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Document Type
Article
Publication Date
2019
College/Unit
School of Medicine
Department/Program/Center
Exercise Physiology
Abstract
Background: Diabetes mellitus is a chronic disease that impacts an increasing percentage of people each year. Among its comorbidities, diabetics are two to four times more likely to develop cardiovascular diseases. While HbA1c remains the primary diagnostic for diabetics, its ability to predict long-term, health outcomes across diverse demographics, ethnic groups, and at a personalized level are limited. The purpose of this study was to provide a model for precision medicine through the implementation of machine-learning algorithms using multiple cardiac biomarkers as a means for predicting diabetes mellitus development. Methods: Right atrial appendages from 50 patients, 30 non-diabetic and 20 type 2 diabetic, were procured from the WVU Ruby Memorial Hospital. Machine-learning was applied to physiological, biochemical, and sequencing data for each patient. Supervised learning implementing SHapley Additive exPlanations (SHAP) allowed binary (no diabetes or type 2 diabetes) and multiple classifcation (no diabetes, prediabetes, and type 2 diabetes) of the patient cohort with and without the inclusion of HbA1c levels. Findings were validated through Logistic Regression (LR), Linear Discriminant Analysis (LDA), Gaussian Naïve Bayes (NB), Support Vector Machine (SVM), and Classifcation and Regression Tree (CART) models with tenfold cross validation. Results: Total nuclear methylation and hydroxymethylation were highly correlated to diabetic status, with nuclear methylation and mitochondrial electron transport chain (ETC) activities achieving superior testing accuracies in the predictive model (~84% testing, binary). Mitochondrial DNA SNPs found in the D-Loop region (SNP-73G, -16126C, and -16362C) were highly associated with diabetes mellitus. The CpG island of transcription factor A, mitochondrial (TFAM) revealed CpG24 (chr10:58385262, P=0.003) and CpG29 (chr10:58385324, P=0.001) as markers correlating with diabetic progression. When combining the most predictive factors from each set, total nuclear methylation and CpG24 methylation were the best diagnostic measures in both binary and multiple classifcation sets. Conclusions: Using machine-learning, we were able to identify novel as well as the most relevant biomarkers associated with type 2 diabetes mellitus by integrating physiological, biochemical, and sequencing datasets. Ultimately, this approach may be used as a guideline for future investigations into disease pathogenesis and novel biomarker discovery
Digital Commons Citation
Hathaway, Quincy A.; Roth, Skyler M.; Pinti, Mark V.; Sprando, Daniel C.; Kunovac, Amina; Durr, Andrya J.; Cook, Chris C.; Fink, Garret K.; Cheuvront, Tristen B.; Grossman, Jasmine H.; Aljahli, Ghadah A.; Taylor, Andrew D.; Giromini, Andrew P.; Allen, Jessica L.; and Hollander, John M., "Machine-learning to Stratify Diabetic Patients Using Novel Cardiac Biomarkers and Integrative Genomics" (2019). Faculty & Staff Scholarship. 2001.
https://researchrepository.wvu.edu/faculty_publications/2001
Source Citation
Hathaway, Q. A., Roth, S. M., Pinti, M. V., Sprando, D. C., Kunovac, A., Durr, A. J., Cook, C. C., Fink, G. K., Cheuvront, T. B., Grossman, J. H., Aljahli, G. A., Taylor, A. D., Giromini, A. P., Allen, J. L., & Hollander, J. M. (2019). Machine-learning to stratify diabetic patients using novel cardiac biomarkers and integrative genomics. Cardiovascular Diabetology, 18(1). https://doi.org/10.1186/s12933-019-0879-0
Comments
© The Author(s) 2019. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/ publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.