Predictive utilities of lipid traits, lipoprotein subfractions and other risk factors for incident diabetes: A machine learning approach in the Diabetes Prevention Program

Tibor V. Varga, Jinxi Liu, Ronald B. Goldberg, Guannan Chen, Samuel Dagogo-Jack, Carlos Lorenzo, Kieren J. Mather, Xavier Pi-Sunyer, Søren Brunak, Marinella Temprosa

Research output: Contribution to journalArticlepeer-review

Abstract

Introduction Although various lipid and non-lipid analytes measured by nuclear magnetic resonance (NMR) spectroscopy have been associated with type 2 diabetes, a structured comparison of the ability of NMR-derived biomarkers and standard lipids to predict individual diabetes risk has not been undertaken in larger studies nor among individuals at high risk of diabetes. Research design and methods Cumulative discriminative utilities of various groups of biomarkers including NMR lipoproteins, related non-lipid biomarkers, standard lipids, and demographic and glycemic traits were compared for short-term (3.2 years) and long-term (15 years) diabetes development in the Diabetes Prevention Program, a multiethnic, placebo-controlled, randomized controlled trial of individuals with pre-diabetes in the USA (N=2590). Logistic regression, Cox proportional hazards model and six different hyperparameter-tuned machine learning algorithms were compared. The Matthews Correlation Coefficient (MCC) was used as the primary measure of discriminative utility. Results Models with baseline NMR analytes and their changes did not improve the discriminative utility of simpler models including standard lipids or demographic and glycemic traits. Across all algorithms, models with baseline 2-hour glucose performed the best (max MCC=0.36). Sophisticated machine learning algorithms performed similarly to logistic regression in this study. Conclusions NMR lipoproteins and related non-lipid biomarkers were associated but did not augment discrimination of diabetes risk beyond traditional diabetes risk factors except for 2-hour glucose. Machine learning algorithms provided no meaningful improvement for discrimination compared with logistic regression, which suggests a lack of influential latent interactions among the analytes assessed in this study. Trial registration number Diabetes Prevention Program: NCT00004992; Diabetes Prevention Program Outcomes Study: NCT00038727.

Original languageEnglish (US)
Article number001953
JournalBMJ Open Diabetes Research and Care
Volume9
Issue number1
DOIs
StatePublished - Mar 31 2021

Keywords

  • diabetes mellitus
  • lipids
  • lipoproteins
  • prediabetic state
  • type 2

ASJC Scopus subject areas

  • Endocrinology, Diabetes and Metabolism

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