10/05/2022] [Accepted: 10/07/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND In the recent years, artificial intelligence (AI) algorithms have been used to accurately diagnose musculoskeletal diseases. However, it is not known whether the particular regions of interest (ROI) delineation method would affect the performance of the AI algorithm. PURPOSE The purpose of this study was to investigate the influence of ROI delineation methods on model performance and observer consistency. METHODS In this retrospective analysis, ultrasound (US) measures of median nerves affected with carpal tunnel syndrome (CTS) were compared to median nerves in a control group without CTS. Two methods were used for delineation of the ROI: (1) the ROI along the hyperechoic medial edge of the median nerve but not including the epineurium (MN) (ROI1); and (2) the ROI including the hyperechoic epineurium (ROI2), respectively. The intra group correlation coefficient (ICC) was used to compare the observer consistency of ROI features (i.e. the corresponding radiomics parameters). Parameters α1 and α2 were obtained based on the ICC of ROI1 features and ROI2 features. The ROC analysis was used to determine the area under the curve (AUC) and evaluate the performance of the radiologists and network. In addition, four indices, namely sensitivity, specificity, positive prediction and negative prediction were analyzed too. RESULTS A total of 136 wrists of 77 CTS group and 136 wrists of 74 control group were included in the study. Control group was matched to CTS group according to the age and sex. The observer consistency of ROI features delineated by the two schemes was different, and the consistency of ROI1 features was higher (α1 ˃ α2). The intra-observer consistency was higher than the inter-observer consistency regardless of the scheme, and the intra-observer consistency was higher when chose scheme one. The performances of models based on the two ROI features were different, although the AUC of each model was greater than 0.8.The model performed better when the MN epineurium was included in the ROI. Among five artificial intelligence algorithms, the Forest models (model1 achieved an AUC of 0.921 in training datasets and 0.830 in testing datasets; model2 achieved an AUC of 0.967 in training datasets and 0.872 in testing datasets.) obtained the highest performance, followed by the support vector machine (SVM) models and the Logistic models. The performances of the models were significantly better than the inexperienced radiologist (Dr. B. Z. achieved an AUC of 0.702). CONCLUSION Different ROI delineation methods may affect the performance of the model and the consistency of observers. Model performance was better when the ROI contained the MN epineurium, and observer consistency was higher when the ROI was delineated along the hyperechoic medial border of the MN.
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Affiliation(s)
- Shuyi Lyu
- Department of Interventional Therapy, Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, People's Republic of China
- Ningbo Clinical Research Center for Medical Imaging, Ningbo, China
- Provinicial and Municipal Co-construction Key Discipline for Medical Imaging, Ningbo, China
| | - Yan Zhang
- Department of Interventional Therapy, Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, People's Republic of China
- Ningbo Clinical Research Center for Medical Imaging, Ningbo, China
- Provinicial and Municipal Co-construction Key Discipline for Medical Imaging, Ningbo, China
| | - Meiwu Zhang
- Department of Interventional Therapy, Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, People's Republic of China
- Ningbo Clinical Research Center for Medical Imaging, Ningbo, China
- Provinicial and Municipal Co-construction Key Discipline for Medical Imaging, Ningbo, China
| | - Maoqing Jiang
- Ningbo Clinical Research Center for Medical Imaging, Ningbo, China
- Provinicial and Municipal Co-construction Key Discipline for Medical Imaging, Ningbo, China
- Department of PET-CT and Nuclear Medicine, Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, People's Republic of China
| | - Jianjun Yu
- Department of Neuroelectrophysiology, Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, People's Republic of China
| | - Jiazhen Zhu
- Ningbo Clinical Research Center for Medical Imaging, Ningbo, China
- Provinicial and Municipal Co-construction Key Discipline for Medical Imaging, Ningbo, China
- Multi-disciplinary diagnosis and treatment department, Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, People's Republic of China
| | - Baisong Zhang
- Department of Interventional Therapy, Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, People's Republic of China
- Ningbo Clinical Research Center for Medical Imaging, Ningbo, China
- Provinicial and Municipal Co-construction Key Discipline for Medical Imaging, Ningbo, China
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11
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Lafcı O, Celepli P, Seher Öztekin P, Koşar PN. DCE-MRI Radiomics Analysis in Differentiating Luminal A and Luminal B Breast Cancer Molecular Subtypes. Acad Radiol 2023; 30:22-29. [PMID: 35595629 DOI: 10.1016/j.acra.2022.04.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 03/30/2022] [Accepted: 04/06/2022] [Indexed: 12/26/2022]
Abstract
RATIONALE AND OBJECTIVES The aim of the present study was to investigate the association between Luminal A and Luminal B molecular subtypes and radiomic features of dynamic contrast‑enhanced magnetic resonance imaging in patients with invasive breast cancer. MATERIALS AND METHODS Seventy-three patients with histopathologically proven invasive ductal cancer (IDC) were selected. Tumors were classified into molecular subtypes: Luminal A (estrogen receptor (ER)-positive and/or progesterone receptor (PR)-positive, human epidermal growth factor receptor type 2 (HER2) -negative, proliferation marker Ki-67<20) and Luminal B (ER-positive and/or PR-positive, HER2-positive or HER2-negative with high Ki-67 ≥20). A total of 81 tumoral lesions were evaluated on T1-weighted fat-suppressed sagittal post-contrast late-phase MRI images after the required "pre-process" steps and 3D segmentations were made. Forty-three radiomic features including: 1 conventional, 4 shape, 6 histogram, 7 Grey-Level Co-occurrence Matrix (GLCM), 11 Grey-Level Run-Length Matrix (GLRLM), 3 Neighborhood Grey-Level Difference Matrix (NGLDM), 11 Grey-Level Zone-Length Matrix (GLZLM) were extracted by using the software LIFEX. RESULTS A statistically significant difference was found in radiomic features including; a) Histogram: "skewness", b) Shape: "volume-ml, volume-voxel," c) GLCM: "entropy.log10, entropy.log2, energy", d) GLRLM: "GLNU, RLNU, HGRE," e) NGLDM: "busyness," f) GLZLM: "GLNU, HGZE, ZLNU, SZE" between two different molecular subtypes. The model combining Shape-volume (ml) and GLZLM-HGZE yielded 0.746 area under the curve (AUC), 0.744 sensitivity, 0.643 specificity and 0.694 accuracy. CONCLUSION Radiomic properties that may distinguish Luminal A and Luminal B molecular subtypes of IDC were identified. The radiomic features were thought to reflect the intratumoral heterogeneity in molecular subtypes. This study demonstrated that the characterization of Luminal A and Luminal B tumors could be made non-invasively by radiomics analysis.
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Affiliation(s)
- Oğuz Lafcı
- Department of Radiology, Ankara Training and Research Hospital, University of Health Sciences, Hacettepe Mh. Ulucanlar Cd. No:89 Altındağ, Ankara, Turkey.
| | - Pınar Celepli
- Department of Pathology, Ankara Training and Research Hospital, University of Health Sciences, Ankara, Turkey
| | - Pelin Seher Öztekin
- Department of Radiology, Ankara Training and Research Hospital, University of Health Sciences, Hacettepe Mh. Ulucanlar Cd. No:89 Altındağ, Ankara, Turkey
| | - Pınar Nercis Koşar
- Department of Radiology, Ankara Training and Research Hospital, University of Health Sciences, Hacettepe Mh. Ulucanlar Cd. No:89 Altındağ, Ankara, Turkey
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12
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Zhang Y, Li G, Bian W, Bai Y, He S, Liu Y, Liu H, Liu J. Value of genomics- and radiomics-based machine learning models in the identification of breast cancer molecular subtypes: a systematic review and meta-analysis. ANNALS OF TRANSLATIONAL MEDICINE 2022; 10:1394. [PMID: 36660694 PMCID: PMC9843333 DOI: 10.21037/atm-22-5986] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 12/20/2022] [Indexed: 01/01/2023]
Abstract
Background In the era of precision therapy, early classification of breast cancer (BRCA) molecular subtypes has clinical significance for disease management and prognosis. We explored the accuracy of machine learning (ML) models for early classification of BRCA molecular subtypes through a systematic review of the literature currently available. Methods We retrieved relevant studies published in PubMed, EMBASE, Cochrane, and Web of Science until 15 April 2022. A prediction model risk of bias assessment tool (PROBAST) was applied for the assessment of risk of bias of a genomics-based ML model, and the Radiomics Quality Score (RQS) was simultaneously used to evaluate the quality of this radiomics-based ML model. A random effects model was adopted to analyze the predictive accuracy of genomics-based ML and radiomics-based ML for Luminal A, Luminal B, Basal-like or triple-negative breast cancer (TNBC), and human epidermal growth factor receptor 2 (HER2). The PROSPERO of our study was prospectively registered (CRD42022333611). Results Of the 38 studies were selected for analysis, 14 ML models were based on gene-transcriptomic, with only 4 external validations; and 43 ML models were based on radiomics, with only 14 external validations. Meta-analysis results showed that c-statistic values of the ML based on radiomics for the identification of BRCA molecular subtypes Luminal A, Luminal B, Basal-like or TNBC, and HER2 were 0.76 [95% confidence interval (CI): 0.60-0.96], 0.78 (95% CI: 0.69-0.87), 0.89 (95% CI: 0.83-0.91), and 0.83 (95% CI: 0.81-0.86), respectively. The c-statistic values of ML based on the gene-transcriptomic analysis cohort for the identification of the previously described BRCA molecular subtypes were 0.96 (95% CI: 0.93-0.99), 0.96 (95% CI: 0.93-0.99), 0.98 (95% CI: 0.95-1.00), and 0.97 (95% CI: 0.96-0.98) respectively. Additionally, the sensitivity of the ML model based on radiomics for each molecular subtype ranged from 0.79 to 0.85, while the sensitivity of the ML model based on gene-transcriptomic was between 0.92 and 0.99. Conclusions Both radiomics and gene transcriptomics produced ideal effects on BRCA molecular subtype prediction. Compared with radiomics, gene transcriptomics yielded better prediction results, but radiomics was simpler and more convenient from a clinical point of view.
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Affiliation(s)
- Yiwen Zhang
- College of Chinese Medicine, Changchun University of Chinese Medicine, Changchun, China
| | - Guofeng Li
- Department of Traditional Chinese Medicine Surgery, Affiliated Hospital of Changchun University of Traditional Chinese Medicine, Changchun, China
| | - Wenqing Bian
- Intensive Care Unit, Zibo Maternal and Child Health Hospital, Zibo, China
| | - Yuzhuo Bai
- Department of Traditional Chinese Medicine Surgery, Affiliated Hospital of Changchun University of Traditional Chinese Medicine, Changchun, China
| | - Shuangyan He
- College of Chinese Medicine, Changchun University of Chinese Medicine, Changchun, China
| | - Yulian Liu
- Department of Colorectal & Anal Surgery, General Surgery Center, First Hospital of Jilin University, Changchun, China
| | - Huan Liu
- College of Chinese Medicine, Changchun University of Chinese Medicine, Changchun, China
| | - Jiaqi Liu
- Department of Breast Thyroid Surgery, Zibo Central Hospital, Zibo, China
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13
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Cellina M, Cè M, Khenkina N, Sinichich P, Cervelli M, Poggi V, Boemi S, Ierardi AM, Carrafiello G. Artificial Intellgence in the Era of Precision Oncological Imaging. Technol Cancer Res Treat 2022; 21:15330338221141793. [PMID: 36426565 PMCID: PMC9703524 DOI: 10.1177/15330338221141793] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Rapid-paced development and adaptability of artificial intelligence algorithms have secured their almost ubiquitous presence in the field of oncological imaging. Artificial intelligence models have been created for a variety of tasks, including risk stratification, automated detection, and segmentation of lesions, characterization, grading and staging, prediction of prognosis, and treatment response. Soon, artificial intelligence could become an essential part of every step of oncological workup and patient management. Integration of neural networks and deep learning into radiological artificial intelligence algorithms allow for extrapolating imaging features otherwise inaccessible to human operators and pave the way to truly personalized management of oncological patients.Although a significant proportion of currently available artificial intelligence solutions belong to basic and translational cancer imaging research, their progressive transfer to clinical routine is imminent, contributing to the development of a personalized approach in oncology. We thereby review the main applications of artificial intelligence in oncological imaging, describe the example of their successful integration into research and clinical practice, and highlight the challenges and future perspectives that will shape the field of oncological radiology.
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Affiliation(s)
- Michaela Cellina
- Radiology Department, Fatebenefratelli Hospital, Milano, Italy,Michaela Cellina, MD, Radiology Department, Fatebenefratelli Hospital, ASST Fatebenefratelli Sacco, Milano, Piazza Principessa Clotilde 3, 20121, Milano, Italy.
| | - Maurizio Cè
- Postgraduate School in Radiodiagnostics, Università degli Studi di Milano, Milan, Italy
| | - Natallia Khenkina
- Postgraduate School in Radiodiagnostics, Università degli Studi di Milano, Milan, Italy
| | - Polina Sinichich
- Postgraduate School in Radiodiagnostics, Università degli Studi di Milano, Milan, Italy
| | - Marco Cervelli
- Postgraduate School in Radiodiagnostics, Università degli Studi di Milano, Milan, Italy
| | - Vittoria Poggi
- Postgraduate School in Radiodiagnostics, Università degli Studi di Milano, Milan, Italy
| | - Sara Boemi
- Postgraduate School in Radiodiagnostics, Università degli Studi di Milano, Milan, Italy
| | | | - Gianpaolo Carrafiello
- Postgraduate School in Radiodiagnostics, Università degli Studi di Milano, Milan, Italy,Radiology Department, Fondazione IRCCS Cà Granda, Milan, Italy
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Wu J, Mayer AT, Li R. Integrated imaging and molecular analysis to decipher tumor microenvironment in the era of immunotherapy. Semin Cancer Biol 2022; 84:310-328. [PMID: 33290844 PMCID: PMC8319834 DOI: 10.1016/j.semcancer.2020.12.005] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 11/29/2020] [Accepted: 12/02/2020] [Indexed: 02/07/2023]
Abstract
Radiological imaging is an integral component of cancer care, including diagnosis, staging, and treatment response monitoring. It contains rich information about tumor phenotypes that are governed not only by cancer cellintrinsic biological processes but also by the tumor microenvironment, such as the composition and function of tumor-infiltrating immune cells. By analyzing the radiological scans using a quantitative radiomics approach, robust relations between specific imaging and molecular phenotypes can be established. Indeed, a number of studies have demonstrated the feasibility of radiogenomics for predicting intrinsic molecular subtypes and gene expression signatures in breast cancer based on MRI. In parallel, promising results have been shown for inferring the amount of tumor-infiltrating lymphocytes, a key factor for the efficacy of cancer immunotherapy, from standard-of-care radiological images. Compared with the biopsy-based approach, radiogenomics offers a unique avenue to profile the molecular makeup of the tumor and immune microenvironment as well as its evolution in a noninvasive and holistic manner through longitudinal imaging scans. Here, we provide a systematic review of the state of the art radiogenomics studies in the era of immunotherapy and discuss emerging paradigms and opportunities in AI and deep learning approaches. These technical advances are expected to transform the radiogenomics field, leading to the discovery of reliable imaging biomarkers. This will pave the way for their clinical translation to guide precision cancer therapy.
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Affiliation(s)
- Jia Wu
- Department of Imaging Physics, MD Anderson Cancer Center, Texas, 77030, USA; Department of Thoracic/Head & Neck Medical Oncology, MD Anderson Cancer Center, Texas, 77030, USA.
| | - Aaron T Mayer
- Department of Bioengineering, Stanford University, Stanford, California, 94305, USA; Department of Radiology, Stanford University, Stanford, California, 94305, USA; Molecular Imaging Program at Stanford, Stanford University, Stanford, California, 94305, USA; BioX Program at Stanford, Stanford University, Stanford, California, 94305, USA
| | - Ruijiang Li
- Department of Radiation Oncology, Stanford University, Stanford, California, 94305, USA
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15
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Jones MA, Islam W, Faiz R, Chen X, Zheng B. Applying artificial intelligence technology to assist with breast cancer diagnosis and prognosis prediction. Front Oncol 2022; 12:980793. [PMID: 36119479 PMCID: PMC9471147 DOI: 10.3389/fonc.2022.980793] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 08/04/2022] [Indexed: 12/27/2022] Open
Abstract
Breast cancer remains the most diagnosed cancer in women. Advances in medical imaging modalities and technologies have greatly aided in the early detection of breast cancer and the decline of patient mortality rates. However, reading and interpreting breast images remains difficult due to the high heterogeneity of breast tumors and fibro-glandular tissue, which results in lower cancer detection sensitivity and specificity and large inter-reader variability. In order to help overcome these clinical challenges, researchers have made great efforts to develop computer-aided detection and/or diagnosis (CAD) schemes of breast images to provide radiologists with decision-making support tools. Recent rapid advances in high throughput data analysis methods and artificial intelligence (AI) technologies, particularly radiomics and deep learning techniques, have led to an exponential increase in the development of new AI-based models of breast images that cover a broad range of application topics. In this review paper, we focus on reviewing recent advances in better understanding the association between radiomics features and tumor microenvironment and the progress in developing new AI-based quantitative image feature analysis models in three realms of breast cancer: predicting breast cancer risk, the likelihood of tumor malignancy, and tumor response to treatment. The outlook and three major challenges of applying new AI-based models of breast images to clinical practice are also discussed. Through this review we conclude that although developing new AI-based models of breast images has achieved significant progress and promising results, several obstacles to applying these new AI-based models to clinical practice remain. Therefore, more research effort is needed in future studies.
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Affiliation(s)
- Meredith A. Jones
- School of Biomedical Engineering, University of Oklahoma, Norman, OK, United States
| | - Warid Islam
- School of Electrical and Computer Engineering, University of Oklahoma, Norman, OK, United States
| | - Rozwat Faiz
- School of Electrical and Computer Engineering, University of Oklahoma, Norman, OK, United States
| | - Xuxin Chen
- School of Electrical and Computer Engineering, University of Oklahoma, Norman, OK, United States
| | - Bin Zheng
- School of Electrical and Computer Engineering, University of Oklahoma, Norman, OK, United States
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16
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Ming W, Zhu Y, Bai Y, Gu W, Li F, Hu Z, Xia T, Dai Z, Yu X, Li H, Gu Y, Yuan S, Zhang R, Li H, Zhu W, Ding J, Sun X, Liu Y, Liu H, Liu X. Radiogenomics analysis reveals the associations of dynamic contrast-enhanced–MRI features with gene expression characteristics, PAM50 subtypes, and prognosis of breast cancer. Front Oncol 2022; 12:943326. [PMID: 35965527 PMCID: PMC9366134 DOI: 10.3389/fonc.2022.943326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 06/29/2022] [Indexed: 11/17/2022] Open
Abstract
Background To investigate reliable associations between dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) features and gene expression characteristics in breast cancer (BC) and to develop and validate classifiers for predicting PAM50 subtypes and prognosis from DCE-MRI non-invasively. Methods Two radiogenomics cohorts with paired DCE-MRI and RNA-sequencing (RNA-seq) data were collected from local and public databases and divided into discovery (n = 174) and validation cohorts (n = 72). Six external datasets (n = 1,443) were used for prognostic validation. Spatial–temporal features of DCE-MRI were extracted, normalized properly, and associated with gene expression to identify the imaging features that can indicate subtypes and prognosis. Results Expression of genes including RBP4, MYBL2, and LINC00993 correlated significantly with DCE-MRI features (q-value < 0.05). Importantly, genes in the cell cycle pathway exhibited a significant association with imaging features (p-value < 0.001). With eight imaging-associated genes (CHEK1, TTK, CDC45, BUB1B, PLK1, E2F1, CDC20, and CDC25A), we developed a radiogenomics prognostic signature that can distinguish BC outcomes in multiple datasets well. High expression of the signature indicated a poor prognosis (p-values < 0.01). Based on DCE-MRI features, we established classifiers to predict BC clinical receptors, PAM50 subtypes, and prognostic gene sets. The imaging-based machine learning classifiers performed well in the independent dataset (areas under the receiver operating characteristic curve (AUCs) of 0.8361, 0.809, 0.7742, and 0.7277 for estrogen receptor (ER), human epidermal growth factor receptor 2 (HER2)-enriched, basal-like, and obtained radiogenomics signature). Furthermore, we developed a prognostic model directly using DCE-MRI features (p-value < 0.0001). Conclusions Our results identified the DCE-MRI features that are robust and associated with the gene expression in BC and displayed the possibility of using the features to predict clinical receptors and PAM50 subtypes and to indicate BC prognosis.
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Affiliation(s)
- Wenlong Ming
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Yanhui Zhu
- Department of Breast Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yunfei Bai
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Wanjun Gu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
- Collaborative Innovation Center of Jiangsu Province of Cancer Prevention and Treatment of Chinese Medicine, School of Artificial Intelligence and Information Technology, Nanjing University of Chinese Medicine, Nanjing, China
| | - Fuyu Li
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Zixi Hu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Tiansong Xia
- Department of Breast Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Zuolei Dai
- Department of Information, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Xiafei Yu
- Department of Breast Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Huamei Li
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Yu Gu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Shaoxun Yuan
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Rongxin Zhang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Haitao Li
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Wenyong Zhu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Jianing Ding
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Xiao Sun
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Yun Liu
- Department of Information, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- *Correspondence: Yun Liu, ; Hongde Liu, ; Xiaoan Liu,
| | - Hongde Liu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
- *Correspondence: Yun Liu, ; Hongde Liu, ; Xiaoan Liu,
| | - Xiaoan Liu
- Department of Breast Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- *Correspondence: Yun Liu, ; Hongde Liu, ; Xiaoan Liu,
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Role of Artificial Intelligence in Radiogenomics for Cancers in the Era of Precision Medicine. Cancers (Basel) 2022; 14:cancers14122860. [PMID: 35740526 PMCID: PMC9220825 DOI: 10.3390/cancers14122860] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 06/03/2022] [Accepted: 06/07/2022] [Indexed: 12/12/2022] Open
Abstract
Simple Summary Recently, radiogenomics has played a significant role and offered a new understanding of cancer’s biology and behavior in response to standard therapy. It also provides a more precise prognosis, investigation, and analysis of the patient’s cancer. Over the years, Artificial Intelligence (AI) has provided a significant strength in radiogenomics. In this paper, we offer computational and oncological prospects of the role of AI in radiogenomics, as well as its offers, achievements, opportunities, and limitations in the current clinical practices. Abstract Radiogenomics, a combination of “Radiomics” and “Genomics,” using Artificial Intelligence (AI) has recently emerged as the state-of-the-art science in precision medicine, especially in oncology care. Radiogenomics syndicates large-scale quantifiable data extracted from radiological medical images enveloped with personalized genomic phenotypes. It fabricates a prediction model through various AI methods to stratify the risk of patients, monitor therapeutic approaches, and assess clinical outcomes. It has recently shown tremendous achievements in prognosis, treatment planning, survival prediction, heterogeneity analysis, reoccurrence, and progression-free survival for human cancer study. Although AI has shown immense performance in oncology care in various clinical aspects, it has several challenges and limitations. The proposed review provides an overview of radiogenomics with the viewpoints on the role of AI in terms of its promises for computational as well as oncological aspects and offers achievements and opportunities in the era of precision medicine. The review also presents various recommendations to diminish these obstacles.
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Xu A, Chu X, Zhang S, Zheng J, Shi D, Lv S, Li F, Weng X. Prediction Breast Molecular Typing of Invasive Ductal Carcinoma Based on Dynamic Contrast Enhancement Magnetic Resonance Imaging Radiomics Characteristics: A Feasibility Study. Front Oncol 2022; 12:799232. [PMID: 35664741 PMCID: PMC9160981 DOI: 10.3389/fonc.2022.799232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 04/14/2022] [Indexed: 11/13/2022] Open
Abstract
Objective To investigate the feasibility of radiomics in predicting molecular subtype of breast invasive ductal carcinoma (IDC) based on dynamic contrast enhancement magnetic resonance imaging (DCE-MRI). Methods A total of 303 cases with pathologically confirmed IDC from January 2018 to March 2021 were enrolled in this study, including 223 cases from Fudan University Shanghai Cancer Center (training/test set) and 80 cases from Shaoxing Central Hospital (validation set). All the cases were classified as HR+/Luminal, HER2-enriched, and TNBC according to immunohistochemistry. DCE-MRI original images were treated by semi-automated segmentation to initially extract original and wavelet-transformed radiomic features. The extended logistic regression with least absolute shrinkage and selection operator (LASSO) penalty was applied to identify the optimal radiomic features, which were then used to establish predictive models combined with significant clinical risk factors. Receiver operating characteristic curve (ROC), calibration curve, and decision curve analysis were adopted to evaluate the effectiveness and clinical benefit of the models established. Results Of the 223 cases from Fudan University Shanghai Cancer Center, HR+/Luminal cancers were diagnosed in 116 cases (52.02%), HER2-enriched in 71 cases (31.84%), and TNBC in 36 cases (16.14%). Based on the training set, 788 radiomic features were extracted in total and 8 optimal features were further identified, including 2 first-order features, 1 gray-level run length matrix (GLRLM), 4 gray-level co-occurrence matrices (GLCM), and 1 3D shape feature. Three multi-class classification models were constructed by extended logistic regression: clinical model (age, menopause, tumor location, Ki-67, histological grade, and lymph node metastasis), radiomic model, and combined model. The macro-average areas under the ROC curve (macro-AUC) for the three models were 0.71, 0.81, and 0.84 in the training set, 0.73, 0.81, and 0.84 in the test set, and 0.76, 0.82, and 0.83 in the validation set, respectively. Conclusion The DCE-MRI-based radiomic features are significant biomarkers for distinguishing molecular subtypes of breast cancer noninvasively. Notably, the classification performance could be improved with the fusion analysis of multi-modal features.
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Affiliation(s)
- Aqiao Xu
- Department of Radiology, The Central Hospital Affiliated to Shaoxing University (Shaoxing Central Hospital), Shaoxing, China
| | - Xiufeng Chu
- Department of Surgical, The Central Hospital Affiliated to Shaoxing University (Shaoxing Central Hospital), Shaoxing, China
| | - Shengjian Zhang
- Department of Radiology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Jing Zheng
- Department of Radiology, The Central Hospital Affiliated to Shaoxing University (Shaoxing Central Hospital), Shaoxing, China
| | - Dabao Shi
- Department of Radiology, The Central Hospital Affiliated to Shaoxing University (Shaoxing Central Hospital), Shaoxing, China
| | - Shasha Lv
- Department of Radiology, The Central Hospital Affiliated to Shaoxing University (Shaoxing Central Hospital), Shaoxing, China
| | - Feng Li
- Department of Research Collaboration, Research & Development Center (R&D), Beijing Deepwise & League of Doctor of Philosophy (PHD) Technology Co., Ltd, Beijing, China
| | - Xiaobo Weng
- Department of Radiology, The Central Hospital Affiliated to Shaoxing University (Shaoxing Central Hospital), Shaoxing, China
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Sha Y, Chen J. MRI-based radiomics for the diagnosis of triple-negative breast cancer: a meta-analysis. Clin Radiol 2022; 77:655-663. [DOI: 10.1016/j.crad.2022.04.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 04/21/2022] [Indexed: 11/03/2022]
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20
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Radiogenomics: A Valuable Tool for the Clinical Assessment and Research of Ovarian Cancer. J Comput Assist Tomogr 2022; 46:371-378. [DOI: 10.1097/rct.0000000000001279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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21
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Liu D, Zhang W, Hu F, Yu P, Zhang X, Yin H, Yang L, Fang X, Song B, Wu B, Hu J, Huang Z. A Bounding Box-Based Radiomics Model for Detecting Occult Peritoneal Metastasis in Advanced Gastric Cancer: A Multicenter Study. Front Oncol 2021; 11:777760. [PMID: 34926287 PMCID: PMC8678129 DOI: 10.3389/fonc.2021.777760] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 11/09/2021] [Indexed: 02/05/2023] Open
Abstract
Purpose To develop a bounding box (BBOX)-based radiomics model for the preoperative diagnosis of occult peritoneal metastasis (OPM) in advanced gastric cancer (AGC) patients. Materials and Methods 599 AGC patients from 3 centers were retrospectively enrolled and were divided into training, validation, and testing cohorts. The minimum circumscribed rectangle of the ROIs for the largest tumor area (R_BBOX), the nonoverlapping area between the tumor and R_BBOX (peritumoral area; PERI) and the smallest rectangle that could completely contain the tumor determined by a radiologist (M_BBOX) were used as inputs to extract radiomic features. Multivariate logistic regression was used to construct a radiomics model to estimate the preoperative probability of OPM in AGC patients. Results The M_BBOX model was not significantly different from R_BBOX in the validation cohort [AUC: M_BBOX model 0.871 (95% CI, 0.814–0.940) vs. R_BBOX model 0.873 (95% CI, 0.820–0.940); p = 0.937]. M_BBOX was selected as the final radiomics model because of its extremely low annotation cost and superior OPM discrimination performance (sensitivity of 85.7% and specificity of 82.8%) over the clinical model, and this radiomics model showed comparable diagnostic efficacy in the testing cohort. Conclusions The BBOX-based radiomics could serve as a simpler reliable and powerful tool for the preoperative diagnosis of OPM in AGC patients. And M_BBOX-based radiomics is simpler and less time consuming.
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Affiliation(s)
- Dan Liu
- Department of Radiology, West China Hospital, Sichuan University, Chengdu, China
| | - Weihan Zhang
- Department of Gastrointestinal Surgery and Laboratory of Gastric Cancer, Collaborative Innovation Center for Biotherapy, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Fubi Hu
- Department of Radiology, First Affiliated Hospital of Chengdu Medical College, Chengdu, China
| | - Pengxin Yu
- Institute of Advanced Research, Infervision, Beijing, China
| | - Xiao Zhang
- Department of Radiology, People's Hospital of Leshan, Leshan, China
| | - Hongkun Yin
- Institute of Advanced Research, Infervision, Beijing, China
| | - Lanqing Yang
- Department of Radiology, West China Hospital, Sichuan University, Chengdu, China
| | - Xin Fang
- Department of Radiology, West China Hospital, Sichuan University, Chengdu, China
| | - Bin Song
- Department of Radiology, West China Hospital, Sichuan University, Chengdu, China
| | - Bing Wu
- Department of Radiology, West China Hospital, Sichuan University, Chengdu, China
| | - Jiankun Hu
- Department of Gastrointestinal Surgery and Laboratory of Gastric Cancer, Collaborative Innovation Center for Biotherapy, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Zixing Huang
- Department of Radiology, West China Hospital, Sichuan University, Chengdu, China
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22
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Frankhouser DE, Dietze E, Mahabal A, Seewaldt VL. Vascularity and Dynamic Contrast-Enhanced Breast Magnetic Resonance Imaging. FRONTIERS IN RADIOLOGY 2021; 1:735567. [PMID: 37492179 PMCID: PMC10364989 DOI: 10.3389/fradi.2021.735567] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Accepted: 11/11/2021] [Indexed: 07/27/2023]
Abstract
Angiogenesis is a key step in the initiation and progression of an invasive breast cancer. High microvessel density by morphological characterization predicts metastasis and poor survival in women with invasive breast cancers. However, morphologic characterization is subject to variability and only can evaluate a limited portion of an invasive breast cancer. Consequently, breast Magnetic Resonance Imaging (MRI) is currently being evaluated to assess vascularity. Recently, through the new field of radiomics, dynamic contrast enhanced (DCE)-MRI is being used to evaluate vascular density, vascular morphology, and detection of aggressive breast cancer biology. While DCE-MRI is a highly sensitive tool, there are specific features that limit computational evaluation of blood vessels. These include (1) DCE-MRI evaluates gadolinium contrast and does not directly evaluate biology, (2) the resolution of DCE-MRI is insufficient for imaging small blood vessels, and (3) DCE-MRI images are very difficult to co-register. Here we review computational approaches for detection and analysis of blood vessels in DCE-MRI images and present some of the strategies we have developed for co-registry of DCE-MRI images and early detection of vascularization.
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Affiliation(s)
- David E. Frankhouser
- Department of Population Sciences, City of Hope National Medical Center, Duarte, CA, United States
| | - Eric Dietze
- Department of Population Sciences, City of Hope National Medical Center, Duarte, CA, United States
| | - Ashish Mahabal
- Department of Astronomy, Division of Physics, Mathematics, and Astronomy, California Institute of Technology (Caltech), Pasadena, CA, United States
| | - Victoria L. Seewaldt
- Department of Population Sciences, City of Hope National Medical Center, Duarte, CA, United States
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Segovia-Mendoza M, García-Quiroz J, Díaz L, García-Becerra R. Combinations of Calcitriol with Anticancer Treatments for Breast Cancer: An Update. Int J Mol Sci 2021; 22:12741. [PMID: 34884550 PMCID: PMC8657847 DOI: 10.3390/ijms222312741] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 11/16/2021] [Accepted: 11/19/2021] [Indexed: 12/12/2022] Open
Abstract
Preclinical, clinical, and epidemiological studies indicate that vitamin D3 (VD) deficiency is a risk factor for the development of breast cancer. Underlying mechanisms include the ability of calcitriol to induce cell differentiation, inhibit oncogenes expression, and modify different signaling pathways involved in the control of cell proliferation. In addition, calcitriol combined with different kinds of antineoplastic drugs has been demonstrated to enhance their beneficial effects in an additive or synergistic fashion. However, a recognized adjuvant regimen based on calcitriol for treating patients with breast cancer has not yet been fully established. Accordingly, in the present work, we review and discuss the preclinical and clinical studies about the combination of calcitriol with different oncological drugs, aiming to emphasize its main therapeutic benefits and opportunities for the treatment of this pathology.
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Affiliation(s)
- Mariana Segovia-Mendoza
- Departamento de Farmacología, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico;
| | - Janice García-Quiroz
- Departamento de Biología de la Reproducción Dr. Carlos Gual Castro, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Vasco de Quiroga No. 15, Belisario Domínguez Sección XVI, Tlalpan, Ciudad de México 14080, Mexico;
| | - Lorenza Díaz
- Departamento de Biología de la Reproducción Dr. Carlos Gual Castro, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Vasco de Quiroga No. 15, Belisario Domínguez Sección XVI, Tlalpan, Ciudad de México 14080, Mexico;
| | - Rocío García-Becerra
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
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Yang X, Liu M, Ren Y, Chen H, Yu P, Wang S, Zhang R, Dai H, Wang C. Using contrast-enhanced CT and non-contrast-enhanced CT to predict EGFR mutation status in NSCLC patients-a radiomics nomogram analysis. Eur Radiol 2021; 32:2693-2703. [PMID: 34807270 PMCID: PMC8921110 DOI: 10.1007/s00330-021-08366-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 09/08/2021] [Accepted: 09/28/2021] [Indexed: 12/22/2022]
Abstract
Objectives To develop and validate a general radiomics nomogram capable of identifying EGFR mutation status in non-small cell lung cancer (NSCLC) patients, regardless of patient with either contrast-enhanced CT (CE-CT) or non-contrast-enhanced CT (NE-CT). Methods A total of 412 NSCLC patients were retrospectively enrolled in this study. Patients’ radiomics features not significantly different between NE-CT and CE-CT were defined as general features, and were further used to construct the general radiomics signature. Fivefold cross-validation was used to select the best machine learning algorithm. Finally, a general radiomics nomogram was developed using general radiomics signature, and clinical and radiological characteristics. Two groups of data collected at different time periods were used as two test sets to access the discrimination and clinical usefulness. Area under the receiver operating characteristic curve (ROC-AUC) was applied to performance evaluation. Result The general radiomics signature yielded the highest AUC of 0.756 and 0.739 in the two test sets, respectively. When applying to same type of CT, the performance of general radiomics signature was always similar to or higher than that of models built using only NE-CT or CE-CT features. The general radiomics nomogram combining general radiomics signature, smoking history, emphysema, and ILD achieved higher performance whether applying to NE-CT or CE-CT (test set 1, AUC = 0.833 and 0.842; test set 2, AUC = 0.839 and 0.850). Conclusions Our work demonstrated that using general features to construct radiomics signature and nomogram could help identify EGFR mutation status of NSCLC patients and expand its scope of clinical application. Key Points • General features were proposed to construct general radiomics signature using different types of CT of different patients at the same time to identify EGFR mutation status of NSCLC patients. • The general radiomics nomogram based on general radiomics signature, and clinical and radiological characteristics could identify EGFR mutation status of patients with NSCLC and outperformed the general radiomics signature. • The general radiomics nomogram had a wider scope of clinical application; no matter which of NE-CT and CE-CT the patient has, its EGFR mutation status could be predicted. Supplementary Information The online version contains supplementary material available at 10.1007/s00330-021-08366-y.
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Affiliation(s)
- Xiaoyan Yang
- Department of Pulmonary and Critical Care Medicine, China-Japan Friendship Hospital, Capital Medical University, Beijing, China
- National Center for Respiratory Medicine, Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, National Clinical Research Center for Respiratory Diseases, Beijing, China
| | - Min Liu
- Department of Radiology, China-Japan Friendship Hospital, Beijing, China
| | - Yanhong Ren
- Department of Pulmonary and Critical Care Medicine, China-Japan Friendship Hospital, Capital Medical University, Beijing, China
- National Center for Respiratory Medicine, Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, National Clinical Research Center for Respiratory Diseases, Beijing, China
| | - Huang Chen
- Department of Clinical Pathology, China-Japan Friendship Hospital, Beijing, China
| | - Pengxin Yu
- Infervision Medical Technology Co Ltd, Beijing, China
| | - Siyi Wang
- Infervision Medical Technology Co Ltd, Beijing, China
| | - Rongguo Zhang
- Infervision Medical Technology Co Ltd, Beijing, China
| | - Huaping Dai
- Department of Pulmonary and Critical Care Medicine, China-Japan Friendship Hospital, Capital Medical University, Beijing, China.
- National Center for Respiratory Medicine, Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, National Clinical Research Center for Respiratory Diseases, Beijing, China.
| | - Chen Wang
- Department of Pulmonary and Critical Care Medicine, China-Japan Friendship Hospital, Capital Medical University, Beijing, China.
- National Center for Respiratory Medicine, Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, National Clinical Research Center for Respiratory Diseases, Beijing, China.
- Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
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Abstract
This article gives a brief overview of the development of artificial intelligence in clinical breast imaging. For multiple decades, artificial intelligence (AI) methods have been developed and translated for breast imaging tasks such as detection, diagnosis, and assessing response to therapy. As imaging modalities arise to support breast cancer screening programs and diagnostic examinations, including full-field digital mammography, breast tomosynthesis, ultrasound, and MRI, AI techniques parallel the efforts with more complex algorithms, faster computers, and larger data sets. AI methods include human-engineered radiomics algorithms and deep learning methods. Examples of these AI-supported clinical tasks are given along with commentary on the future.
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Affiliation(s)
- Qiyuan Hu
- Committee on Medical Physics, Department of Radiology, The University of Chicago, 5841 S Maryland Avenue, MC2026, Chicago, IL 60637, USA
| | - Maryellen L Giger
- Committee on Medical Physics, Department of Radiology, The University of Chicago, 5841 S Maryland Avenue, MC2026, Chicago, IL 60637, USA.
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26
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Machine Learning: Applications and Advanced Progresses of Radiomics in Endocrine Neoplasms. JOURNAL OF ONCOLOGY 2021; 2021:8615450. [PMID: 34671399 PMCID: PMC8523238 DOI: 10.1155/2021/8615450] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 07/13/2021] [Accepted: 09/20/2021] [Indexed: 12/24/2022]
Abstract
Endocrine neoplasms remain a great threat to human health. It is extremely important to make a clear diagnosis and timely treatment of endocrine tumors. Machine learning includes radiomics, which has long been utilized in clinical cancer research. Radiomics refers to the extraction of valuable information by analyzing a large amount of standard data with high-throughput medical images mainly including computed tomography, positron emission tomography, magnetic resonance imaging, and ultrasound. With the quantitative imaging analysis and model building, radiomics can reflect specific underlying characteristics of a disease that otherwise could not be evaluated visually. More and more promising results of radiomics in oncological practice have been seen in recent years. Radiomics may have the potential to supplement traditional imaging analysis and assist in providing precision medicine for patients. Radiomics had developed rapidly in endocrine neoplasms practice in the past decade. In this review, we would introduce the general workflow of radiomics and summarize the applications and developments of radiomics in endocrine neoplasms in recent years. The limitations of current radiomic research studies and future development directions would also be discussed.
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Davey MG, Davey MS, Boland MR, Ryan ÉJ, Lowery AJ, Kerin MJ. Radiomic differentiation of breast cancer molecular subtypes using pre-operative breast imaging - A systematic review and meta-analysis. Eur J Radiol 2021; 144:109996. [PMID: 34624649 DOI: 10.1016/j.ejrad.2021.109996] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 09/17/2021] [Accepted: 09/30/2021] [Indexed: 01/12/2023]
Abstract
INTRODUCTION Breast cancer has four distinct molecular subtypes which are discriminated using gene expression profiling following biopsy. Radiogenomics is an emerging field which utilises diagnostic imaging to reveal genomic properties of disease. We aimed to perform a systematic review of the current literature to evaluate the value radiomics in differentiating breast cancers into their molecular subtypes using diagnostic imaging. METHODS A systematic review was performed as per PRISMA guidelines. Studies assessing radiomictumour analysis in differentiatingbreast cancer molecular subtypeswere included. Quality was assessed using the radiomics quality score (RQS). Diagnostic sensitivity and specificity of radiomic analyses were included for meta-analysis; Study specific sensitivity and specificity were retrieved and summary ROC analysis were performed to compile pooled sensitivities and specificities. RESULTS Forty-one studies were included. Overall, there were 10,090 female patients (mean age of 47.6 ± 11.7 years, range: 21-93) and molecular subtypewas reported in 7,693 of cases, with Luminal A (LABC), Luminal B (LBBC), Human Epidermal Growth Factor Receptor-2 overexpressing (HER2+), and Triple Negative (TNBC) breast cancers representing 51.3%, 19.9%, 12.3% and 16.3% of tumour respectively. Seven studies provided radiomic analysis to determine molecular subtypes using mammography to differentiateTNBCvs.others (sensitivity: 0.82,specificity:0.79). Thirty-five studies reported on radiomic analysis of magnetic resonance imaging (MRI); LABC versus others(sensitivity:0.78,specificity:0.83),HER2+versusothers(sensitivity:0.87,specificity:0.88), andLBBCversusTNBC (sensitivity: 0.79,specificity:0.88) respectively. CONCLUSION Radiomic tumour assessment of contemporary breast imaging provide a novel option in determining breast cancer molecular subtypes. However, amelioration of such techniques are required and genetic expression assessment will remain the gold standard.
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Affiliation(s)
- Matthew G Davey
- The Lambe Institute for Translational Research, National University of Ireland, Galway H91 YR91, Ireland.
| | - Martin S Davey
- The Lambe Institute for Translational Research, National University of Ireland, Galway H91 YR91, Ireland
| | - Michael R Boland
- The Lambe Institute for Translational Research, National University of Ireland, Galway H91 YR91, Ireland
| | - Éanna J Ryan
- The Lambe Institute for Translational Research, National University of Ireland, Galway H91 YR91, Ireland
| | - Aoife J Lowery
- The Lambe Institute for Translational Research, National University of Ireland, Galway H91 YR91, Ireland
| | - Michael J Kerin
- The Lambe Institute for Translational Research, National University of Ireland, Galway H91 YR91, Ireland
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Chalfant JS, Mortazavi S, Lee-Felker SA. Background Parenchymal Enhancement on Breast MRI: Assessment and Clinical Implications. CURRENT RADIOLOGY REPORTS 2021. [DOI: 10.1007/s40134-021-00386-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Abstract
Purpose of Review
To present recent literature regarding the assessment and clinical implications of background parenchymal enhancement on breast MRI.
Recent Findings
The qualitative assessment of BPE remains variable within the literature, as well as in clinical practice. Several different quantitative approaches have been investigated in recent years, most commonly region of interest-based and segmentation-based assessments. However, quantitative assessment has not become standard in clinical practice to date. Numerous studies have demonstrated a clear association between higher BPE and future breast cancer risk. While higher BPE does not appear to significantly impact cancer detection, it may result in a higher abnormal interpretation rate. BPE is also likely a marker of pathologic complete response after neoadjuvant chemotherapy, with decreases in BPE during and after neoadjuvant chemotherapy correlated with pCR. In contrast, pre-treatment BPE does not appear to be predictive of pCR. The association between BPE and prognosis is less clear, with heterogeneous results in the literature.
Summary
Assessment of BPE continues to evolve, with heterogeneity in approaches to both qualitative and quantitative assessment. The level of BPE has important clinical implications, with associations with future breast cancer risk and treatment response. BPE may also be an imaging marker of prognosis, but future research is needed on this topic.
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Bitencourt A, Daimiel Naranjo I, Lo Gullo R, Rossi Saccarelli C, Pinker K. AI-enhanced breast imaging: Where are we and where are we heading? Eur J Radiol 2021; 142:109882. [PMID: 34392105 PMCID: PMC8387447 DOI: 10.1016/j.ejrad.2021.109882] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 07/15/2021] [Accepted: 07/26/2021] [Indexed: 12/22/2022]
Abstract
Significant advances in imaging analysis and the development of high-throughput methods that can extract and correlate multiple imaging parameters with different clinical outcomes have led to a new direction in medical research. Radiomics and artificial intelligence (AI) studies are rapidly evolving and have many potential applications in breast imaging, such as breast cancer risk prediction, lesion detection and classification, radiogenomics, and prediction of treatment response and clinical outcomes. AI has been applied to different breast imaging modalities, including mammography, ultrasound, and magnetic resonance imaging, in different clinical scenarios. The application of AI tools in breast imaging has an unprecedented opportunity to better derive clinical value from imaging data and reshape the way we care for our patients. The aim of this study is to review the current knowledge and future applications of AI-enhanced breast imaging in clinical practice.
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Affiliation(s)
- Almir Bitencourt
- Department of Imaging, A.C.Camargo Cancer Center, Sao Paulo, SP, Brazil; Dasa, Sao Paulo, SP, Brazil
| | - Isaac Daimiel Naranjo
- Department of Radiology, Breast Imaging Service, Guy's and St. Thomas' NHS Trust, Great Maze Pond, London, UK
| | - Roberto Lo Gullo
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Katja Pinker
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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30
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You C, Zhang Y, Chen Y, Hu X, Hu D, Wu J, Gu Y, Peng W. Evaluation of Background Parenchymal Enhancement and Histogram-Based Diffusion-Weighted Image in Determining the Molecular Subtype of Breast Cancer. J Comput Assist Tomogr 2021; 45:711-716. [PMID: 34546678 DOI: 10.1097/rct.0000000000001239] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
RATIONALE AND OBJECTIVES This study aimed to evaluate the value of background parenchymal enhancement (BPE) and diffusion-weighted image (DWI) histogram features in differentiating among different molecular subtypes of breast cancers and investigate the relationship between BPE and DWI features. MATERIALS AND METHODS We prospectively enrolled 142 patients with breast cancer between January and November 2018. All patients underwent breast magnetic resonance imaging before core needle biopsy. The quantitative BPE from dynamic enhanced images and the first-order histogram features extracted from DWI were analyzed. Univariate analysis of variance was used to compare differences in DWI histogram features and BPE characteristics among different molecular subtypes. Spearman test was used to compare the correlation between these imaging indexes. RESULTS A total of 142 patients had 142 lesions, including 17 cases of triple-negative breast cancer, 12 cases of luminal A type breast cancer, 39 cases of luminal B type breast cancer, and 74 cases of human epidermal growth factor receptor 2-positive breast cancer. The apparent diffusion coefficient (ADC) 95th percentile, ADC kurtosis, and BPE were significantly different among 4 subtype groups (P < 0.05), especially between the triple-negative subtype and any other subtype (P < 0.05 in pairwise comparisons). There was a weak but significant correlation between BPE and kurtosis of ADC (r = -0.176, P = 0.036). CONCLUSIONS Diffusion-weighted image histogram features (95th percentile ADC value and kurtosis value of ADC) and BPE features were different in the 4 molecular subtypes of breast cancer, especially in the triple-negative breast cancer subtype. Background parenchymal enhancement was negatively correlated with the kurtosis value of ADC.
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Affiliation(s)
- Chao You
- From the Department of Radiology, Fudan University Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University
| | - Yunyan Zhang
- Department of Radiology, Shanghai Proton and Heavy Ion Center
| | - Yanqiong Chen
- From the Department of Radiology, Fudan University Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University
| | - Xiaoxin Hu
- From the Department of Radiology, Fudan University Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University
| | - Danting Hu
- From the Department of Radiology, Fudan University Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University
| | - Jiong Wu
- Department of Breast Surgery, Fudan University Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, PR China
| | - Yajia Gu
- From the Department of Radiology, Fudan University Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University
| | - Weijun Peng
- From the Department of Radiology, Fudan University Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University
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31
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Singh A, Chitalia R, Kontos D. Radiogenomics in brain, breast, and lung cancer: opportunities and challenges. J Med Imaging (Bellingham) 2021; 8:031907. [PMID: 34164563 PMCID: PMC8212946 DOI: 10.1117/1.jmi.8.3.031907] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Accepted: 06/04/2021] [Indexed: 01/06/2023] Open
Abstract
The field of radiogenomics largely focuses on developing imaging surrogates for genomic signatures and integrating imaging, genomic, and molecular data to develop combined personalized biomarkers for characterizing various diseases. Our study aims to highlight the current state-of-the-art and the role of radiogenomics in cancer research, focusing mainly on solid tumors, and is broadly divided into four sections. The first section reviews representative studies that establish the biologic basis of radiomic signatures using gene expression and molecular profiling information. The second section includes studies that aim to non-invasively predict molecular subtypes of tumors using radiomic signatures. The third section reviews studies that evaluate the potential to augment the performance of established prognostic signatures by combining complementary information encoded by radiomic and genomic signatures derived from cancer tumors. The fourth section includes studies that focus on ascertaining the biological significance of radiomic phenotypes. We conclude by discussing current challenges and opportunities in the field, such as the importance of coordination between imaging device manufacturers, regulatory organizations, health care providers, pharmaceutical companies, academic institutions, and physicians for the effective standardization of the results from radiogenomic signatures and for the potential use of these findings to improve precision care for cancer patients.
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Affiliation(s)
- Apurva Singh
- University of Pennsylvania, Department of Radiology, Philadelphia, Pennsylvania, United States
| | - Rhea Chitalia
- University of Pennsylvania, Department of Radiology, Philadelphia, Pennsylvania, United States
| | - Despina Kontos
- University of Pennsylvania, Department of Radiology, Philadelphia, Pennsylvania, United States
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Chang X, Guo X, Li X, Han X, Li X, Liu X, Ren J. Potential Value of Radiomics in the Identification of Stage T3 and T4a Esophagogastric Junction Adenocarcinoma Based on Contrast-Enhanced CT Images. Front Oncol 2021; 11:627947. [PMID: 33747947 PMCID: PMC7968370 DOI: 10.3389/fonc.2021.627947] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 01/05/2021] [Indexed: 12/24/2022] Open
Abstract
Purpose This study was designed to evaluate the predictive performance of contrast-enhanced CT-based radiomic features for the personalized, differential diagnosis of esophagogastric junction (EGJ) adenocarcinoma at stages T3 and T4a. Methods Two hundred patients with T3 (n = 44) and T4a (n = 156) EGJ adenocarcinoma lesions were enrolled in this study. Traditional computed tomography (CT) features were obtained from contrast-enhanced CT images, and the traditional model was constructed using a multivariate logistic regression analysis. A radiomic model was established based on radiomic features from venous CT images, and the radiomic score (Radscore) of each patient was calculated. A combined nomogram diagnostic model was constructed based on Radscores and traditional features. The diagnostic performances of these three models (traditional model, radiomic model, and nomogram) were assessed with receiver operating characteristics curves. Sensitivity, specificity, accuracy, positive predictive value, negative predictive value, and areas under the curve (AUC) of models were calculated, and the performances of the models were evaluated and compared. Finally, the clinical effectiveness of the three models was evaluated by conducting a decision curve analysis (DCA). Results An eleven-feature combined radiomic signature and two traditional CT features were constructed as the radiomic and traditional feature models, respectively. The Radscore was significantly different between patients with stage T3 and T4a EGJ adenocarcinoma. The combined nomogram performed the best and has potential clinical usefulness. Conclusions The developed combined nomogram might be useful in differentiating T3 and T4a stages of EGJ adenocarcinoma and may facilitate the decision-making process for the treatment of T3 and T4a EGJ adenocarcinoma.
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Affiliation(s)
- Xu Chang
- Department of Radiology, Heping Hospital Affiliated to Changzhi Medical College, Changzhi, China
| | - Xing Guo
- Department of Radiology, Heping Hospital Affiliated to Changzhi Medical College, Changzhi, China
| | - Xiaole Li
- Department of Radiology, Graduate School of Changzhi Medical College, Changzhi, China
| | - Xiaowei Han
- Department of Radiology, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, China
| | - Xiaoxiao Li
- Department of Radiology, Graduate School of Changzhi Medical College, Changzhi, China
| | - Xiaoyan Liu
- Department of Radiology, Graduate School of Changzhi Medical College, Changzhi, China
| | - Jialiang Ren
- Department of Pharmaceutical Diagnostics, GE Healthcare China, Beijing, China
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Leithner D, Bernard-Davila B, Martinez DF, Horvat JV, Jochelson MS, Marino MA, Avendano D, Ochoa-Albiztegui RE, Sutton EJ, Morris EA, Thakur SB, Pinker K. Radiomic Signatures Derived from Diffusion-Weighted Imaging for the Assessment of Breast Cancer Receptor Status and Molecular Subtypes. Mol Imaging Biol 2021; 22:453-461. [PMID: 31209778 PMCID: PMC7062654 DOI: 10.1007/s11307-019-01383-w] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Purpose To compare annotation segmentation approaches and to assess the value of radiomics analysis applied to diffusion-weighted imaging (DWI) for evaluation of breast cancer receptor status and molecular subtyping. Procedures In this IRB-approved HIPAA-compliant retrospective study, 91 patients with treatment-naïve breast malignancies proven by image-guided breast biopsy, (luminal A, n = 49; luminal B, n = 8; human epidermal growth factor receptor 2 [HER2]-enriched, n = 11; triple negative [TN], n = 23) underwent multiparametric magnetic resonance imaging (MRI) of the breast at 3 T with dynamic contrast-enhanced MRI, T2-weighted and DW imaging. Lesions were manually segmented on high b-value DW images and segmentation ROIS were propagated to apparent diffusion coefficient (ADC) maps. In addition in a subgroup (n = 79) where lesions were discernable on ADC maps alone, these were also directly segmented there. To derive radiomics signatures, the following features were extracted and analyzed: first-order histogram (HIS), co-occurrence matrix (COM), run-length matrix (RLM), absolute gradient, autoregressive model (ARM), discrete Haar wavelet transform (WAV), and lesion geometry. Fisher, probability of error and average correlation, and mutual information coefficients were used for feature selection. Linear discriminant analysis followed by k-nearest neighbor classification with leave-one-out cross-validation was applied for pairwise differentiation of receptor status and molecular subtyping. Histopathologic results were considered the gold standard. Results For lesion that were segmented on DWI and segmentation ROIs were propagated to ADC maps the following classification accuracies > 90% were obtained: luminal B vs. HER2-enriched, 94.7 % (based on COM features); luminal B vs. others, 92.3 % (COM, HIS); and HER2-enriched vs. others, 90.1 % (RLM, COM). For lesions that were segmented directly on ADC maps, better results were achieved yielding the following classification accuracies: luminal B vs. HER2-enriched, 100 % (COM, WAV); luminal A vs. luminal B, 91.5 % (COM, WAV); and luminal B vs. others, 91.1 % (WAV, ARM, COM). Conclusions Radiomic signatures from DWI with ADC mapping allows evaluation of breast cancer receptor status and molecular subtyping with high diagnostic accuracy. Better classification accuracies were obtained when breast tumor segmentations could be performed on ADC maps.
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Affiliation(s)
- Doris Leithner
- Department of Radiology, Breast Imaging Service, Memorial Sloan Kettering Cancer Center, 300 E 66th St, 7th Floor, New York, NY, 10065, USA.,Department of Diagnostic and Interventional Radiology, University Hospital Frankfurt, Frankfurt, Germany
| | - Blanca Bernard-Davila
- Department of Radiology, Breast Imaging Service, Memorial Sloan Kettering Cancer Center, 300 E 66th St, 7th Floor, New York, NY, 10065, USA
| | - Danny F Martinez
- Department of Radiology, Breast Imaging Service, Memorial Sloan Kettering Cancer Center, 300 E 66th St, 7th Floor, New York, NY, 10065, USA
| | - Joao V Horvat
- Department of Radiology, Breast Imaging Service, Memorial Sloan Kettering Cancer Center, 300 E 66th St, 7th Floor, New York, NY, 10065, USA
| | - Maxine S Jochelson
- Department of Radiology, Breast Imaging Service, Memorial Sloan Kettering Cancer Center, 300 E 66th St, 7th Floor, New York, NY, 10065, USA
| | - Maria Adele Marino
- Department of Radiology, Breast Imaging Service, Memorial Sloan Kettering Cancer Center, 300 E 66th St, 7th Floor, New York, NY, 10065, USA.,Department of Biomedical Sciences and Morphologic and Functional Imaging, University of Messina, Messina, Italy
| | - Daly Avendano
- Department of Radiology, Breast Imaging Service, Memorial Sloan Kettering Cancer Center, 300 E 66th St, 7th Floor, New York, NY, 10065, USA.,Department of Breast Imaging, Breast Cancer Center TecSalud, ITESM Monterrey, Monterrey, Nuevo Leon, Mexico
| | - R Elena Ochoa-Albiztegui
- Department of Radiology, Breast Imaging Service, Memorial Sloan Kettering Cancer Center, 300 E 66th St, 7th Floor, New York, NY, 10065, USA
| | - Elizabeth J Sutton
- Department of Radiology, Breast Imaging Service, Memorial Sloan Kettering Cancer Center, 300 E 66th St, 7th Floor, New York, NY, 10065, USA
| | - Elizabeth A Morris
- Department of Radiology, Breast Imaging Service, Memorial Sloan Kettering Cancer Center, 300 E 66th St, 7th Floor, New York, NY, 10065, USA
| | - Sunitha B Thakur
- Department of Radiology, Breast Imaging Service, Memorial Sloan Kettering Cancer Center, 300 E 66th St, 7th Floor, New York, NY, 10065, USA.,Department of Medical Physics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Katja Pinker
- Department of Radiology, Breast Imaging Service, Memorial Sloan Kettering Cancer Center, 300 E 66th St, 7th Floor, New York, NY, 10065, USA. .,Department of Biomedical Imaging and Image-guided Therapy, Molecular and Gender Imaging Service, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria.
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Zhang M, Sadinski M, Haddad D, Bae MS, Martinez D, Morris EA, Gibbs P, Sutton EJ. Background Parenchymal Enhancement on Breast MRI as a Prognostic Surrogate: Correlation With Breast Cancer Oncotype Dx Score. Front Oncol 2021; 10:595820. [PMID: 33614481 PMCID: PMC7890019 DOI: 10.3389/fonc.2020.595820] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 12/11/2020] [Indexed: 12/11/2022] Open
Abstract
Purpose Breast MRI background parenchymal enhancement (BPE) can potentially serve as a prognostic marker, by possible correlation with molecular subtype. Oncotype Dx, a gene assay, is a prognostic and predictive surrogate for tumor aggressiveness and treatment response. The purpose of this study was to investigate the association between contralateral non-tumor breast magnetic resonance imaging (MRI) background parenchymal enhancement and tumor oncotype score. Methods In this retrospective study, patients with ER+ and HER2− early stage invasive ductal carcinoma who underwent preoperative breast MRI, oncotype risk scoring, and breast conservation surgery from 2008–2010 were identified. After registration, BPE from the pre and three post-contrast phases was automatically extracted using a k-means clustering algorithm. Four metrics were calculated: initial enhancement (IE) relative to the pre-contrast signal, late enhancement, overall enhancement (OE), and area under the enhancement curve (AUC). Histogram analysis was performed to determine first order metrics which were compared to oncotype risk score groups using Mann–Whitney tests and Spearman rank correlation analysis. Results This study included 80 women (mean age = 51.1 ± 10.3 years); 46 women were categorized as low risk (≤17) and 34 women were categorized as intermediate/high risk (≥18) according to Oncotype Dx. For the mean of the top 10% pixels, significant differences were noted for IE (p = 0.032), OE (p = 0.049), and AUC (p = 0.044). Using the risk score as a continuous variable, correlation analysis revealed a weak but significant correlation with the mean of the top 10% pixels for IE (r = 0.26, p = 0.02), OE (r = 0.25, p = 0.02), and AUC (r = 0.27, p = 0.02). Conclusion BPE metrics of enhancement in the non-tumor breast are associated with tumor Oncotype Dx recurrence score, suggesting that the breast microenvironment may relate to likelihood of recurrence and magnitude of chemotherapy benefit.
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Affiliation(s)
- Michelle Zhang
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY, United States.,Department of Radiology, McGill University, Montreal, QC, Canada
| | - Meredith Sadinski
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Dana Haddad
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY, United States.,Department of Radiology, Montefiore, New York, NY, United States.,Department of Radiology, Mediclinic Middle East, Dubai, United Arab Emirates.,College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Min Sun Bae
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY, United States.,Department of Radiology, Seoul National University Hospital, Seoul, South Korea
| | - Danny Martinez
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Elizabeth A Morris
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Peter Gibbs
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Elizabeth J Sutton
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY, United States
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Saint Martin MJ, Orlhac F, Akl P, Khalid F, Nioche C, Buvat I, Malhaire C, Frouin F. A radiomics pipeline dedicated to Breast MRI: validation on a multi-scanner phantom study. MAGNETIC RESONANCE MATERIALS IN PHYSICS BIOLOGY AND MEDICINE 2020; 34:355-366. [PMID: 33180226 DOI: 10.1007/s10334-020-00892-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 09/27/2020] [Accepted: 10/23/2020] [Indexed: 12/14/2022]
Abstract
OBJECTIVE Quantitative analysis in MRI is challenging due to variabilities in intensity distributions across patients, acquisitions and scanners and suffers from bias field inhomogeneity. Radiomic studies are impacted by these effects that affect radiomic feature values. This paper describes a dedicated pipeline to increase reproducibility in breast MRI radiomic studies. MATERIALS AND METHODS T1, T2, and T1-DCE MR images of two breast phantoms were acquired using two scanners and three dual breast coils. Images were retrospectively corrected for bias field inhomogeneity and further normalised using Z score or histogram matching. Extracted radiomic features were harmonised between coils by the ComBat method. The whole pipeline was assessed qualitatively and quantitatively using statistical comparisons on two series of radiomic feature values computed in the gel mimicking the normal breast tissue or in dense lesions. RESULTS Intra and inter-acquisition variabilities were strongly reduced by the standardisation pipeline. Harmonisation by ComBat lowered the percentage of radiomic features significantly different between the three coils from 87% after bias field correction and MR normalisation to 3% in the gel, while preserving or improving performance of lesion classification in the phantoms. DISCUSSION A dedicated standardisation pipeline was developed to reduce variabilities in breast MRI, which paves the way for robust multi-scanner radiomic studies but needs to be assessed on patient data.
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Affiliation(s)
- Marie-Judith Saint Martin
- Inserm, Institut Curie,Université Paris-Saclay, Laboratoire d'Imagerie Translationnelle en Oncologie (LITO), Centre de Recherche de l'Institut Curie, Bât 101B rue Henri Becquerel, 91401, Orsay, France.
| | - Fanny Orlhac
- Inserm, Institut Curie,Université Paris-Saclay, Laboratoire d'Imagerie Translationnelle en Oncologie (LITO), Centre de Recherche de l'Institut Curie, Bât 101B rue Henri Becquerel, 91401, Orsay, France
| | - Pia Akl
- Inserm, Institut Curie,Université Paris-Saclay, Laboratoire d'Imagerie Translationnelle en Oncologie (LITO), Centre de Recherche de l'Institut Curie, Bât 101B rue Henri Becquerel, 91401, Orsay, France
- HCL, Radiologie du Groupement Hospitalier Est, Hôpital Femme Mère Enfant, Unité Fonctionnelle: Imagerie de la Femme, 3 Quai des Célestins, 69002, Lyon, France
- Institut Curie, Service de Radiodiagnostic, 26 rue d'Ulm, 75005, Paris, France
| | - Fahad Khalid
- Inserm, Institut Curie,Université Paris-Saclay, Laboratoire d'Imagerie Translationnelle en Oncologie (LITO), Centre de Recherche de l'Institut Curie, Bât 101B rue Henri Becquerel, 91401, Orsay, France
| | - Christophe Nioche
- Inserm, Institut Curie,Université Paris-Saclay, Laboratoire d'Imagerie Translationnelle en Oncologie (LITO), Centre de Recherche de l'Institut Curie, Bât 101B rue Henri Becquerel, 91401, Orsay, France
| | - Irène Buvat
- Inserm, Institut Curie,Université Paris-Saclay, Laboratoire d'Imagerie Translationnelle en Oncologie (LITO), Centre de Recherche de l'Institut Curie, Bât 101B rue Henri Becquerel, 91401, Orsay, France
| | - Caroline Malhaire
- Inserm, Institut Curie,Université Paris-Saclay, Laboratoire d'Imagerie Translationnelle en Oncologie (LITO), Centre de Recherche de l'Institut Curie, Bât 101B rue Henri Becquerel, 91401, Orsay, France
- Institut Curie, Service de Radiodiagnostic, 26 rue d'Ulm, 75005, Paris, France
| | - Frédérique Frouin
- Inserm, Institut Curie,Université Paris-Saclay, Laboratoire d'Imagerie Translationnelle en Oncologie (LITO), Centre de Recherche de l'Institut Curie, Bât 101B rue Henri Becquerel, 91401, Orsay, France
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Martin-Gonzalez P, Crispin-Ortuzar M, Rundo L, Delgado-Ortet M, Reinius M, Beer L, Woitek R, Ursprung S, Addley H, Brenton JD, Markowetz F, Sala E. Integrative radiogenomics for virtual biopsy and treatment monitoring in ovarian cancer. Insights Imaging 2020; 11:94. [PMID: 32804260 PMCID: PMC7431480 DOI: 10.1186/s13244-020-00895-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 07/16/2020] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Ovarian cancer survival rates have not changed in the last 20 years. The majority of cases are High-grade serous ovarian carcinomas (HGSOCs), which are typically diagnosed at an advanced stage with multiple metastatic lesions. Taking biopsies of all sites of disease is infeasible, which challenges the implementation of stratification tools based on molecular profiling. MAIN BODY In this review, we describe how these challenges might be overcome by integrating quantitative features extracted from medical imaging with the analysis of paired genomic profiles, a combined approach called radiogenomics, to generate virtual biopsies. Radiomic studies have been used to model different imaging phenotypes, and some radiomic signatures have been associated with paired molecular profiles to monitor spatiotemporal changes in the heterogeneity of tumours. We describe different strategies to integrate radiogenomic information in a global and local manner, the latter by targeted sampling of tumour habitats, defined as regions with distinct radiomic phenotypes. CONCLUSION Linking radiomics and biological correlates in a targeted manner could potentially improve the clinical management of ovarian cancer. Radiogenomic signatures could be used to monitor tumours during the course of therapy, offering additional information for clinical decision making. In summary, radiogenomics may pave the way to virtual biopsies and treatment monitoring tools for integrative tumour analysis.
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Affiliation(s)
- Paula Martin-Gonzalez
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, CB2 0RE, UK
- Cancer Research UK Cambridge Centre, University of Cambridge, Cambridge, CB2 0RE, UK
| | - Mireia Crispin-Ortuzar
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, CB2 0RE, UK
- Cancer Research UK Cambridge Centre, University of Cambridge, Cambridge, CB2 0RE, UK
| | - Leonardo Rundo
- Cancer Research UK Cambridge Centre, University of Cambridge, Cambridge, CB2 0RE, UK
- Department of Radiology, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Maria Delgado-Ortet
- Cancer Research UK Cambridge Centre, University of Cambridge, Cambridge, CB2 0RE, UK
- Department of Radiology, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Marika Reinius
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, CB2 0RE, UK
- Cancer Research UK Cambridge Centre, University of Cambridge, Cambridge, CB2 0RE, UK
| | - Lucian Beer
- Cancer Research UK Cambridge Centre, University of Cambridge, Cambridge, CB2 0RE, UK
- Department of Radiology, University of Cambridge, Cambridge, CB2 0QQ, UK
- Department of Biomedical Imaging and Image-guided Therapy, Medical University Vienna, 1090, Vienna, Austria
| | - Ramona Woitek
- Cancer Research UK Cambridge Centre, University of Cambridge, Cambridge, CB2 0RE, UK
- Department of Radiology, University of Cambridge, Cambridge, CB2 0QQ, UK
- Department of Biomedical Imaging and Image-guided Therapy, Medical University Vienna, 1090, Vienna, Austria
| | - Stephan Ursprung
- Cancer Research UK Cambridge Centre, University of Cambridge, Cambridge, CB2 0RE, UK
- Department of Radiology, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Helen Addley
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, CB2 0RE, UK
- Department of Radiology, University of Cambridge, Cambridge, CB2 0QQ, UK
- Cambridge University Hospitals NHS Foundation Trust, Addenbrooke's Hospital, Cambridge, CB2 0QQ, UK
| | - James D Brenton
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, CB2 0RE, UK
- Cancer Research UK Cambridge Centre, University of Cambridge, Cambridge, CB2 0RE, UK
| | - Florian Markowetz
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, CB2 0RE, UK
- Cancer Research UK Cambridge Centre, University of Cambridge, Cambridge, CB2 0RE, UK
| | - Evis Sala
- Cancer Research UK Cambridge Centre, University of Cambridge, Cambridge, CB2 0RE, UK.
- Department of Radiology, University of Cambridge, Cambridge, CB2 0QQ, UK.
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A comprehensive hierarchical classification based on multi-features of breast DCE-MRI for cancer diagnosis. Med Biol Eng Comput 2020; 58:2413-2425. [DOI: 10.1007/s11517-020-02232-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 07/17/2020] [Indexed: 11/27/2022]
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Orlando A, Dimarco M, Cannella R, Bartolotta TV. Breast dynamic contrast-enhanced-magnetic resonance imaging and radiomics: State of art. Artif Intell Med Imaging 2020; 1:6-18. [DOI: 10.35711/aimi.v1.i1.6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 06/17/2020] [Accepted: 06/19/2020] [Indexed: 02/06/2023] Open
Abstract
Breast cancer represents the most common malignancy in women, being one of the most frequent cause of cancer-related mortality. Ultrasound, mammography, and magnetic resonance imaging (MRI) play a pivotal role in the diagnosis of breast lesions, with different levels of accuracy. Particularly, dynamic contrast-enhanced MRI has shown high diagnostic value in detecting multifocal, multicentric, or contralateral breast cancers. Radiomics is emerging as a promising tool for quantitative tumor evaluation, allowing the extraction of additional quantitative data from radiological imaging acquired with different modalities. Radiomics analysis may provide novel information through the quantification of lesions heterogeneity, that may be relevant in clinical practice for the characterization of breast lesions, prediction of tumor response to systemic therapies and evaluation of prognosis in patients with breast cancers. Several published studies have explored the value of radiomics with good-to-excellent diagnostic and prognostic performances for the evaluation of breast lesions. Particularly, the integrations of radiomics data with other clinical and histopathological parameters have demonstrated to improve the prediction of tumor aggressiveness with high accuracy and provided precise models that will help to guide clinical decisions and patients management. The purpose of this article in to describe the current application of radiomics in breast dynamic contrast-enhanced MRI.
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Affiliation(s)
- Alessia Orlando
- Section of Radiology - BiND, University Hospital “Paolo Giaccone”, Palermo 90127, Italy
| | - Mariangela Dimarco
- Section of Radiology - BiND, University Hospital “Paolo Giaccone”, Palermo 90127, Italy
| | - Roberto Cannella
- Section of Radiology - BiND, University Hospital “Paolo Giaccone”, Palermo 90127, Italy
| | - Tommaso Vincenzo Bartolotta
- Section of Radiology - BiND, University Hospital “Paolo Giaccone”, Palermo 90127, Italy
- Department of Radiology, Fondazione Istituto Giuseppe Giglio, Ct.da Pietrapollastra, Palermo 90015, Italy
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Feng Q, Hu Q, Liu Y, Yang T, Yin Z. Diagnosis of triple negative breast cancer based on radiomics signatures extracted from preoperative contrast-enhanced chest computed tomography. BMC Cancer 2020; 20:579. [PMID: 32571245 PMCID: PMC7309976 DOI: 10.1186/s12885-020-07053-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 06/08/2020] [Indexed: 12/13/2022] Open
Abstract
Background To explore the diagnostic value of radiomics features of preoperative computed tomography (CT) for triple negative breast cancer (TNBC) for better treatment of patients with breast cancer. Methods A total of 890 patients with breast cancer admitted to our hospital from June 2016 to January 2018 were analyzed. They were diagnosed by surgery and pathology to have mass and invasive breast cancer and had contrast-enhanced chest CT examination before operation. 300 patients were randomly selected for the study, including 100 TNBC and 200 non-TNBC (NTNBC) patients. Among them 180 were used in discovery group and 120 were used in validation group. The molecular subtypes of breast cancer in the patients were determined immunohistochemistrially. Radiomics features were extracted from three dimensional CT-images. The LASSO logistic method was used to select image features and calculate radiomics scores. Receiver operating characteristic (ROC) curve analysis was performed to evaluate the diagnostic value of radiomics scores for TNBC. Results Five image features were found to be related to TNBC subtype (P < 0.001). These image features based-radiomic signatures had good predictive values for TNBC with the areas under ROC curve (AUC) of 0.881 (95% CI: 0.781–0.921) in the discovery group and 0.851 (95% CI: 0.761–0.961) in the validation group, respectively. The sensitivities and specificities were 0.767, and 0.873 in the discovery group and 0.785 and 0.915 in the validation group. Conclusions Radiomic signature based on preoperative CT is capable of distinguishing patients with TNBC and NTNBC. It adds additional value for conventional chest contrast-enhanced CT and helps plan the strategy for clinical treatment of the patients.
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Affiliation(s)
- Qingliang Feng
- Department of Radiology, Linyi Central Hospital, Linyi, China
| | - Qiang Hu
- Department of Radiology, Linyi Central Hospital, Linyi, China
| | - Yan Liu
- Department of Healthcare, Linyi Central Hospital, Linyi, China
| | - Tao Yang
- Department of Radiology, Linyi Central Hospital, Linyi, China
| | - Ziyi Yin
- Department of Surgery, Beijing Tiantan Hospital, Capital Medical University, 119 South 4th Ring West Road, Beijing, 100070, China.
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Lu H, Yin J. Texture Analysis of Breast DCE-MRI Based on Intratumoral Subregions for Predicting HER2 2+ Status. Front Oncol 2020; 10:543. [PMID: 32373531 PMCID: PMC7186477 DOI: 10.3389/fonc.2020.00543] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 03/26/2020] [Indexed: 01/04/2023] Open
Abstract
Background: Breast tumor heterogeneity is related to risk factors that lead to aggressive tumor growth; however, such heterogeneity has not been thoroughly investigated. Purpose: To evaluate the performance of texture features extracted from heterogeneity subregions on subtraction MRI images for identifying human epidermal growth factor receptor 2 (HER2) 2+ status of breast cancers. Materials and Methods: Seventy-six patients with HER2 2+ breast cancer who underwent dynamic contrast-enhanced magnetic resonance imaging were enrolled, including 42 HER2 positive and 34 negative cases confirmed by fluorescence in situ hybridization. The lesion area was delineated semi-automatically on the subtraction MRI images at the second, fourth, and sixth phases (P-1, P-2, and P-3). A regionalization method was used to segment the lesion area into three subregions (rapid, medium, and slow) according to peak arrival time of the contrast agent. We extracted 488 texture features from the whole lesion area and three subregions independently. Wrapper, least absolute shrinkage and selection operator (LASSO), and stepwise methods were used to identify the optimal feature subsets. Univariate analysis was performed as well as support vector machine (SVM) with a leave-one-out-based cross-validation method. The area under the receiver operating characteristic curve (AUC) was calculated to evaluate the performance of the classifiers. Results: In univariate analysis, the variance from medium subregion at P-2 was the best-performing feature for distinguishing HER2 2+ status (AUC = 0.836); for the whole lesion region, the variance at P-2 achieved the best performance (AUC = 0.798). There was no significant difference between the two methods (P = 0.271). In the machine learning with SVM, the best performance (AUC = 0.929) was achieved with LASSO from rapid subregion at P-2; for the whole region, the highest AUC value was 0.847 obtained at P-2 with LASSO. The difference was significant between the two methods (P = 0.021). Conclusion: The texture analysis of heterogeneity subregions based on intratumoral regionalization method showed potential value for recognizing HER2 2+ status in breast cancer.
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Affiliation(s)
- Hecheng Lu
- School of Medicine and Bioinformatics Engineering, Northeastern University, Shenyang, China.,Department of Radiology, ShengJing Hospital of China Medical University, Shenyang, China
| | - Jiandong Yin
- Department of Radiology, ShengJing Hospital of China Medical University, Shenyang, China
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42
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Grimm LJ, Mazurowski MA. Breast Cancer Radiogenomics: Current Status and Future Directions. Acad Radiol 2020; 27:39-46. [PMID: 31818385 DOI: 10.1016/j.acra.2019.09.012] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Revised: 07/17/2019] [Accepted: 09/08/2019] [Indexed: 12/13/2022]
Abstract
Radiogenomics is an area of research that aims to identify associations between imaging phenotypes ("radio-") and tumor genome ("-genomics"). Breast cancer radiogenomics research in particular has been an especially prolific area of investigation in recent years as evidenced by the wide number and variety of publications and conferences presentations. To date, research has primarily been focused on dynamic contrast enhanced pre-operative breast MRI and breast cancer molecular subtypes, but investigations have extended to all breast imaging modalities as well as multiple additional genetic markers including those that are commercially available. Furthermore, both human and computer-extracted features as well as deep learning techniques have been explored. This review will summarize the specific imaging modalities used in radiogenomics analysis, describe the methods of extracting imaging features, and present the types of genomics, molecular, and related information used for analysis. Finally, the limitations and future directions of breast cancer radiogenomics research will be discussed.
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Whitney HM, Li H, Ji Y, Liu P, Giger ML. Comparison of Breast MRI Tumor Classification Using Human-Engineered Radiomics, Transfer Learning From Deep Convolutional Neural Networks, and Fusion Methods. PROCEEDINGS OF THE IEEE. INSTITUTE OF ELECTRICAL AND ELECTRONICS ENGINEERS 2020; 108:163-177. [PMID: 34045769 PMCID: PMC8152568 DOI: 10.1109/jproc.2019.2950187] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Digital image-based signatures of breast tumors may ultimately contribute to the design of patient-specific breast cancer diagnostics and treatments. Beyond traditional human-engineered computer vision methods, tumor classification methods using transfer learning from deep convolutional neural networks (CNNs) are actively under development. This article will first discuss our progress in using CNN-based transfer learning to characterize breast tumors for various diagnostic, prognostic, or predictive image-based tasks across multiple imaging modalities, including mammography, digital breast tomosynthesis, ultrasound (US), and magnetic resonance imaging (MRI), compared to both human-engineered feature-based radiomics and fusion classifiers created through combination of such features. Second, a new study is presented that reports on a comprehensive comparison of the classification performances of features derived from human-engineered radiomic features, CNN transfer learning, and fusion classifiers for breast lesions imaged with MRI. These studies demonstrate the utility of transfer learning for computer-aided diagnosis and highlight the synergistic improvement in classification performance using fusion classifiers.
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Affiliation(s)
- Heather M Whitney
- Department of Radiology, The University of Chicago, Chicago, IL 60637 USA, and also with the Department of Physics, Wheaton College, Wheaton, IL 60187 USA
| | - Hui Li
- Department of Radiology, The University of Chicago, Chicago, IL 60637 USA
| | - Yu Ji
- Department of Breast Imaging, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin Medical University, Tianjin 30060, China
| | - Peifang Liu
- Department of Breast Imaging, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin Medical University, Tianjin 30060, China
| | - Maryellen L Giger
- Department of Radiology, The University of Chicago, Chicago, IL 60637 USA
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TCGA-TCIA Impact on Radiogenomics Cancer Research: A Systematic Review. Int J Mol Sci 2019; 20:ijms20236033. [PMID: 31795520 PMCID: PMC6929079 DOI: 10.3390/ijms20236033] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 11/26/2019] [Accepted: 11/28/2019] [Indexed: 12/11/2022] Open
Abstract
In the last decade, the development of radiogenomics research has produced a significant amount of papers describing relations between imaging features and several molecular 'omic signatures arising from next-generation sequencing technology and their potential role in the integrated diagnostic field. The most vulnerable point of many of these studies lies in the poor number of involved patients. In this scenario, a leading role is played by The Cancer Genome Atlas (TCGA) and The Cancer Imaging Archive (TCIA), which make available, respectively, molecular 'omic data and linked imaging data. In this review, we systematically collected and analyzed radiogenomic studies based on TCGA-TCIA data. We organized literature per tumor type and molecular 'omic data in order to discuss salient imaging genomic associations and limitations of each study. Finally, we outlined the potential clinical impact of radiogenomics to improve the accuracy of diagnosis and the prediction of patient outcomes in oncology.
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Molecular Subtypes Recognition of Breast Cancer in Dynamic Contrast-Enhanced Breast Magnetic Resonance Imaging Phenotypes from Radiomics Data. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2019; 2019:6978650. [PMID: 31827586 PMCID: PMC6885255 DOI: 10.1155/2019/6978650] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 10/10/2019] [Indexed: 12/28/2022]
Abstract
Background and Objective Breast cancer is a major cause of mortality among women if not treated in early stages. Recognizing molecular markers from DCE-MRI directly to distinguish the four molecular subtypes without invasive biopsy is helpful for guiding treatment plans for breast cancer, which provides a fast way to consequential treatment plan decision in early time and best opportunity for patients. Methods This study presents an approach of molecular subtypes recognition from breast cancer image phenotypes by radiomics. An improved region growth algorithm with dynamic threshold without user interaction is proposed for cancer lesion segmentation, which gives the precise border of lesion other than area with background. The lesions are extracted automatically based on radiologists' annotation which guarantees the lesion is segmented correctly. Various features are extracted on lesions data including texture, morphology, dynamic kinetics, and statistics features carried out on a large patient cohort, which are used to validate the relationship between image phenotypes and the molecular subtypes. A new algorithm of multimodel-based recursive feature elimination is applied on the radiomics data generated by the feature extraction process. This method obtains the feature subset with stable performance for different classification models, and the gradient boosting decision tree model gets the best results of both classification performance and imbalance performance on molecular subtypes. Result From the experimental results, 69 optimal features from 143 original features are found by the multimodel-based recursive feature elimination algorithms and the gradient boosting decision tree classifier obtains a good performance with accuracy 0.87, precise 0.88, recall 0.87, and F1-score 0.87. The dataset with 637 patients in this paper has serious imbalance problem on different molecular subtypes, and the the robust features that are generated by multimodel-based recursive feature eliminiation algorithm make the gradient boosting decision tree classifier have good behaviors. The recognition precision for the four molecular subtypes of luminal A, luminal B, HER-2, and basal-like are 0.91, 0.89, 0.83, and 0.87, respectively. Conclusions The improved lesion segmentation method gives more precise lesion edge, which not only saves the time of automatic extraction of lesion region of interest without threshold setting for each case, but also prevents the segmentation error by manual and prejudice from different radiologists. The feature selection algorithm of multimodel-based recursive feature elimination has the ability to find robust and optimal features that distinguish the four molecular subtypes from image phenotypes. The gradient boosting decision tree classifier rather plays a main role in recognition than other models used in this paper.
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46
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Li X, Yin G, Zhang Y, Dai D, Liu J, Chen P, Zhu L, Ma W, Xu W. Predictive Power of a Radiomic Signature Based on 18F-FDG PET/CT Images for EGFR Mutational Status in NSCLC. Front Oncol 2019; 9:1062. [PMID: 31681597 PMCID: PMC6803612 DOI: 10.3389/fonc.2019.01062] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 09/30/2019] [Indexed: 12/13/2022] Open
Abstract
Radiomics has become an area of interest for tumor characterization in 18F-Fluorodeoxyglucose positron emission tomography/computed tomography (18F-FDG PET/CT) imaging. The aim of the present study was to demonstrate how imaging phenotypes was connected to somatic mutations through an integrated analysis of 115 non-small cell lung cancer (NSCLC) patients with somatic mutation testings and engineered computed PET/CT image analytics. A total of 38 radiomic features quantifying tumor morphological, grayscale statistic, and texture features were extracted from the segmented entire-tumor region of interest (ROI) of the primary PET/CT images. The ensembles for boosting machine learning scheme were employed for classification, and the least absolute shrink age and selection operator (LASSO) method was used to select the most predictive radiomic features for the classifiers. A radiomic signature based on both PET and CT radiomic features outperformed individual radiomic features, the PET or CT radiomic signature, and the conventional PET parameters including the maximum standardized uptake value (SUVmax), SUVmean, SUVpeak, metabolic tumor volume (MTV), and total lesion glycolysis (TLG), in discriminating between mutant-type of epidermal growth factor receptor (EGFR) and wild-type of EGFR- cases with an AUC of 0.805, an accuracy of 80.798%, a sensitivity of 0.826 and a specificity of 0.783. Consistently, a combined radiomic signature with clinical factors exhibited a further improved performance in EGFR mutation differentiation in NSCLC. In conclusion, tumor imaging phenotypes that are driven by somatic mutations may be predicted by radiomics based on PET/CT images.
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Affiliation(s)
- Xiaofeng Li
- Department of Molecular Imaging and Nuclear Medicine, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China.,National Clinical Research Center for Cancer, Tianjin, China.,Key Laboratory of Cancer Prevention and Therapy, Tianjin, China.,Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Guotao Yin
- Department of Molecular Imaging and Nuclear Medicine, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China.,National Clinical Research Center for Cancer, Tianjin, China.,Key Laboratory of Cancer Prevention and Therapy, Tianjin, China.,Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Yufan Zhang
- Department of Molecular Imaging and Nuclear Medicine, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China.,National Clinical Research Center for Cancer, Tianjin, China.,Key Laboratory of Cancer Prevention and Therapy, Tianjin, China.,Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Dong Dai
- Department of Molecular Imaging and Nuclear Medicine, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China.,National Clinical Research Center for Cancer, Tianjin, China.,Key Laboratory of Cancer Prevention and Therapy, Tianjin, China.,Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Jianjing Liu
- Department of Molecular Imaging and Nuclear Medicine, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China.,National Clinical Research Center for Cancer, Tianjin, China.,Key Laboratory of Cancer Prevention and Therapy, Tianjin, China.,Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Peihe Chen
- Department of Molecular Imaging and Nuclear Medicine, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China.,National Clinical Research Center for Cancer, Tianjin, China.,Key Laboratory of Cancer Prevention and Therapy, Tianjin, China.,Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Lei Zhu
- Department of Molecular Imaging and Nuclear Medicine, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China.,National Clinical Research Center for Cancer, Tianjin, China.,Key Laboratory of Cancer Prevention and Therapy, Tianjin, China.,Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Wenjuan Ma
- National Clinical Research Center for Cancer, Tianjin, China.,Key Laboratory of Cancer Prevention and Therapy, Tianjin, China.,Tianjin's Clinical Research Center for Cancer, Tianjin, China.,Department of Breast Imaging, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Wengui Xu
- Department of Molecular Imaging and Nuclear Medicine, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China.,National Clinical Research Center for Cancer, Tianjin, China.,Key Laboratory of Cancer Prevention and Therapy, Tianjin, China.,Tianjin's Clinical Research Center for Cancer, Tianjin, China
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47
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Leithner D, Horvat JV, Marino MA, Bernard-Davila B, Jochelson MS, Ochoa-Albiztegui RE, Martinez DF, Morris EA, Thakur S, Pinker K. Radiomic signatures with contrast-enhanced magnetic resonance imaging for the assessment of breast cancer receptor status and molecular subtypes: initial results. Breast Cancer Res 2019; 21:106. [PMID: 31514736 PMCID: PMC6739929 DOI: 10.1186/s13058-019-1187-z] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 08/14/2019] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND To evaluate the diagnostic performance of radiomic signatures extracted from contrast-enhanced magnetic resonance imaging (CE-MRI) for the assessment of breast cancer receptor status and molecular subtypes. METHODS One hundred and forty-three patients with biopsy-proven breast cancer who underwent CE-MRI at 3 T were included in this IRB-approved HIPAA-compliant retrospective study. The training dataset comprised 91 patients (luminal A, n = 49; luminal B, n = 8; HER2-enriched, n = 11; triple negative, n = 23), while the validation dataset comprised 52 patients from a second institution (luminal A, n = 17; luminal B, n = 17; triple negative, n = 18). Radiomic analysis of manually segmented tumors included calculation of features derived from the first-order histogram (HIS), co-occurrence matrix (COM), run-length matrix (RLM), absolute gradient (GRA), autoregressive model (ARM), discrete Haar wavelet transform (WAV), and lesion geometry (GEO). Fisher, probability of error and average correlation (POE + ACC), and mutual information coefficients were used for feature selection. Linear discriminant analysis followed by k-nearest neighbor classification (with leave-one-out cross-validation) was used for pairwise radiomic-based separation of receptor status and molecular subtypes. Histopathology served as the standard of reference. RESULTS In the training dataset, radiomic signatures yielded the following accuracies > 80%: luminal B vs. luminal A, 84.2% (mainly based on COM features); luminal B vs. triple negative, 83.9% (mainly based on GEO features); luminal B vs. all others, 89% (mainly based on COM features); and HER2-enriched vs. all others, 81.3% (mainly based on COM features). Radiomic signatures were successfully validated in the separate validation dataset for luminal A vs. luminal B (79.4%) and luminal B vs. triple negative (77.1%). CONCLUSIONS In this preliminary study, radiomic signatures with CE-MRI enable the assessment of breast cancer receptor status and molecular subtypes with high diagnostic accuracy. These results need to be confirmed in future larger studies.
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Affiliation(s)
- Doris Leithner
- Department of Radiology, Breast Imaging Service, Memorial Sloan Kettering Cancer Center, 300 E 66th St, 7th Floor, New York, NY, 10065, USA.,Department of Diagnostic and Interventional Radiology, University Hospital Frankfurt, Frankfurt, Germany
| | - Joao V Horvat
- Department of Radiology, Breast Imaging Service, Memorial Sloan Kettering Cancer Center, 300 E 66th St, 7th Floor, New York, NY, 10065, USA
| | - Maria Adele Marino
- Department of Radiology, Breast Imaging Service, Memorial Sloan Kettering Cancer Center, 300 E 66th St, 7th Floor, New York, NY, 10065, USA.,Department of Biomedical Sciences and Morphologic and Functional Imaging, University of Messina, Messina, Italy
| | - Blanca Bernard-Davila
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Maxine S Jochelson
- Department of Radiology, Breast Imaging Service, Memorial Sloan Kettering Cancer Center, 300 E 66th St, 7th Floor, New York, NY, 10065, USA
| | - R Elena Ochoa-Albiztegui
- Department of Radiology, Breast Imaging Service, Memorial Sloan Kettering Cancer Center, 300 E 66th St, 7th Floor, New York, NY, 10065, USA
| | - Danny F Martinez
- Department of Radiology, Breast Imaging Service, Memorial Sloan Kettering Cancer Center, 300 E 66th St, 7th Floor, New York, NY, 10065, USA
| | - Elizabeth A Morris
- Department of Radiology, Breast Imaging Service, Memorial Sloan Kettering Cancer Center, 300 E 66th St, 7th Floor, New York, NY, 10065, USA
| | - Sunitha Thakur
- Department of Medical Physics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Katja Pinker
- Department of Radiology, Breast Imaging Service, Memorial Sloan Kettering Cancer Center, 300 E 66th St, 7th Floor, New York, NY, 10065, USA. .,Department of Biomedical Imaging and Image-guided Therapy, Division of Molecular and Gender Imaging, Medical University Vienna, Vienna, Austria.
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48
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Sheth D, Giger ML. Artificial intelligence in the interpretation of breast cancer on MRI. J Magn Reson Imaging 2019; 51:1310-1324. [PMID: 31343790 DOI: 10.1002/jmri.26878] [Citation(s) in RCA: 89] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 07/08/2019] [Indexed: 12/13/2022] Open
Abstract
Advances in both imaging and computers have led to the rise in the potential use of artificial intelligence (AI) in various tasks in breast imaging, going beyond the current use in computer-aided detection to include diagnosis, prognosis, response to therapy, and risk assessment. The automated capabilities of AI offer the potential to enhance the diagnostic expertise of clinicians, including accurate demarcation of tumor volume, extraction of characteristic cancer phenotypes, translation of tumoral phenotype features to clinical genotype implications, and risk prediction. The combination of image-specific findings with the underlying genomic, pathologic, and clinical features is becoming of increasing value in breast cancer. The concurrent emergence of newer imaging techniques has provided radiologists with greater diagnostic tools and image datasets to analyze and interpret. Integrating an AI-based workflow within breast imaging enables the integration of multiple data streams into powerful multidisciplinary applications that may lead the path to personalized patient-specific medicine. In this article we describe the goals of AI in breast cancer imaging, in particular MRI, and review the literature as it relates to the current application, potential, and limitations in breast cancer. Level of Evidence: 3 Technical Efficacy: Stage 3 J. Magn. Reson. Imaging 2020;51:1310-1324.
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Affiliation(s)
- Deepa Sheth
- Department of Radiology, University of Chicago, Chicago, Illinois, USA
| | - Maryellen L Giger
- Department of Radiology, University of Chicago, Chicago, Illinois, USA
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49
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Reig B, Heacock L, Geras KJ, Moy L. Machine learning in breast MRI. J Magn Reson Imaging 2019; 52:998-1018. [PMID: 31276247 DOI: 10.1002/jmri.26852] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 06/18/2019] [Accepted: 06/19/2019] [Indexed: 12/13/2022] Open
Abstract
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.
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Affiliation(s)
- Beatriu Reig
- The Department of Radiology, New York University School of Medicine, New York, New York, USA
| | - Laura Heacock
- Bernard and Irene Schwartz Center for Biomedical Imaging, Department of Radiology, New York University School of Medicine, New York, New York, USA
| | - Krzysztof J Geras
- Bernard and Irene Schwartz Center for Biomedical Imaging, Department of Radiology, New York University School of Medicine, New York, New York, USA
| | - Linda Moy
- Bernard and Irene Schwartz Center for Biomedical Imaging, Department of Radiology, New York University School of Medicine, New York, New York, USA.,Center for Advanced Imaging Innovation and Research (CAI2 R), New York University School of Medicine, New York, New York, USA
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50
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Zhu Z, Albadawy E, Saha A, Zhang J, Harowicz MR, Mazurowski MA. Deep learning for identifying radiogenomic associations in breast cancer. Comput Biol Med 2019; 109:85-90. [PMID: 31048129 DOI: 10.1016/j.compbiomed.2019.04.018] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 03/05/2019] [Accepted: 04/20/2019] [Indexed: 11/27/2022]
Abstract
RATIONALE AND OBJECTIVES To determine whether deep learning models can distinguish between breast cancer molecular subtypes based on dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI). MATERIALS AND METHODS In this institutional review board-approved single-center study, we analyzed DCE-MR images of 270 patients at our institution. Lesions of interest were identified by radiologists. The task was to automatically determine whether the tumor is of the Luminal A subtype or of another subtype based on the MR image patches representing the tumor. Three different deep learning approaches were used to classify the tumor according to their molecular subtypes: learning from scratch where only tumor patches were used for training, transfer learning where networks pre-trained on natural images were fine-tuned using tumor patches, and off-the-shelf deep features where the features extracted by neural networks trained on natural images were used for classification with a support vector machine. Network architectures utilized in our experiments were GoogleNet, VGG, and CIFAR. We used 10-fold crossvalidation method for validation and area under the receiver operating characteristic (AUC) as the measure of performance. RESULTS The best AUC performance for distinguishing molecular subtypes was 0.65 (95% CI:[0.57,0.71]) and was achieved by the off-the-shelf deep features approach. The highest AUC performance for training from scratch was 0.58 (95% CI:[0.51,0.64]) and the best AUC performance for transfer learning was 0.60 (95% CI:[0.52,0.65]) respectively. For the off-the-shelf approach, the features extracted from the fully connected layer performed the best. CONCLUSION Deep learning may play a role in discovering radiogenomic associations in breast cancer.
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Affiliation(s)
- Zhe Zhu
- Department of Radiology, Duke University, USA.
| | | | | | - Jun Zhang
- Department of Radiology, Duke University, USA.
| | | | - Maciej A Mazurowski
- Department of Radiology and Department of Electrical and Computer Engineering, Duke University, USA.
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