Dataset Information

Nomogram based on preoperative CT imaging predicts the EGFR mutation status in lung adenocarcinoma.

ABSTRACT: Tyrosine kinase inhibitors (TKIs) provide clinical benefits to the lung cancer patients with epidermal growth factor receptor (EGFR) mutations. However, non-invasively determine EGFR mutation status in patients before targeted therapy remains a challenge. This study aimed to develop and validate a nomogram for preoperative prediction of EGFR mutation status in patients with lung adenocarcinoma. The medical records of 403 patients with lung adenocarcinoma confirmed by histology from January 2016 to June 2020 were retrospectively collected. We combined CT features and clinical risk factors and used them to build a prediction nomogram. The performance of the nomogram was evaluated in terms of calibration, discrimination, and clinical usefulness. The nomogram was further validated in an independent external cohort. Finally, a nomogram that contained CT features and clinical risk factors, which could conveniently and non-invasively predict EGFR mutation status in patients with lung adenocarcinoma before surgery.

SUBMITTER: Zhang G

PROVIDER: S-EPMC7691609 | biostudies-literature | 2020 Nov

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Nomogram based on preoperative CT imaging predicts the EGFR mutation status in lung adenocarcinoma.

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

Translational oncology 20201121 1

Tyrosine kinase inhibitors (TKIs) provide clinical benefits to the lung cancer patients with epidermal growth factor receptor (EGFR) mutations. However, non-invasively determine EGFR mutation status in patients before targeted therapy remains a challenge. This study aimed to develop and validate a nomogram for preoperative prediction of EGFR mutation status in patients with lung adenocarcinoma. The medical records of 403 patients with lung adenocarcinoma confirmed by histology from January 2016 ...[more]

PMID: 33232920

Similar Datasets

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:ObjectivesTo 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).MethodsA 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.ResultThe 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).ConclusionsOur 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.

Project description:Background Identifying epidermal growth factor receptor (EGFR) mutations in lung adenocarcinoma (LADC) is vital for treatment decision-making. This study aimed to establish a convenient and noninvasive nomogram prediction model based on 18F-fluorodeoxyglucose positron emission tomography/computed tomography (18F-FDG PET/CT) imaging and clinical features to predict EGFR mutation status in patients with LADC. Methods A total of 274 patients (male 130, female 144, median age 65 years) were enrolled in this retrospective study. Imaging data from 18F-FDG PET/CT and clinical information were analyzed, with the Mann-Whitney U test, Student’s t-test, and chi-square test used to compare categorical or continuous covariates as appropriate. Logistic regression analyses were performed to identify independent variables associated with EGFR mutation status, from which the nomogram prediction model was constructed. Leave-one-out cross-validation was performed, and the discrimination ability and calibration of the nomogram were assessed by calculating the area under the curve of the receiver operating characteristic curve and the calibration curve. The clinical net benefit of the nomogram was evaluated. Results Of the 274 patients, 143 (52.2%) had EGFR mutations. Female sex [odds ratios (OR): 2.64, 95% confidence interval (CI): 1.29–5.45, P=0.008], non-smoking status (OR: 2.78, 95% CI: 1.30–5.88, P=0.008), mean standardized uptake value ≤9.23 (OR: 2.44, 95% CI: 1.35–4.55, P=0.004), metabolic tumor volume ≤17.72 cm3 (OR: 5.00, 95% CI: 2.38–12.50, P<0.001) and the presence of pleural retraction (OR: 1.88, 95% CI: 1.05–3.40, P=0.034) were independent predictors for EGFR mutations in LADCs. The nomogram based on these risk factors showed good predictive efficacy, with an area under the curve of 0.805 (95% CI: 0.753–0.857), a sensitivity of 90.2%, a specificity of 59.5% and an accuracy of 73.0%. Conclusions The nomogram prediction model incorporating sex, smoking status, mean standardized uptake value, metabolic tumor volume, and the presence of pleural retraction could effectively discriminate EGFR-mutant from wild-type LADCs.

Project description:IntroductionIn lung adenocarcinoma, the mutational spectrum is dominated by EGFR and KRAS mutations. Improved knowledge about genomic and transcriptional alterations in and between mutation-defined subgroups may identify genes involved in disease development or progression.MethodsGenomic profiles from 457 adenocarcinomas, including 113 EGFR-mutated, 134 KRAS-mutated and 210 EGFR and KRAS-wild type tumors (EGFRwt/KRASwt), and gene expression profiles from 914 adenocarcinomas, including 309 EGFR-mutated, 192 KRAS-mutated, and 413 EGFRwt/KRASwt tumors, were assembled from different repositories. Genomic and transcriptional differences between the three mutational groups were analyzed by both supervised and unsupervised methods.ResultsEGFR-mutated adenocarcinomas displayed a larger number of copy number alterations and recurrent amplifications, a higher fraction of total loss-of-heterozygosity, higher genomic complexity, and a more distinct expression pattern than EGFR-wild type adenocarcinomas. Several of these differences were also consistent when the three mutational groups were stratified by stage, gender and smoking status. Specific copy number alterations were associated with mutation status, predominantly including regions of gain with the highest frequency in EGFR-mutated tumors. Differential regions included both large and small regions of gain on 1p, 5q34-q35.3, 7p, 7q11.21, 12p12.1, 16p, and 21q, and losses on 6q16.3-q21, 8p, and 9p, with 20-40% frequency differences between the mutational groups. Supervised gene expression analyses identified 96 consistently differentially expressed genes between the mutational groups, and together with unsupervised analyses these analyses highlighted the difficulty in broadly resolving the three mutational groups into distinct transcriptional entities.ConclusionsWe provide a comprehensive overview of the genomic and transcriptional landscape in lung adenocarcinoma stratified by EGFR and KRAS mutations. Our analyses suggest that the overall genomic and transcriptional landscape of lung adenocarcinoma is affected, but only to a minor extent, by EGFR and KRAS mutation status.

Dataset Information

Nomogram based on preoperative CT imaging predicts the EGFR mutation status in lung adenocarcinoma.

Publications

Nomogram based on preoperative CT imaging predicts the EGFR mutation status in lung adenocarcinoma.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets