Radiomic Model for Determining the Value of Elasticity and Grayscale Ultrasound Diagnoses for Predicting BRAFV600E Mutations in Papillary Thyroid Carcinoma

Ultrasound-based radiogenomics: status, applications, and future direction

Radiogenomics, an extension of radiomics, explores the relationship between imaging features and underlying gene expression patterns. This field is instrumental in providing reliable imaging surrogates, thus potentially representing an alternative to genetic testing. The rapidly growing area of radiogenomics that utilizes ultrasound (US) imaging seeks to elucidate the connections between US image characteristics and genomic data. In this review, the authors outline the radiogenomics workflow and summarize the applications of US-based radiogenomics. These include the prediction of gene variations, molecular subtypes, and other biological characteristics, as well as the exploration of the relationships between US phenotypes and cancer gene profiles. Although the field faces various challenges, US-based radiogenomics offers promising prospects and avenues for future research.

Quantitative ultrasound radiomics analysis to evaluate lymph nodes in patients with cancer: a systematic review

This systematic review aims to evaluate the role of ultrasound (US) radiomics in assessing lymphadenopathy in patients with cancer and the ability of radiomics to predict metastatic lymph node involvement. A systematic literature search was performed in the PubMed (MEDLINE), Cochrane Central Register of Controlled Trials (CENTRAL), and EMBASE (Ovid) databases up to June 13, 2023. 42 articles were included in which the lymph node mass was assessed with a US exam, and the analysis was performed using radiomics methods. From the survey of the selected articles, experimental evidence suggests that radiomics features extracted from US images can be a useful tool for predicting and characterizing lymphadenopathy in patients with breast, head and neck, and cervical cancer. This noninvasive and effective method allows the extraction of important information beyond mere morphological characteristics, extracting features that may be related to lymph node involvement. Future studies are needed to investigate the role of US-radiomics in other types of cancers, such as melanoma.

Research on ultrasound-based radiomics: a bibliometric analysis

Background

A large number of studies related to ultrasound-based radiomics have been published in recent years; however, a systematic bibliometric analysis of this topic has not yet been conducted. In this study, we attempted to identify the hotspots and frontiers in ultrasound-based radiomics through bibliometrics and to systematically characterize the overall framework and characteristics of studies through mapping and visualization.

Methods

A literature search was carried out in Web of Science Core Collection (WoSCC) database from January 2016 to December 2023 according to a predetermined search formula. Bibliometric analysis and visualization of the results were performed using CiteSpace, VOSviewer, R, and other platforms.

Results

Ultimately, 466 eligible papers were included in the study. Publication trend analysis showed that the annual publication trend of journals in ultrasound-based radiomics could be divided into three phases: there were no more than five documents published in this field in any year before 2018, a small yearly increase in the number of annual publications occurred between 2018 and 2022, and a high, stable number of publications appeared after 2022. In the analysis of publication sources, China was found to be the main contributor, with a much higher number of publications than other countries, and was followed by the United States and Italy. Frontiers in Oncology was the journal with the highest number of papers in this field, publishing 60 articles. Among the academic institutions, Fudan University, Sun Yat-sen University, and the Chinese Academy of Sciences ranked as the top three in terms of the number of documents. In the analysis of authors and cocited authors, the author with the most publications was Yuanyuan Wang, who has published 19 articles in 8 years, while Philippe Lambin was the most cited author, with 233 citations. Visualization of the results from the cocitation analysis of the literature revealed a strong centrality of the subject terms papillary thyroid cancer, biological behavior, potential biomarkers, and comparative assessment, which may be the main focal points of research in this subject. Based on the findings of the keyword analysis and cluster analysis, the keywords can be categorized into two major groups: (I) technological innovations that enable the construction of radiomics models such as machine learning and deep learning and (II) applications of predictive models to support clinical decision-making in certain diseases, such as papillary thyroid cancer, hepatocellular carcinoma (HCC), and breast cancer.

Conclusions

Ultrasound-based radiomics has received widespread attention in the medical field and has been gradually been applied in clinical research. Radiomics, a relatively late development in medical technology, has made substantial contributions to the diagnosis, prediction, and prognostic evaluation of diseases. Additionally, the coupling of artificial intelligence techniques with ultrasound imaging has yielded a number of promising tools that facilitate clinical decision-making and enable the practice of precision medicine. Finally, the development of ultrasound-based radiomics requires multidisciplinary cooperation and joint efforts from the field biomedicine, information technology, statistics, and clinical medicine.

Ultrasound radiomics based XGBoost model to differential diagnosis thyroid nodules and unnecessary biopsy rate: Individual application of SHapley additive exPlanations

OBJECTIVES

Radiomics-based eXtreme gradient boosting (XGBoost) model was developed to differentiate benign thyroid nodules from malignant thyroid nodules and to prevent unnecessary thyroid biopsies, including positive and negative effects.

METHODS

The study evaluated a data set of ultrasound images of thyroid nodules in patients retrospectively, who initially received ultrasound-guided fine-needle aspiration biopsy (FNAB) for diagnostic purposes. According to ACR TI-RADS, a total of five ultrasound feature categories and the maximum size of the nodule were determined by four radiologists. A radiomics score was developed by the LASSO algorithm from the ultrasound-based radiomics features. An interpretative method based on Shapley additive explanation (SHAP) was developed. XGBoost was compared with ACR TI-RADS for its diagnostic performance and FNAB rate and was compared with six other machine learning models to evaluate the model performance.

RESULTS

Finally, 191 thyroid nodules were examined from 177 patients. The radiomics score were calculated using 8 features, which were selected among 789 candidate features generated from the ultrasound images. The model yielded an AUC of 93% in the training cohort and 92% in the test cohort. It outperformed traditional machine learning models in assessing the nature of thyroid nodules. Compared with ACR TI-RADS, the FNAB rate decreased from 34% to 30% in training and from 35% to 41% in test.

CONCLUSIONS

The radiomics-based XGBoost model proposed could distinguish benign and malignant thyroid nodules, thereby reduced significantly the number of unnecessary FNAB. It was effective in making preoperative decisions and managing selected patients using the SHAP visual interpretation tools.

Radiomics-based ultrasound models for thyroid nodule differentiation in Hashimoto's thyroiditis

Background

Previous models for differentiating benign and malignant thyroid nodules(TN) have predominantly focused on the characteristics of the nodules themselves, without considering the specific features of the thyroid gland(TG) in patients with Hashimoto's thyroiditis(HT). In this study, we analyzed the clinical and ultrasound radiomics(USR) features of TN in patients with HT and constructed a model for differentiating benign and malignant nodules specifically in this population.

Methods

We retrospectively collected clinical and ultrasound data from 227 patients with TN and concomitant HT(161 for training, 66 for testing). Two experienced sonographers delineated the TG and TN regions, and USR features were extracted using Python. Lasso regression and logistic analysis were employed to select relevant USR features and clinical data to construct the model for differentiating benign and malignant TN. The performance of the model was evaluated using area under the curve(AUC), calibration curves, and decision curve analysis(DCA).

Results

A total of 1,162 USR features were extracted from TN and the TG in the 227 patients with HT. Lasso regression identified 14 features, which were used to construct the TN score, TG score, and TN+TG score. Univariate analysis identified six clinical predictors: TI-RADS, echoic type, aspect ratio, boundary, calcification, and thyroid function. Multivariable analysis revealed that incorporating USR scores improved the performance of the model for differentiating benign and malignant TN in patients with HT. Specifically, the TN+TG score resulted in the highest increase in AUC(from 0.83 to 0.94) in the clinical prediction model. Calibration curves and DCA demonstrated higher accuracy and net benefit for the TN+TG+clinical model.

Conclusion

USR features of both the TG and TN can be utilized for differentiating benign and malignant TN in patients with HT. These findings highlight the importance of considering the entire TG in the evaluation of TN in HT patients, providing valuable insights for clinical decision-making in this population.

Predicting BRAFV600E mutations in papillary thyroid carcinoma using six machine learning algorithms based on ultrasound elastography

The most common BRAF mutation is thymine (T) to adenine (A) missense mutation in nucleotide 1796 (T1796A, V600E). The BRAFV600E gene encodes a protein-dependent kinase (PDK), which is a key component of the mitogen-activated protein kinase pathway and essential for controlling cell proliferation, differentiation, and death. The BRAFV600E mutation causes PDK to be activated improperly and continuously, resulting in abnormal proliferation and differentiation in PTC. Based on elastography ultrasound (US) radiomic features, this study seeks to create and validate six distinct machine learning algorithms to predict BRAFV6OOE mutation in PTC patients prior to surgery. This study employed routine US strain elastography image data from 138 PTC patients. The patients were separated into two groups: those who did not have the BRAFV600E mutation (n = 75) and those who did have the mutation (n = 63). The patients were randomly assigned to one of two data sets: training (70%), or validation (30%). From strain elastography US images, a total of 479 radiomic features were retrieved. Pearson's Correlation Coefficient (PCC) and Recursive Feature Elimination (RFE) with stratified tenfold cross-validation were used to decrease the features. Based on selected radiomic features, six machine learning algorithms including support vector machine with the linear kernel (SVM_L), support vector machine with radial basis function kernel (SVM_RBF), logistic regression (LR), Naïve Bayes (NB), K-nearest neighbors (KNN), and linear discriminant analysis (LDA) were compared to predict the possibility of BRAFV600E. The accuracy (ACC), the area under the curve (AUC), sensitivity (SEN), specificity (SPEC), positive predictive value (PPV), negative predictive value (NPV), decision curve analysis (DCA), and calibration curves of the machine learning algorithms were used to evaluate their performance. ① The machine learning algorithms' diagnostic performance depended on 27 radiomic features. ② AUCs for NB, KNN, LDA, LR, SVM_L, and SVM_RBF were 0.80 (95% confidence interval [CI]: 0.65-0.91), 0.87 (95% CI 0.73-0.95), 0.91(95% CI 0.79-0.98), 0.92 (95% CI 0.80-0.98), 0.93 (95% CI 0.80-0.98), and 0.98 (95% CI 0.88-1.00), respectively. ③ There was a significant difference in echogenicity,vertical and horizontal diameter ratios, and elasticity between PTC patients with BRAFV600E and PTC patients without BRAFV600E. Machine learning algorithms based on US elastography radiomic features are capable of predicting the likelihood of BRAFV600E in PTC patients, which can assist physicians in identifying the risk of BRAFV600E in PTC patients. Among the six machine learning algorithms, the support vector machine with radial basis function (SVM_RBF) achieved the best ACC (0.93), AUC (0.98), SEN (0.95), SPEC (0.90), PPV (0.91), and NPV (0.95).

Update on the Applications of Radiomics in Diagnosis, Staging, and Recurrence of Intrahepatic Cholangiocarcinoma

BACKGROUND

This paper offers an assessment of radiomics tools in the evaluation of intrahepatic cholangiocarcinoma.

METHODS

The PubMed database was searched for papers published in the English language no earlier than October 2022.

RESULTS

We found 236 studies, and 37 satisfied our research criteria. Several studies addressed multidisciplinary topics, especially diagnosis, prognosis, response to therapy, and prediction of staging (TNM) or pathomorphological patterns. In this review, we have covered diagnostic tools developed through machine learning, deep learning, and neural network for the recurrence and prediction of biological characteristics. The majority of the studies were retrospective.

CONCLUSIONS

It is possible to conclude that many performing models have been developed to make differential diagnosis easier for radiologists to predict recurrence and genomic patterns. However, all the studies were retrospective, lacking further external validation in prospective and multicentric cohorts. Furthermore, the radiomics models and the expression of results should be standardized and automatized to be applicable in clinical practice.

Clinical-Radiomics Nomogram Based on Contrast-Enhanced Ultrasound for Preoperative Prediction of Cervical Lymph Node Metastasis in Papillary Thyroid Carcinoma

This study aimed to establish a new clinical-radiomics nomogram based on ultrasound (US) for cervical lymph node metastasis (LNM) in papillary thyroid carcinoma (PTC). We collected 211 patients with PTC between June 2018 and April 2020, then we randomly divided these patients into the training set (n = 148) and the validation set (n = 63). 837 radiomics features were extracted from B-mode ultrasound (BMUS) images and contrast-enhanced ultrasound (CEUS) images. The maximum relevance minimum redundancy (mRMR) algorithm, least absolute shrinkage and selection operator (LASSO) algorithm, and backward stepwise logistic regression (LR) were applied to select key features and establish a radiomics score (Radscore), including BMUS Radscore and CEUS Radscore. The clinical model and clinical-radiomics model were established using the univariate analysis and multivariate backward stepwise LR. The clinical-radiomics model was finally presented as a clinical-radiomics nomogram, the performance of which was evaluated by the receiver operating characteristic curves, Hosmer-Lemeshow test, calibration curves, and decision curve analysis (DCA). The results show that the clinical-radiomics nomogram was constructed by four predictors, including gender, age, US-reported LNM, and CEUS Radscore. The clinical-radiomics nomogram performed well in both the training set (AUC = 0.820) and the validation set (AUC = 0.814). The Hosmer-Lemeshow test and the calibration curves demonstrated good calibration. The DCA showed that the clinical-radiomics nomogram had satisfactory clinical utility. The clinical-radiomics nomogram constructed by CEUS Radscore and key clinical features can be used as an effective tool for individualized prediction of cervical LNM in PTC.

Ultrasound images-based deep learning radiomics nomogram for preoperative prediction of RET rearrangement in papillary thyroid carcinoma

PURPOSE

To create an ultrasound -based deep learning radiomics nomogram (DLRN) for preoperatively predicting the presence of RET rearrangement among patients with papillary thyroid carcinoma (PTC).

METHODS

We retrospectively enrolled 650 patients with PTC. Patients were divided into the RET/PTC rearrangement group (n = 103) and the non-RET/PTC rearrangement group (n = 547). Radiomics features were extracted based on hand-crafted features from the ultrasound images, and deep learning networks were used to extract deep transfer learning features. The least absolute shrinkage and selection operator regression was applied to select the features of nonzero coefficients from radiomics and deep transfer learning features; then, we established the deep learning radiomics signature. DLRN was constructed using a logistic regression algorithm by combining clinical and deep learning radiomics signatures. The prediction performance was evaluated using the receiver operating characteristic curve, calibration curve, and decision curve analysis.

RESULTS

Comparing the effectiveness of the models by linking the area under the receiver operating characteristic curve of each model, we found that the area under the curve of DLRN could reach 0.9545 (95% confidence interval: 0.9133-0.9558) in the test cohort and 0.9396 (95% confidence interval: 0.9185-0.9607) in the training cohort, indicating that the model has an excellent performance in predicting RET rearrangement in PTC. The decision curve analysis demonstrated that the combined model was clinically useful.

CONCLUSION

The novel ultrasonic-based DLRN has an important clinical value for predicting RET rearrangement in PTC. It can provide physicians with a preoperative non-invasive primary screening method for RET rearrangement diagnosis, thus facilitating targeted patients with purposeful molecular sequencing to avoid unnecessary medical investment and improve treatment outcomes.