Development and validation of a machine learning model to predict the risk of lymph node metastasis in renal carcinoma

Abstract

Simple summary: Studies have shown that about 30% of kidney cancer patients will have metastasis, and lymph node metastasis (LNM) may be related to a poor prognosis. Our retrospective study aims to provide a reliable machine learning-based model to predict the occurrence of LNM in kidney cancer. We screened the pathological grade, liver metastasis, M staging, primary site, T staging, and tumor size from the training group (n=39016) formed by the SEER database and the validation group (n=771) formed by the medical center. Independent predictors of LNM in cancer patients. Using six different algorithms to build a prediction model, it is found that the prediction performance of the XGB model in the training group and the validation group is significantly better than any other machine learning model. The results show that prediction tools based on machine learning can accurately predict the probability of LNM in patients with kidney cancer and have satisfactory clinical application prospects.

Background: Lymph node metastasis (LNM) is associated with the prognosis of patients with kidney cancer. This study aimed to provide reliable machine learning-based (ML-based) models to predict the probability of LNM in kidney cancer.

Methods: Data on patients diagnosed with kidney cancer were extracted from the Surveillance, Epidemiology and Outcomes (SEER) database from 2010 to 2017, and variables were filtered by least absolute shrinkage and selection operator (LASSO), univariate and multivariate logistic regression analyses. Statistically significant risk factors were used to build predictive models. We used 10-fold cross-validation in the validation of the model. The area under the receiver operating characteristic curve (AUC) was used to assess the performance of the model. Correlation heat maps were used to investigate the correlation of features using permutation analysis to assess the importance of predictors. Probability density functions (PDFs) and clinical utility curves (CUCs) were used to determine clinical utility thresholds.

Results: The training cohort of this study included 39,016 patients, and the validation cohort included 771 patients. In the two cohorts, 2544 (6.5%) and 66 (8.1%) patients had LNM, respectively. Pathological grade, liver metastasis, M stage, primary site, T stage, and tumor size were independent predictive factors of LNM. In both model validation, the XGB model significantly outperformed any of the machine learning models with an AUC value of 0.916.A web calculator (https://share.streamlit.io/liuwencai4/renal_lnm/main/renal_lnm.py) were built based on the XGB model. Based on the PDF and CUC, we suggested 54.6% as a threshold probability for guiding the diagnosis of LNM, which could distinguish about 89% of LNM patients.

Conclusions: The predictive tool based on machine learning can precisely indicate the probability of LNM in kidney cancer patients and has a satisfying application prospect in clinical practice.

Keywords: kidney cancer; lymph node metastasis; machine learning; predictive model; renal cell cancer; web calculator.