Diagnostics (Nov 2022)

Metabolomic Selection in the Progression of Type 2 Diabetes Mellitus: A Genetic Algorithm Approach

  • Jorge Morgan-Benita,
  • Ana G. Sánchez-Reyna,
  • Carlos H. Espino-Salinas,
  • Juan José Oropeza-Valdez,
  • Huizilopoztli Luna-García,
  • Carlos E. Galván-Tejada,
  • Jorge I. Galván-Tejada,
  • Hamurabi Gamboa-Rosales,
  • Jose Antonio Enciso-Moreno,
  • José Celaya-Padilla

DOI
https://doi.org/10.3390/diagnostics12112803
Journal volume & issue
Vol. 12, no. 11
p. 2803

Abstract

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According to the World Health Organization (WHO), type 2 diabetes mellitus (T2DM) is a result of the inefficient use of insulin by the body. More than 95% of people with diabetes have T2DM, which is largely due to excess weight and physical inactivity. This study proposes an intelligent feature selection of metabolites related to different stages of diabetes, with the use of genetic algorithms (GA) and the implementation of support vector machines (SVMs), K-Nearest Neighbors (KNNs) and Nearest Centroid (NEARCENT) and with a dataset obtained from the Instituto Mexicano del Seguro Social with the protocol name of the following: “Análisis metabolómico y transcriptómico diferencial en orina y suero de pacientes pre diabéticos, diabéticos y con nefropatía diabética para identificar potenciales biomarcadores pronósticos de daño renal” (differential metabolomic and transcriptomic analyses in the urine and serum of pre-diabetic, diabetic and diabetic nephropathy patients to identify potential prognostic biomarkers of kidney damage). In order to analyze which machine learning (ML) model is the most optimal for classifying patients with some stage of T2DM, the novelty of this work is to provide a genetic algorithm approach that detects significant metabolites in each stage of progression. More than 100 metabolites were identified as significant between all stages; with the data analyzed, the average accuracies obtained in each of the five most-accurate implementations of genetic algorithms were in the range of 0.8214–0.9893 with respect to average accuracy, providing a precise tool to use in detections and backing up a diagnosis constructed entirely with metabolomics. By providing five potential biomarkers for progression, these extremely significant metabolites are as follows: “Cer(d18:1/24:1) i2”, “PC(20:3-OH/P-18:1)”, “Ganoderic acid C2”, “TG(16:0/17:1/18:1)” and “GPEtn(18:0/20:4)”.

Keywords