Dataset Information

Predicting EGFR mutation status in lung adenocarcinoma: development and validation of a computed tomography-based radiomics signature.

ABSTRACT: Patients with epidermal growth factor receptor (EGFR) mutations in lung adenocarcinoma can benefit from targeted therapy. However, noninvasively determination of EGFR mutation status before targeted therapy remains a challenge. This study constructed a nomogram based on a combination of radiomics features with the clinical and radiological features to predict the EGFR mutation status. The least absolute shrinkage and selection operator (LASSO) and Wilcoxon test were used for feature selection. Decision tree (DT), logistic regression (LR), and support vector machine (SVM) classifiers were used for radiomics model building. Used the clinical and radiological features establish clinical-radiology (C-R) model. The C-R model with the best radiomics model to establish clinical-radiological-radiomics (C-R-R) model. The predictive performance of the model was evaluated by ROC and calibration curves, and the clinical usefulness was assessed by a decision curve analysis. The current study showed that twelve radiomics features were significantly associated with EGFR mutations. The best radiomics signature model was obtained using the SVM classifier. The C-R-R model had the best distinguishing ability for predicting the EGFR mutation status, with an AUC of 0.849 (95% CI, 0.805-0.893) and 0.835 (95% CI, 0.761-0.909) in the development and validation cohorts, respectively. Our study provides a non-invasive C-R-R model that combines CT-based radiomics features with clinical and radiological features, which can provide useful image-based biological information for targeted therapy candidates.

SUBMITTER: Zhang G

PROVIDER: S-EPMC7868761 | biostudies-literature | 2021

REPOSITORIES: biostudies-literature

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Predicting <i>EGFR</i> mutation status in lung adenocarcinoma: development and validation of a computed tomography-based radiomics signature.

Zhang Guojin G Cao Yuntai Y Zhang Jing J Ren Jialiang J Zhao Zhiyong Z Zhang Xiaodi X Li Shenglin S Deng Liangna L Zhou Junlin J

American journal of cancer research 20210201 2

Patients with epidermal growth factor receptor (EGFR) mutations in lung adenocarcinoma can benefit from targeted therapy. However, noninvasively determination of EGFR mutation status before targeted therapy remains a challenge. This study constructed a nomogram based on a combination of radiomics features with the clinical and radiological features to predict the EGFR mutation status. The least absolute shrinkage and selection operator (LASSO) and Wilcoxon test were used for feature selection. D ...[more]

PMID: 33575086

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Project description:IntroductionMolecular markers are important variables in the selection of treatment for cancer patients and highly associated with their survival. Therefore, a nomogram that can predict survival probability by incorporating epidermal growth factor receptor mutation status and treatments for patients with advanced adenocarcinoma would be highly valuable. The aim of the study is to develop and validate a novel nomogram, incorporating epidermal growth factor receptor mutation status and treatments, for predicting 1-year and 2-year survival probability of patients with advanced adenocarcinoma.Material and methodsData on 13,043 patients between June 1, 2011, and December 31, 2014 were collected. Seventy percent of them were randomly assigned to the training cohort for nomogram development, and the remaining 30% assigned to the validation cohort. The most important factors for constructing the nomogram were identified using multivariable Cox regression analysis. The discriminative ability and calibration of the nomograms were tested using C-statistics, calibration plots, and Kaplan-Meier curves.ResultsIn the training cohort, 1-year and 2-year OS were 52.8% and 28.5% in EGFR(-) patients, and 73.9% and 44.1% in EGFR(+) patients, respectively. In EGFR(+) group, factors selected were age, gender, congestive heart failure, renal disease, number of lymph node examined, tumor stage, surgical intervention, radiotherapy, first-line chemotherapy, ECOG performance status, malignant pleural effusion, and smoking. In EGFR(-) group, factors selected were age, gender, myocardial infarction, cerebrovascular disease, chronic pulmonary disease, number of lymph node examined, tumor stage, surgical intervention, radiotherapy, ECOG performance status, malignant pleural effusion, and a history of smoking. Two nomograms show good accuracy in predicting OS, with a concordance index of 0.83 in EGFR(+) and of 0.88 in EGFR(-).ConclusionsThe survival prediction models can be used to make individualized predictions with different EGFR mutation status and a useful tool for selecting regimens for treating advanced adenocarcinoma.

Project description:To recognize the epidermal growth factor receptor (EGFR) gene mutation status in lung adenocarcinoma (LADC) has become a prerequisite of deciding whether EGFR-tyrosine kinase inhibitor (EGFR-TKI) medicine can be used. Polymerase chain reaction assay or gene sequencing is for measuring EGFR status, however, the tissue samples by surgery or biopsy are required. We propose to develop deep learning models to recognize EGFR status by using radiomics features extracted from non-invasive CT images. Preoperative CT images, EGFR mutation status and clinical data have been collected in a cohort of 709 patients (the primary cohort) and an independent cohort of 205 patients. After 1,037 CT-based radiomics features are extracted from each lesion region, 784 discriminative features are selected for analysis and construct a feature mapping. One Squeeze-and-Excitation (SE) Convolutional Neural Network (SE-CNN) has been designed and trained to recognize EGFR status from the radiomics feature mapping. SE-CNN model is trained and validated by using 638 patients from the primary cohort, tested by using the rest 71 patients (the internal test cohort), and further tested by using the independent 205 patients (the external test cohort). Furthermore, SE-CNN model is compared with machine learning (ML) models using radiomics features, clinical features, and both features. EGFR(-) patients show the smaller age, higher odds of female, larger lesion volumes, and lower odds of subtype of acinar predominant adenocarcinoma (APA), compared with EGFR(+). The most discriminative features are for texture (614, 78.3%) and the features of first order of intensity (158, 20.1%) and the shape features (12, 1.5%) follow. SE-CNN model can recognize EGFR mutation status with an AUC of 0.910 and 0.841 for the internal and external test cohorts, respectively. It outperforms the CNN model without SE, the fine-tuned VGG16 and VGG19, three ML models, and the state-of-art models. Utilizing radiomics feature mapping extracted from non-invasive CT images, SE-CNN can precisely recognize EGFR mutation status of LADC patients. The proposed method combining radiomics features and deep leaning is superior to ML methods and can be expanded to other medical applications. The proposed SE-CNN model may help make decision on usage of EGFR-TKI medicine.

Project description:BackgroundClear cell renal cell carcinoma (ccRCC) is the most common renal cancer and it has the worst prognosis among all renal cancers. However, traditional radiological characteristics on computed tomography (CT) scans of ccRCC have been insufficient to predict the pathological grade of ccRCC before surgery.MethodsPatients with ccRCC were retrospectively enrolled into this study and were separated into two groups according to the World Health Organization (WHO)/International Society of Urological Pathology (ISUP) grading system, i.e., low-grade (Grade I and II) group and high-grade (Grade III and IV) group. Traditional CT radiological characteristics such as tumor size, pre- and post-enhancing CT densities were assessed. In addition, radiomic texture analysis based on the CT imaging of the ccRCC were also performed. A CT-based machine learning method combining the traditional radiological characteristics and radiomic features was used in the predictive modeling for differentiating the low-grade from the high-grade ccRCC. Model performance was evaluated with the receiver operating characteristic curve (ROC) analysis.ResultsA total of 264 patients with pathologically confirmed ccRCC were included in this study. In this cohort, 206 patients had the low-grade tumors and 58 had the high-grade tumors. The model built with traditional radiological characteristics achieved an area under the curve (AUC) of 0.9175 (95% CI: 0.8765-0.9585) and 0.8088 (95% CI: 0.7064-0.9113) in differentiating the low-grade from the high-grade ccRCC for the training cohort and the validation cohort respectively. The model built with the radiomic textural features yielded an AUC value of 0.8170 (95% CI: 0.7353-0.8987) and 0.8017 (95% CI: 0.6878-0.9157) for the training cohort and the validation cohort, respectively. The combined model integrating both the traditional radiological characteristics and the radiomic textural features achieved the highest efficacy, with an AUC of 0.9235 (95% CI: 0.8646-0.9824) and an AUC of 0.9099 (95% CI: 0.8324-0.9873) for the training cohort and validation cohort, respectively.ConclusionWe developed a machine learning radiomic model achieving a satisfying performance in differentiating the low-grade from the high-grade ccRCC. Our study presented a potentially useful non-invasive imaging-focused method to predict the pathological grade of renal cancers prior to surgery.

Project description:ObjectiveConsidering the essential role of KRAS mutation in NSCLC and the limited experience of PET radiomic features in KRAS mutation, a prediction model was built in our current analysis. Our model aims to evaluate the status of KRAS mutants in lung adenocarcinoma by combining PET radiomics and machine learning.MethodPatients were retrospectively selected from our database and screened from the NSCLC radiogenomic dataset from TCIA. The dataset was randomly divided into three subgroups. Two open-source software programs, 3D Slicer and Python, were used to segment lung tumours and extract radiomic features from 18F-FDG-PET images. Feature selection was performed by the Mann-Whitney U test, Spearman's rank correlation coefficient, and RFE. Logistic regression was used to build the prediction models. AUCs from ROCs were used to compare the predictive abilities of the models. Calibration plots were obtained to examine the agreements of observed and predictive values in the validation and testing groups. DCA curves were performed to check the clinical impact of the best model. Finally, a nomogram was obtained to present the selected model.ResultsOne hundred and nineteen patients with lung adenocarcinoma were included in our study. The whole group was divided into three datasets: a training set (n = 96), a validation set (n = 11), and a testing set (n = 12). In total, 1781 radiomic features were extracted from PET images. One hundred sixty-three predictive models were established according to each original feature group and their combinations. After model comparison and selection, one model, including wHLH_fo_IR, wHLH_glrlm_SRHGLE, wHLH_glszm_SAHGLE, and smoking habits, was validated with the highest predictive value. The model obtained AUCs of 0.731 (95% CI: 0.619~0.843), 0.750 (95% CI: 0.248~1.000), and 0.750 (95% CI: 0.448~1.000) in the training set, the validation set and the testing set, respectively. Results from calibration plots in validation and testing groups indicated that there was no departure between observed and predictive values in the two datasets (p = 0.377 and 0.861, respectively).ConclusionsOur model combining 18F-FDG-PET radiomics and machine learning indicated a good predictive ability of KRAS status in lung adenocarcinoma. It may be a helpful non-invasive method to screen the KRAS mutation status of heterogenous lung adenocarcinoma before selected biopsy sampling.

Project description:Vulnerable carotid atherosclerotic plaque (CAP) significantly contributes to ischemic stroke. Neovascularization within plaques is an emerging biomarker linked to plaque vulnerability that can be detected using contrast-enhanced ultrasound (CEUS). Computed tomography angiography (CTA) is a common method used in clinical cerebrovascular assessments that can be employed to evaluate the vulnerability of CAPs. Radiomics is a technique that automatically extracts radiomic features from images. This study aimed to identify radiomic features associated with the neovascularization of CAP and construct a prediction model for CAP vulnerability based on radiomic features. CTA data and clinical data of patients with CAPs who underwent CTA and CEUS between January 2018 and December 2021 in Beijing Hospital were retrospectively collected. The data were divided into a training cohort and a testing cohort using a 7:3 split. According to the examination of CEUS, CAPs were dichotomized into vulnerable and stable groups. 3D Slicer software was used to delineate the region of interest in CTA images, and the Pyradiomics package was used to extract radiomic features in Python. Machine learning algorithms containing logistic regression (LR), support vector machine (SVM), random forest (RF), light gradient boosting machine (LGBM), adaptive boosting (AdaBoost), extreme gradient boosting (XGBoost), and multi-layer perception (MLP) were used to construct the models. The confusion matrix, receiver operating characteristic (ROC) curve, accuracy, precision, recall, and f-1 score were used to evaluate the performance of the models. A total of 74 patients with 110 CAPs were included. In all, 1,316 radiomic features were extracted, and 10 radiomic features were selected for machine-learning model construction. After evaluating several models on the testing cohorts, it was discovered that model_RF outperformed the others, achieving an AUC value of 0.93 (95% CI: 0.88-0.99). The accuracy, precision, recall, and f-1 score of model_RF in the testing cohort were 0.85, 0.87, 0.85, and 0.85, respectively. Radiomic features associated with the neovascularization of CAP were obtained. Our study highlights the potential of radiomics-based models for improving the accuracy and efficiency of diagnosing vulnerable CAP. In particular, the model_RF, utilizing radiomic features extracted from CTA, provides a noninvasive and efficient method for accurately predicting the vulnerability status of CAP. This model shows great potential for offering clinical guidance for early detection and improving patient outcomes.

Dataset Information

Predicting EGFR mutation status in lung adenocarcinoma: development and validation of a computed tomography-based radiomics signature.

Publications

Predicting <i>EGFR</i> mutation status in lung adenocarcinoma: development and validation of a computed tomography-based radiomics signature.

Similar Datasets

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