Dataset Information

An Immune-Related Gene Panel for Preoperative Lymph Node Status Evaluation in Advanced Gastric Cancer.

ABSTRACT: Background and Aim: Gastric cancer (GC) is the common leading cause of cancer-related death worldwide. Immune-related genes (IRGs) may potentially predict lymph node metastasis (LNM). We aimed to develop a preoperative model to predict LNM based on these IRGs. Methods: In this paper, we compared and evaluated three machine learning models to predict LNM based on publicly available gene expression data from TCGA-STAD. The Pearson correlation coefficient (PCC) method was utilized to feature selection according to its relationships with LN status. The performance of the model was assessed using the area under the curve (AUC) and F1 score. Results: The Naive Bayesian model showed better performance and was constructed based on 26 selected gene features, with AUCs of 0.741 in the training set and 0.688 in the test set. The F1 score in the training set and test set was 0.652 and 0.597, respectively. Furthermore, Naive Bayesian model based on 26 IRGs is the first diagnostic tool for the identification of LNM in advanced GC. Conclusion: These results indicate that our new methods have the value of auxiliary diagnosis with promising clinical potential.

SUBMITTER: Yang Y

PROVIDER: S-EPMC7789469 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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An Immune-Related Gene Panel for Preoperative Lymph Node Status Evaluation in Advanced Gastric Cancer.

Yang Yuan Y Zheng Ya Y Zhang Hongling H Miao Yandong Y Wu Guozhi G Zhou Lingshan L Wang Haoying H Ji Rui R Guo Qinghong Q Chen Zhaofeng Z Wang Jiangtao J Wang Yuping Y Zhou Yongning Y

BioMed research international 20201207

<i>Background and Aim</i>: Gastric cancer (GC) is the common leading cause of cancer-related death worldwide. Immune-related genes (IRGs) may potentially predict lymph node metastasis (LNM). We aimed to develop a preoperative model to predict LNM based on these IRGs. <i>Methods</i>: In this paper, we compared and evaluated three machine learning models to predict LNM based on publicly available gene expression data from TCGA-STAD. The Pearson correlation coefficient (PCC) method was utilized to ...[more]

PMID: 33490257

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Project description:Objective: To develop and evaluate a diffusion-weighted imaging (DWI)-based radiomic nomogram for lymph node metastasis (LNM) prediction in advanced gastric cancer (AGC) patients. Overall Study: This retrospective study was conducted with 146 consecutively included pathologically confirmed AGC patients from two centers. All patients underwent preoperative 3.0 T magnetic resonance imaging (MRI) examination. The dataset was allocated to a training cohort (n = 71) and an internal validation cohort (n = 47) from one center along with an external validation cohort (n = 28) from another. A summary of 1,305 radiomic features were extracted per patient. The least absolute shrinkage and selection operator (LASSO) logistic regression and learning vector quantization (LVQ) methods with cross-validations were adopted to select significant features in a radiomic signature. Combining the radiomic signature and independent clinical factors, a radiomic nomogram was established. The MRI-reported N staging and the MRI-derived model were built for comparison. Model performance was evaluated considering receiver operating characteristic (ROC) analysis, calibration curves, and decision curve analysis (DCA). Results: A two-feature radiomic signature was found significantly associated with LNM (p < 0.01, training and internal validation cohorts). A radiomic nomogram was established by incorporating the clinical minimum apparent diffusion coefficient (ADC) and MRI-reported N staging. The radiomic nomogram showed a favorable classification ability with an area under ROC curve of 0.850 [95% confidence interval (CI), 0.758-0.942] in the training cohort, which was then confirmed with an AUC of 0.857 (95% CI, 0.714-1.000) in internal validation cohort and 0.878 (95% CI, 0.696-1.000) in external validation cohort. Meanwhile, the specificity, sensitivity, and accuracy were 0.846, 0.853, and 0.851 in internal validation cohort, and 0.714, 0.952, and 0.893 in external validation cohort, compensating for the MRI-reported N staging and MRI-derived model. DCA demonstrated good clinical use of radiomic nomogram. Conclusions: This study put forward a DWI-based radiomic nomogram incorporating the radiomic signature, minimum ADC, and MRI-reported N staging for individualized preoperative detection of LNM in patients with AGC.

Project description:IntroductionThe axillary lymph node (ALN) status of breast cancer patients is an important prognostic indicator. The use of primary breast mass features for the prediction of ALN status is rare. Two nomograms based on preoperative ultrasound (US) images of breast tumors and ALNs were developed for the prediction of ALN status.MethodsA total of 743 breast cancer cases collected from 2016 to 2019 at the Second Affiliated Hospital of Harbin Medical University were randomly divided into a training set (n = 523) and a test set (n = 220). A primary tumor feature model (PTFM) and ALN feature model (ALNFM) were separately generated based on tumor features alone, and a combination of features was used for the prediction of ALN status. Logistic regression analysis was used to construct the nomograms. A receiver operating characteristic curve was plotted to obtain the area under the curve (AUC) to evaluate accuracy, and bias-corrected AUC values and calibration curves were obtained by bootstrap resampling for internal and external verification. Decision curve analysis was applied to assess the clinical utility of the models.ResultsThe AUCs of the PTFM were 0.69 and 0.67 for the training and test sets, respectively, and the bias-corrected AUCs of the PTFM were 0.67 and 0.67, respectively. Moreover, the AUCs of the ALNFM were 0.86 and 0.84, respectively, and the bias-corrected AUCs were 0.85 and 0.81, respectively. Compared with the PTFM, the ALNFM showed significantly improved prediction accuracy (p < 0.001). Both the calibration and decision curves of the ALNFM nomogram indicated greater accuracy and clinical practicality. When the US tumor size was ≤21.5 mm, the Spe was 0.96 and 0.92 in the training and test sets, respectively. When the US tumor size was greater than 21.5 mm, the Sen was 0.85 in the training set and 0.87 in the test set. Our further research showed that when the US tumor size was larger than 35 mm, the Sen was 0.90 in the training set and 0.93 in the test set.ConclusionThe ALNFM could effectively predict ALN status based on US images especially for different US tumor size.

Project description:Purpose: Accurate lymph node (LN) status evaluation for intrahepatic cholangiocarcinoma (ICC) patients is essential for surgical planning. This study aimed to develop and validate a prediction model for preoperative LN status evaluation in ICC patients. Methods and Materials: A group of 106 ICC patients, who were diagnosed between April 2011 and February 2016, was used for prediction model training. Image features were extracted from T1-weighted contrast-enhanced MR images. A support vector machine (SVM) model was built by using the most LN status-related features, which were selected using the maximum relevance minimum redundancy (mRMR) algorithm. The mRMR method ranked each feature according to its relevance to the LN status and redundancy with other features. An SVM score was calculated for each patient to reflect the LN metastasis (LNM) probability from the SVM model. Finally, a combination nomogram was constructed by incorporating the SVM score and clinical features. An independent group of 42 patients who were diagnosed from March 2016 to November 2017 was used to validate the prediction models. The model performances were evaluated on discrimination, calibration, and clinical utility. Results: The SVM model was constructed based on five selected image features. Significant differences were found between patients with LNM and non-LNM in SVM scores in both groups (the training group: 0.5466 (interquartile range (IQR), 0.4059-0.6985) vs. 0.3226 (IQR, 0.0527-0.4659), P<0.0001; the validation group: 0.5831 (IQR, 0.3641-0.8162) vs. 0.3101 (IQR, 0.1029-0.4661), P=0.0015). The combination nomogram based on the SVM score, the CA 19-9 level, and the MR-reported LNM factor showed better discrimination in separating patients with LNM and non-LNM, comparing to the SVM model alone (AUC: the training group: 0.842 vs. 0.788; the validation group: 0.870 vs. 0.787). Favorable clinical utility was observed using the decision curve analysis for the nomogram. Conclusion: The nomogram, incorporating the SVM score, CA 19-9 level and the MR-reported LNM factor, provided an individualized LN status evaluation and helped clinicians guide the surgical decisions.

Project description:BackgroundPreoperative evaluation of lymph node (LN) state is of pivotal significance for informing therapeutic decisions in gastric cancer (GC) patients. However, there are no non-invasive methods that can be used to preoperatively identify such status. We aimed at developing a genomic biosignature based model to predict the possibility of LN metastasis in GC patients.MethodsWe used the RNA profile retrieving strategy and performed RNA expression profiling in a large GC cohort (GSE62254, n = 300) from Gene Expression Ominus (GEO). In the exploratory stage, 300 GC patients from GSE62254 were involved and the differentially expressed RNAs (DERs) for LN-status were determined using the R software. GC samples in GSE62254 were randomly allocated into a learning set (n = 210) and a verification set (n = 90). By using the Least absolute shrinkage and selection operator (LASSO) regression approach, a set of 23-RNA signatures were established and the signature based nomogram was subsequently built for distinguishing LN condition. The diagnostic efficiency, as well as the clinical performance of this model were assessed using the decision curve analysis (DCA). Metascape was used for bioinformatic analysis of the DERs.ResultsBased on the genomic signature, we established a nomogram that robustly distinguished LN status in the learning (AUC = 0.916, 95% CI 0.833-0.999) and verification sets (AUC = 0.775, 95% CI 0.647-0.903). DCA demonstrated the clinical value of this nomogram. Functional enrichment analysis of the DERs was performed using bioinformatics methods which revealed that these DERs were involved in several lymphangiogenesis-correlated cascades.ConclusionsIn this study, we present a genomic signature based nomogram that integrates the 23-RNA biosignature based scores and Lauren classification. This model can be utilized to estimate the probability of LN metastasis with good performance in GC. The functional analysis of the DERs reveals the prospective biogenesis of LN metastasis in GC.

Dataset Information

An Immune-Related Gene Panel for Preoperative Lymph Node Status Evaluation in Advanced Gastric Cancer.

Publications

An Immune-Related Gene Panel for Preoperative Lymph Node Status Evaluation in Advanced Gastric Cancer.

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