Application of machine learning in the prediction of deficient mismatch repair in patients with colorectal cancer based on routine preoperative characterization
Authors: Xu Dong , Chen Rujie , Jiang Yu , Wang Shuai , Liu Zhiyu , Chen Xihao , Fan Xiaoyan , Zhu Jun , Li Jipeng 
Published: December 2022

Simple summary

Detecting deficient mismatch repair (dMMR) in patients with colorectal cancer is essential for clinical decision-making, including evaluation of prognosis, guidance of adjuvant chemotherapy and immunotherapy, and primary screening for Lynch syndrome. However, outside of tertiary care centers, existing detection methods are not widely disseminated and highly depend on the experienced pathologist. Therefore, it is of great clinical significance to develop a broadly accessible and low-cost tool for dMMR prediction, particularly prior to surgery. In this study, we developed a convenient and reliable model for predicting dMMR status in CRC patients on routine preoperative characterization utilizing multiple machine learning algorithms. This model will work as an automated screening tool for identifying patients suitable for mismatch repair testing and consequently for improving the detection rate of dMMR, while reducing unnecessary labor and cost in patients with proficient mismatch repair.

Background

Deficient mismatch repair (dMMR) indicates a sustained anti-tumor immune response and has a favorable prognosis in patients with colorectal cancer (CRC). Although all CRC patients are recommended to undergo dMMR testing after surgery, current diagnostic approaches are not available for all country hospitals and patients. Therefore, efficient and low-cost predictive models for dMMR, especially for preoperative evaluations, are warranted.

Methods

A large scale of 5596 CRC patients who underwent surgical resection and mismatch repair testing were enrolled and randomly divided into training and validation cohorts. The clinical features exploited for predicting dMMR comprised the demographic characteristics, preoperative laboratory data, and tumor burden information. Machine learning (ML) methods involving eight basic algorithms, ensemble learning methods, and fusion algorithms were adopted with 10-fold cross-validation, and their performance was evaluated based on the area under the receiver operating characteristic curve (AUC) and calibration curves. The clinical net benefits were assessed using a decision curve analysis (DCA), and a nomogram was developed to facilitate model clinical practicality.

Results

All models achieved an AUC of nearly 0.80 in the validation cohort, with the stacking model exhibiting the best performance (AUC = 0.832). Logistical DCA revealed that the stacking model yielded more clinical net benefits than the conventional regression models. In the subgroup analysis, the stacking model also predicted dMMR regardless of the clinical stage. The nomogram showed a favorable consistence with the actual outcome in the calibration curve.

Conclusion

With the aid of ML algorithms, we developed a novel and robust model for predicting dMMR in CRC patients with satisfactory discriminative performance and designed a user-friendly and convenient nomogram.